Starting phenix.real_space_refine on Tue Apr 9 14:27:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc6_16555/04_2024/8cc6_16555_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.065 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 45 5.16 5 Cl 5 4.86 5 C 10965 2.51 5 N 2690 2.21 5 O 2935 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 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C ASP 327": "OD1" <-> "OD2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 312": "OD1" <-> "OD2" Residue "E ASP 327": "OD1" <-> "OD2" Residue "E GLU 405": "OE1" <-> "OE2" Residue "E GLU 418": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16640 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 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: 9.20, per 1000 atoms: 0.55 Number of scatterers: 16640 At special positions: 0 Unit cell: (95.035, 96.18, 168.315, 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 45 16.00 O 2935 8.00 N 2690 7.00 C 10965 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 E1002 " - " 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: 6.93 Conformation dependent library (CDL) restraints added in 2.9 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: 56 helices and 20 sheets defined 44.9% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 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: 3.874A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.826A 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: 4.590A 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: 4.853A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 459 removed outlier: 3.614A 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 80 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: 3.908A pdb=" N ALA B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU B 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 5.602A 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: 4.539A 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: 4.800A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 459 removed outlier: 3.591A 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 243 removed outlier: 3.878A pdb=" N ALA C 224 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL C 225 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU C 228 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU C 229 " --> pdb=" O SER C 226 " (cutoff:3.500A) Proline residue: C 230 - end of helix 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: 4.595A 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: 4.826A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 459 removed outlier: 3.603A 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 80 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 243 removed outlier: 3.859A pdb=" N ALA D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL D 225 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU D 228 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU D 229 " --> pdb=" O SER D 226 " (cutoff:3.500A) Proline residue: D 230 - end of helix 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: 4.572A 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: 4.851A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 459 removed outlier: 3.661A 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 243 removed outlier: 3.864A pdb=" N ALA E 224 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL E 225 " --> pdb=" O PHE E 222 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU E 228 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU E 229 " --> pdb=" O SER E 226 " (cutoff:3.500A) Proline residue: E 230 - end of helix 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: 4.622A 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: 4.845A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 459 removed outlier: 3.619A 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: 6.050A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.058A 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: 4.401A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.286A 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: 6.055A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.052A 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: 4.503A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.281A 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: 6.067A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 132 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP C 105 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA C 134 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE C 103 " --> pdb=" O ALA C 134 " (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: 4.442A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.263A 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: 6.038A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.084A 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: 4.411A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.284A 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: 6.034A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.045A 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: 4.449A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 864 hydrogen bonds defined for protein. 2028 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: 4.99 Time building geometry restraints manager: 7.46 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: 3561 1.46 - 1.57: 8414 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 17105 Sorted by residual: bond pdb=" C11 U9L D 502 " pdb=" C12 U9L D 502 " ideal model delta sigma weight residual 1.349 1.425 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C11 U9L C 502 " pdb=" C12 U9L C 502 " ideal model delta sigma weight residual 1.349 1.424 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C11 U9L B 502 " pdb=" C12 U9L B 502 " ideal model delta sigma weight residual 1.349 1.424 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C11 U9L E1001 " pdb=" C12 U9L E1001 " ideal model delta sigma weight residual 1.349 1.424 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C11 U9L A 502 " pdb=" C12 U9L A 502 " ideal model delta sigma weight residual 1.349 1.424 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 17100 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.42: 338 105.42 - 112.57: 9317 112.57 - 119.72: 5497 119.72 - 126.87: 7876 126.87 - 134.02: 347 Bond angle restraints: 23375 Sorted by residual: angle pdb=" C20 U9L E1001 " pdb=" N21 U9L E1001 " pdb=" C26 U9L E1001 " ideal model delta sigma weight residual 109.47 126.59 -17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" C20 U9L D 502 " pdb=" N21 U9L D 502 " pdb=" C26 U9L D 502 " ideal model delta sigma weight residual 109.47 126.41 -16.94 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C20 U9L B 502 " pdb=" N21 U9L B 502 " pdb=" C26 U9L B 502 " ideal model delta sigma weight residual 109.47 126.31 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C20 U9L C 502 " pdb=" N21 U9L C 502 " pdb=" C26 U9L C 502 " ideal model delta sigma weight residual 109.47 126.31 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C20 U9L A 502 " pdb=" N21 U9L A 502 " pdb=" C26 U9L A 502 " ideal model delta sigma weight residual 109.47 125.84 -16.37 3.00e+00 1.11e-01 2.98e+01 ... (remaining 23370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 9513 22.27 - 44.54: 692 44.54 - 66.81: 98 66.81 - 89.08: 23 89.08 - 111.35: 24 Dihedral angle restraints: 10350 sinusoidal: 4535 harmonic: 5815 Sorted by residual: dihedral pdb=" C23 U9L A 502 " pdb=" C25 U9L A 502 " pdb=" N24 U9L A 502 " pdb=" C26 U9L A 502 " ideal model delta sinusoidal sigma weight residual 52.95 -58.40 111.35 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C23 U9L C 502 " pdb=" C25 U9L C 502 " pdb=" N24 U9L C 502 " pdb=" C26 U9L C 502 " ideal model delta sinusoidal sigma weight residual 52.95 -58.07 111.02 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" C23 U9L B 502 " pdb=" C25 U9L B 502 " pdb=" N24 U9L B 502 " pdb=" C26 U9L B 502 " ideal model delta sinusoidal sigma weight residual 52.95 -57.93 110.88 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1880 0.036 - 0.072: 589 0.072 - 0.107: 207 0.107 - 0.143: 79 0.143 - 0.179: 5 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 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-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 -2.22 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2757 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 325 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C VAL D 325 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL D 325 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 326 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 325 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C VAL B 325 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL B 325 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 326 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 325 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C VAL E 325 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL E 325 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 326 " 0.011 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1470 2.75 - 3.28: 16267 3.28 - 3.82: 28604 3.82 - 4.36: 32541 4.36 - 4.90: 58461 Nonbonded interactions: 137343 Sorted by model distance: nonbonded pdb=" OH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 2.248 2.440 ... (remaining 137338 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: 1.120 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: 4.580 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 46.750 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.160 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.004 0.076 17105 Z= 0.292 Angle : 0.705 17.117 23375 Z= 0.332 Chirality : 0.043 0.179 2760 Planarity : 0.004 0.036 2820 Dihedral : 16.301 111.354 6560 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.05 % Allowed : 11.81 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1930 helix: 2.46 (0.18), residues: 815 sheet: -1.62 (0.21), residues: 445 loop : 0.41 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.012 0.001 PHE D 242 TYR 0.011 0.001 TYR C 67 ARG 0.009 0.000 ARG E 420 *********************** 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 140 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.839 Fit side-chains REVERT: B 410 ARG cc_start: 0.7175 (ttp-170) cc_final: 0.6931 (ttp-170) REVERT: E 235 MET cc_start: 0.7769 (tpp) cc_final: 0.7557 (mmm) outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.3195 time to fit residues: 66.4815 Evaluate side-chains 123 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0070 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17105 Z= 0.212 Angle : 0.542 6.570 23375 Z= 0.278 Chirality : 0.043 0.134 2760 Planarity : 0.005 0.029 2820 Dihedral : 9.314 96.953 2717 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.88 % Allowed : 13.13 % Favored : 85.99 % 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: 0.85 (0.20), residues: 1930 helix: 1.99 (0.18), residues: 815 sheet: -1.36 (0.21), residues: 500 loop : 0.56 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 459 HIS 0.003 0.001 HIS B 323 PHE 0.008 0.001 PHE A 242 TYR 0.018 0.001 TYR E 67 ARG 0.004 0.000 ARG D 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 160 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.770 Fit side-chains REVERT: A 136 SER cc_start: 0.8712 (m) cc_final: 0.8492 (p) REVERT: A 235 MET cc_start: 0.7671 (tpp) cc_final: 0.7276 (mmm) REVERT: B 172 GLU cc_start: 0.7743 (pm20) cc_final: 0.7542 (pm20) REVERT: B 410 ARG cc_start: 0.7223 (ttp-170) cc_final: 0.7017 (ttp-170) REVERT: D 136 SER cc_start: 0.8737 (m) cc_final: 0.8490 (p) REVERT: E 17 ASP cc_start: 0.8186 (m-30) cc_final: 0.7981 (t0) REVERT: E 235 MET cc_start: 0.7259 (tpp) cc_final: 0.6983 (mmm) outliers start: 16 outliers final: 5 residues processed: 154 average time/residue: 0.3030 time to fit residues: 70.2714 Evaluate side-chains 142 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17105 Z= 0.194 Angle : 0.524 7.851 23375 Z= 0.263 Chirality : 0.042 0.138 2760 Planarity : 0.005 0.027 2820 Dihedral : 7.080 86.552 2715 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.37 % Allowed : 13.57 % Favored : 85.05 % 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: 0.61 (0.20), residues: 1930 helix: 1.80 (0.18), residues: 790 sheet: -1.41 (0.21), residues: 500 loop : 0.42 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 459 HIS 0.003 0.001 HIS C 323 PHE 0.008 0.001 PHE C 254 TYR 0.017 0.001 TYR E 67 ARG 0.004 0.000 ARG D 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 176 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.945 Fit side-chains REVERT: A 136 SER cc_start: 0.8736 (m) cc_final: 0.8529 (p) REVERT: A 235 MET cc_start: 0.7642 (tpp) cc_final: 0.7339 (mmm) REVERT: B 410 ARG cc_start: 0.7223 (ttp-170) cc_final: 0.6993 (ttp-170) REVERT: C 50 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8371 (t0) REVERT: C 136 SER cc_start: 0.8837 (m) cc_final: 0.8631 (p) REVERT: D 136 SER cc_start: 0.8747 (m) cc_final: 0.8522 (p) REVERT: D 311 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7380 (pp30) REVERT: E 172 GLU cc_start: 0.8081 (pt0) cc_final: 0.7447 (mp0) REVERT: E 235 MET cc_start: 0.7155 (tpp) cc_final: 0.6840 (mmm) REVERT: E 242 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.6926 (t80) outliers start: 25 outliers final: 12 residues processed: 164 average time/residue: 0.3070 time to fit residues: 75.5727 Evaluate side-chains 158 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 chunk 168 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17105 Z= 0.180 Angle : 0.503 5.388 23375 Z= 0.254 Chirality : 0.042 0.135 2760 Planarity : 0.004 0.027 2820 Dihedral : 6.429 87.775 2715 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.87 % Allowed : 14.01 % Favored : 84.12 % 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: 0.53 (0.20), residues: 1930 helix: 1.67 (0.19), residues: 790 sheet: -1.45 (0.21), residues: 500 loop : 0.47 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.008 0.001 PHE A 254 TYR 0.016 0.001 TYR E 67 ARG 0.005 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 188 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 1.944 Fit side-chains REVERT: A 172 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A 235 MET cc_start: 0.7593 (tpp) cc_final: 0.7208 (mmm) REVERT: A 311 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7480 (pp30) REVERT: B 311 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.7428 (pp30) REVERT: C 50 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8358 (t0) REVERT: C 235 MET cc_start: 0.7436 (tpp) cc_final: 0.7128 (mmm) REVERT: C 311 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7145 (pp30) REVERT: D 136 SER cc_start: 0.8754 (m) cc_final: 0.8551 (p) REVERT: D 311 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: E 172 GLU cc_start: 0.8096 (pt0) cc_final: 0.7439 (mp0) REVERT: E 235 MET cc_start: 0.7217 (tpp) cc_final: 0.6890 (mmm) REVERT: E 242 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.6933 (t80) REVERT: E 311 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7363 (pp30) outliers start: 34 outliers final: 17 residues processed: 178 average time/residue: 0.3062 time to fit residues: 83.1361 Evaluate side-chains 173 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.0770 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 160 optimal weight: 0.0030 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 47 optimal weight: 0.4980 overall best weight: 0.2548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17105 Z= 0.120 Angle : 0.475 7.205 23375 Z= 0.242 Chirality : 0.042 0.203 2760 Planarity : 0.004 0.027 2820 Dihedral : 6.124 89.901 2715 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 13.90 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1930 helix: 1.71 (0.19), residues: 790 sheet: -1.42 (0.21), residues: 500 loop : 0.63 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 459 HIS 0.003 0.000 HIS B 323 PHE 0.006 0.001 PHE E 254 TYR 0.015 0.001 TYR D 67 ARG 0.006 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 198 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.892 Fit side-chains REVERT: A 172 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: A 235 MET cc_start: 0.7474 (tpp) cc_final: 0.7134 (mmm) REVERT: A 311 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7503 (pp30) REVERT: B 172 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 311 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7484 (pp30) REVERT: C 50 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8331 (t0) REVERT: C 235 MET cc_start: 0.7323 (tpp) cc_final: 0.7012 (mmm) REVERT: C 311 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7348 (pp30) REVERT: D 136 SER cc_start: 0.8750 (m) cc_final: 0.8547 (p) REVERT: D 311 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7507 (pp30) REVERT: E 172 GLU cc_start: 0.8092 (pt0) cc_final: 0.7461 (mp0) REVERT: E 235 MET cc_start: 0.7145 (tpp) cc_final: 0.6824 (mmm) REVERT: E 242 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7043 (t80) REVERT: E 311 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7442 (pp30) outliers start: 31 outliers final: 14 residues processed: 189 average time/residue: 0.2896 time to fit residues: 84.1315 Evaluate side-chains 178 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 446 LEU 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: 0.9990 chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 156 optimal weight: 0.0040 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17105 Z= 0.164 Angle : 0.483 5.483 23375 Z= 0.245 Chirality : 0.042 0.159 2760 Planarity : 0.004 0.026 2820 Dihedral : 6.074 89.811 2715 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.54 % Allowed : 14.34 % Favored : 84.12 % 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: 0.62 (0.20), residues: 1930 helix: 1.67 (0.18), residues: 790 sheet: -1.41 (0.21), residues: 500 loop : 0.64 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.007 0.001 PHE A 254 TYR 0.016 0.001 TYR E 67 ARG 0.003 0.000 ARG E 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 181 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.874 Fit side-chains REVERT: A 172 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 235 MET cc_start: 0.7473 (tpp) cc_final: 0.7143 (mmm) REVERT: A 311 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7559 (pp30) REVERT: B 172 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: B 311 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.7533 (pp30) REVERT: C 50 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8359 (t0) REVERT: C 210 MET cc_start: 0.9093 (tpt) cc_final: 0.8731 (tpt) REVERT: C 235 MET cc_start: 0.7305 (tpp) cc_final: 0.6893 (mmp) REVERT: C 311 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7282 (pp30) REVERT: D 311 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7526 (pp30) REVERT: E 172 GLU cc_start: 0.8155 (pt0) cc_final: 0.7530 (mp0) REVERT: E 235 MET cc_start: 0.7146 (tpp) cc_final: 0.6816 (mmm) REVERT: E 242 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8167 (t80) REVERT: E 311 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7496 (pp30) outliers start: 28 outliers final: 15 residues processed: 172 average time/residue: 0.2979 time to fit residues: 78.2370 Evaluate side-chains 172 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17105 Z= 0.191 Angle : 0.490 5.401 23375 Z= 0.248 Chirality : 0.043 0.150 2760 Planarity : 0.004 0.026 2820 Dihedral : 6.090 89.628 2715 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.92 % Allowed : 14.56 % Favored : 83.52 % 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: 0.57 (0.20), residues: 1930 helix: 1.64 (0.18), residues: 790 sheet: -1.44 (0.21), residues: 500 loop : 0.60 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.008 0.001 PHE A 254 TYR 0.017 0.001 TYR E 67 ARG 0.003 0.000 ARG B 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 186 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.834 Fit side-chains REVERT: A 172 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 235 MET cc_start: 0.7485 (tpp) cc_final: 0.7142 (mmm) REVERT: A 311 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7562 (pp30) REVERT: B 172 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: B 311 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7438 (pp30) REVERT: B 320 TRP cc_start: 0.8497 (p-90) cc_final: 0.8242 (p-90) REVERT: B 427 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8085 (tt) REVERT: C 50 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8349 (t0) REVERT: C 235 MET cc_start: 0.7285 (tpp) cc_final: 0.6856 (mmp) REVERT: C 311 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7304 (pp30) REVERT: C 406 LEU cc_start: 0.8197 (mt) cc_final: 0.7983 (mt) REVERT: D 311 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.7467 (pp30) REVERT: E 172 GLU cc_start: 0.8211 (pt0) cc_final: 0.7584 (mp0) REVERT: E 235 MET cc_start: 0.7157 (tpp) cc_final: 0.6824 (mmm) REVERT: E 311 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7470 (pp30) outliers start: 35 outliers final: 18 residues processed: 176 average time/residue: 0.2968 time to fit residues: 79.6545 Evaluate side-chains 176 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17105 Z= 0.278 Angle : 0.527 5.565 23375 Z= 0.266 Chirality : 0.044 0.140 2760 Planarity : 0.004 0.029 2820 Dihedral : 6.193 87.080 2715 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.76 % Allowed : 15.05 % Favored : 83.19 % 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: 0.46 (0.20), residues: 1930 helix: 1.57 (0.18), residues: 790 sheet: -1.42 (0.21), residues: 495 loop : 0.42 (0.27), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.010 0.001 PHE A 254 TYR 0.018 0.002 TYR E 67 ARG 0.004 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 178 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.890 Fit side-chains REVERT: A 172 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 235 MET cc_start: 0.7508 (tpp) cc_final: 0.7165 (mmm) REVERT: A 311 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7510 (pp30) REVERT: B 172 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: B 311 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.7441 (pp30) REVERT: B 427 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8083 (tt) REVERT: C 50 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8382 (t0) REVERT: C 172 GLU cc_start: 0.7811 (pm20) cc_final: 0.7398 (mp0) REVERT: C 235 MET cc_start: 0.7396 (tpp) cc_final: 0.6952 (mmp) REVERT: C 311 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7294 (pp30) REVERT: D 172 GLU cc_start: 0.7785 (pm20) cc_final: 0.7481 (mp0) REVERT: D 311 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.7467 (pp30) REVERT: E 103 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: E 172 GLU cc_start: 0.8220 (pt0) cc_final: 0.7615 (mp0) REVERT: E 235 MET cc_start: 0.7287 (tpp) cc_final: 0.6943 (mmm) REVERT: E 311 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7415 (pp30) REVERT: E 417 ASP cc_start: 0.8060 (t0) cc_final: 0.7808 (t0) outliers start: 32 outliers final: 16 residues processed: 171 average time/residue: 0.3147 time to fit residues: 80.1764 Evaluate side-chains 169 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 165 optimal weight: 0.1980 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17105 Z= 0.170 Angle : 0.487 5.533 23375 Z= 0.247 Chirality : 0.042 0.140 2760 Planarity : 0.004 0.027 2820 Dihedral : 6.113 88.029 2715 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.81 % Allowed : 15.16 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1930 helix: 1.60 (0.19), residues: 790 sheet: -1.43 (0.21), residues: 490 loop : 0.50 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.008 0.001 PHE A 254 TYR 0.016 0.001 TYR E 67 ARG 0.004 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 181 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.810 Fit side-chains REVERT: A 172 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: A 235 MET cc_start: 0.7487 (tpp) cc_final: 0.7153 (mmm) REVERT: A 311 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7545 (pp30) REVERT: B 311 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7396 (pp30) REVERT: B 320 TRP cc_start: 0.8498 (p-90) cc_final: 0.8249 (p-90) REVERT: B 427 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8042 (tt) REVERT: C 50 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8379 (t0) REVERT: C 172 GLU cc_start: 0.7715 (pm20) cc_final: 0.7336 (mp0) REVERT: C 235 MET cc_start: 0.7423 (tpp) cc_final: 0.7087 (mmm) REVERT: C 311 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7247 (pp30) REVERT: D 172 GLU cc_start: 0.7780 (pm20) cc_final: 0.7496 (mp0) REVERT: D 311 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7491 (pp30) REVERT: E 103 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: E 172 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: E 235 MET cc_start: 0.7274 (tpp) cc_final: 0.6933 (mmm) REVERT: E 311 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7500 (pp30) outliers start: 33 outliers final: 19 residues processed: 175 average time/residue: 0.3090 time to fit residues: 81.0445 Evaluate side-chains 171 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 16 optimal weight: 0.0770 chunk 119 optimal weight: 0.8980 chunk 94 optimal weight: 0.0470 chunk 122 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17105 Z= 0.155 Angle : 0.478 6.457 23375 Z= 0.244 Chirality : 0.042 0.137 2760 Planarity : 0.004 0.027 2820 Dihedral : 6.054 89.023 2715 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.65 % Allowed : 15.44 % Favored : 82.91 % 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: 0.55 (0.20), residues: 1930 helix: 1.61 (0.19), residues: 790 sheet: -1.42 (0.21), residues: 490 loop : 0.54 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.008 0.001 PHE A 254 TYR 0.016 0.001 TYR D 67 ARG 0.004 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 171 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.841 Fit side-chains REVERT: A 172 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: A 235 MET cc_start: 0.7464 (tpp) cc_final: 0.7143 (mmm) REVERT: A 311 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.7502 (pp30) REVERT: B 311 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: B 320 TRP cc_start: 0.8498 (p-90) cc_final: 0.8264 (p-90) REVERT: B 427 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8058 (tt) REVERT: C 50 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8370 (t0) REVERT: C 172 GLU cc_start: 0.7717 (pm20) cc_final: 0.7341 (mp0) REVERT: C 235 MET cc_start: 0.7414 (tpp) cc_final: 0.7082 (mmm) REVERT: C 311 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7333 (pp30) REVERT: D 172 GLU cc_start: 0.7787 (pm20) cc_final: 0.7502 (mp0) REVERT: D 311 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7440 (pp30) REVERT: E 20 LEU cc_start: 0.8409 (mt) cc_final: 0.8093 (mt) REVERT: E 103 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8019 (m-10) REVERT: E 172 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: E 235 MET cc_start: 0.7268 (tpp) cc_final: 0.7000 (mmm) REVERT: E 311 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.7509 (pp30) outliers start: 30 outliers final: 19 residues processed: 166 average time/residue: 0.3012 time to fit residues: 75.5505 Evaluate side-chains 168 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU 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: 0.4980 chunk 142 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 159 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 136 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102792 restraints weight = 19298.889| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.54 r_work: 0.2905 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17105 Z= 0.164 Angle : 0.478 6.864 23375 Z= 0.243 Chirality : 0.042 0.137 2760 Planarity : 0.004 0.027 2820 Dihedral : 6.029 89.117 2715 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.92 % Allowed : 15.16 % Favored : 82.91 % 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: 0.57 (0.20), residues: 1930 helix: 1.60 (0.19), residues: 790 sheet: -1.28 (0.22), residues: 425 loop : 0.25 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.008 0.001 PHE A 254 TYR 0.015 0.001 TYR E 67 ARG 0.005 0.000 ARG D 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.50 seconds wall clock time: 59 minutes 59.32 seconds (3599.32 seconds total)