Starting phenix.real_space_refine on Fri Mar 15 22:17:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dse_30832/03_2024/7dse_30832.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dse_30832/03_2024/7dse_30832.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dse_30832/03_2024/7dse_30832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dse_30832/03_2024/7dse_30832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dse_30832/03_2024/7dse_30832.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dse_30832/03_2024/7dse_30832.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= -0.002 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8449 2.51 5 N 2086 2.21 5 O 2317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12957 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1837 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1837 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1837 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1837 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1837 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1837 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1837 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 7.48, per 1000 atoms: 0.58 Number of scatterers: 12957 At special positions: 0 Unit cell: (111.54, 112.554, 103.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2317 8.00 N 2086 7.00 C 8449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 139 " " NAG B1001 " - " ASN B 139 " " NAG C1001 " - " ASN C 139 " " NAG D1001 " - " ASN D 139 " " NAG E1001 " - " ASN E 139 " " NAG F1001 " - " ASN F 139 " " NAG G1001 " - " ASN G 139 " Time building additional restraints: 5.65 Conformation dependent library (CDL) restraints added in 2.3 seconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3164 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.600A pdb=" N ALA A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 71 Proline residue: A 59 - end of helix removed outlier: 3.731A pdb=" N ASN A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 Processing helix chain 'A' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 71 Proline residue: B 59 - end of helix removed outlier: 3.732A pdb=" N ASN B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 Processing helix chain 'B' and resid 209 through 250 removed outlier: 3.677A pdb=" N LEU B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 248 " --> pdb=" O CYS B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 71 Proline residue: C 59 - end of helix removed outlier: 3.732A pdb=" N ASN C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 93 through 107 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 Processing helix chain 'C' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR C 248 " --> pdb=" O CYS C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 71 Proline residue: D 59 - end of helix removed outlier: 3.731A pdb=" N ASN D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 93 through 107 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 146 through 156 removed outlier: 3.643A pdb=" N LYS D 156 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 Processing helix chain 'D' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE D 240 " --> pdb=" O HIS D 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 248 " --> pdb=" O CYS D 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 18 Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 71 Proline residue: E 59 - end of helix removed outlier: 3.732A pdb=" N ASN E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 93 through 107 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 Processing helix chain 'E' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 248 " --> pdb=" O CYS E 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 18 Processing helix chain 'F' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 Proline residue: F 59 - end of helix removed outlier: 3.731A pdb=" N ASN F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 93 through 107 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS F 156 " --> pdb=" O LYS F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 Processing helix chain 'F' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR F 248 " --> pdb=" O CYS F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 18 Processing helix chain 'G' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 71 Proline residue: G 59 - end of helix removed outlier: 3.731A pdb=" N ASN G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 93 through 107 Processing helix chain 'G' and resid 107 through 120 Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.643A pdb=" N LYS G 156 " --> pdb=" O LYS G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 Processing helix chain 'G' and resid 209 through 250 removed outlier: 3.677A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE G 240 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN G 247 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR G 248 " --> pdb=" O CYS G 244 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2775 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: 3.40 Time building geometry restraints manager: 6.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3630 1.33 - 1.45: 2203 1.45 - 1.57: 7278 1.57 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 13265 Sorted by residual: bond pdb=" N ALA A 93 " pdb=" CA ALA A 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.55e+00 bond pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.44e+00 bond pdb=" N ALA E 93 " pdb=" CA ALA E 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.30e+00 bond pdb=" N ALA D 93 " pdb=" CA ALA D 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.30e+00 bond pdb=" N ALA B 93 " pdb=" CA ALA B 93 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.10e-02 8.26e+03 6.14e+00 ... (remaining 13260 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.14: 410 107.14 - 113.88: 7507 113.88 - 120.62: 5610 120.62 - 127.36: 4302 127.36 - 134.10: 147 Bond angle restraints: 17976 Sorted by residual: angle pdb=" N LYS C 216 " pdb=" CA LYS C 216 " pdb=" C LYS C 216 " ideal model delta sigma weight residual 111.36 105.39 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" N LYS A 216 " pdb=" CA LYS A 216 " pdb=" C LYS A 216 " ideal model delta sigma weight residual 111.36 105.39 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" N LYS E 216 " pdb=" CA LYS E 216 " pdb=" C LYS E 216 " ideal model delta sigma weight residual 111.36 105.40 5.96 1.09e+00 8.42e-01 2.99e+01 angle pdb=" N LYS D 216 " pdb=" CA LYS D 216 " pdb=" C LYS D 216 " ideal model delta sigma weight residual 111.36 105.42 5.94 1.09e+00 8.42e-01 2.97e+01 angle pdb=" N LYS F 216 " pdb=" CA LYS F 216 " pdb=" C LYS F 216 " ideal model delta sigma weight residual 111.36 105.42 5.94 1.09e+00 8.42e-01 2.97e+01 ... (remaining 17971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.47: 7077 12.47 - 24.94: 631 24.94 - 37.40: 195 37.40 - 49.87: 77 49.87 - 62.34: 21 Dihedral angle restraints: 8001 sinusoidal: 3157 harmonic: 4844 Sorted by residual: dihedral pdb=" N LYS F 82 " pdb=" CA LYS F 82 " pdb=" CB LYS F 82 " pdb=" CG LYS F 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.30 -53.70 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" N LYS D 82 " pdb=" CA LYS D 82 " pdb=" CB LYS D 82 " pdb=" CG LYS D 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.31 -53.69 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LYS G 82 " pdb=" CA LYS G 82 " pdb=" CB LYS G 82 " pdb=" CG LYS G 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.31 -53.69 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 7998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1140 0.028 - 0.055: 586 0.055 - 0.082: 196 0.082 - 0.110: 90 0.110 - 0.137: 39 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA ALA C 93 " pdb=" N ALA C 93 " pdb=" C ALA C 93 " pdb=" CB ALA C 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ALA E 93 " pdb=" N ALA E 93 " pdb=" C ALA E 93 " pdb=" CB ALA E 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ALA G 93 " pdb=" N ALA G 93 " pdb=" C ALA G 93 " pdb=" CB ALA G 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 2048 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 215 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C THR F 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR F 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS F 216 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 215 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C THR B 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR B 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS B 216 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 215 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C THR G 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR G 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS G 216 " 0.018 2.00e-02 2.50e+03 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3776 2.82 - 3.34: 13431 3.34 - 3.86: 20754 3.86 - 4.38: 22653 4.38 - 4.90: 38774 Nonbonded interactions: 99388 Sorted by model distance: nonbonded pdb=" O LEU G 118 " pdb=" OG SER G 182 " model vdw 2.295 2.440 nonbonded pdb=" O LEU E 118 " pdb=" OG SER E 182 " model vdw 2.296 2.440 nonbonded pdb=" O LEU C 118 " pdb=" OG SER C 182 " model vdw 2.296 2.440 nonbonded pdb=" O LEU F 118 " pdb=" OG SER F 182 " model vdw 2.296 2.440 nonbonded pdb=" O LEU D 118 " pdb=" OG SER D 182 " model vdw 2.296 2.440 ... (remaining 99383 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 4.380 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 36.630 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 0.040 13265 Z= 0.318 Angle : 0.647 6.275 17976 Z= 0.408 Chirality : 0.041 0.137 2051 Planarity : 0.004 0.034 2212 Dihedral : 11.843 62.341 4795 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1575 helix: 0.44 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -3.31 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 62 HIS 0.002 0.001 HIS A 220 PHE 0.008 0.001 PHE G 163 TYR 0.011 0.001 TYR F 34 ARG 0.001 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 723 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.8983 (m-80) cc_final: 0.8725 (m-80) REVERT: A 49 TYR cc_start: 0.8924 (t80) cc_final: 0.8646 (t80) REVERT: A 95 LEU cc_start: 0.9332 (mt) cc_final: 0.9039 (pt) REVERT: A 96 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7822 (mtt180) REVERT: A 104 GLN cc_start: 0.8984 (mt0) cc_final: 0.7911 (tp40) REVERT: A 105 ARG cc_start: 0.8831 (tpt170) cc_final: 0.8573 (mmm-85) REVERT: A 177 TYR cc_start: 0.9186 (t80) cc_final: 0.8670 (t80) REVERT: A 227 LYS cc_start: 0.9495 (tttt) cc_final: 0.9188 (ttpt) REVERT: B 95 LEU cc_start: 0.9329 (mt) cc_final: 0.9073 (pt) REVERT: B 96 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7839 (mtt180) REVERT: B 104 GLN cc_start: 0.9059 (mt0) cc_final: 0.8032 (tp40) REVERT: B 105 ARG cc_start: 0.8954 (tpt170) cc_final: 0.8700 (mmm-85) REVERT: B 120 ASP cc_start: 0.8584 (t70) cc_final: 0.8368 (t0) REVERT: B 177 TYR cc_start: 0.9136 (t80) cc_final: 0.8455 (t80) REVERT: B 227 LYS cc_start: 0.9559 (tttt) cc_final: 0.9251 (ttpt) REVERT: C 47 TYR cc_start: 0.8946 (m-80) cc_final: 0.8728 (m-80) REVERT: C 95 LEU cc_start: 0.9218 (mt) cc_final: 0.9015 (pt) REVERT: C 96 ARG cc_start: 0.8082 (mtp180) cc_final: 0.7804 (mtt180) REVERT: C 104 GLN cc_start: 0.9065 (mt0) cc_final: 0.7950 (tm-30) REVERT: C 120 ASP cc_start: 0.8506 (t70) cc_final: 0.8305 (t0) REVERT: C 177 TYR cc_start: 0.9144 (t80) cc_final: 0.8374 (t80) REVERT: C 225 GLU cc_start: 0.9120 (tt0) cc_final: 0.8750 (pt0) REVERT: D 47 TYR cc_start: 0.8959 (m-80) cc_final: 0.8676 (m-80) REVERT: D 95 LEU cc_start: 0.9356 (mt) cc_final: 0.9124 (pt) REVERT: D 96 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7966 (mtt180) REVERT: D 98 MET cc_start: 0.9534 (ttp) cc_final: 0.9270 (ttp) REVERT: D 104 GLN cc_start: 0.9102 (mt0) cc_final: 0.7866 (tm-30) REVERT: D 105 ARG cc_start: 0.9030 (tpt170) cc_final: 0.8709 (mmm-85) REVERT: D 177 TYR cc_start: 0.9189 (t80) cc_final: 0.8521 (t80) REVERT: D 227 LYS cc_start: 0.9558 (tttt) cc_final: 0.9158 (ttpt) REVERT: E 47 TYR cc_start: 0.8933 (m-80) cc_final: 0.8648 (m-80) REVERT: E 95 LEU cc_start: 0.9295 (mt) cc_final: 0.9093 (pt) REVERT: E 96 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7897 (mtt180) REVERT: E 98 MET cc_start: 0.9483 (ttp) cc_final: 0.9278 (ttp) REVERT: E 104 GLN cc_start: 0.8978 (mt0) cc_final: 0.7985 (tm-30) REVERT: E 177 TYR cc_start: 0.9096 (t80) cc_final: 0.8278 (t80) REVERT: E 225 GLU cc_start: 0.9195 (tt0) cc_final: 0.8935 (pt0) REVERT: F 47 TYR cc_start: 0.8944 (m-80) cc_final: 0.8641 (m-80) REVERT: F 95 LEU cc_start: 0.9316 (mt) cc_final: 0.9095 (pt) REVERT: F 96 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7876 (mtt90) REVERT: F 104 GLN cc_start: 0.9062 (mt0) cc_final: 0.8097 (tp40) REVERT: F 105 ARG cc_start: 0.8918 (tpt170) cc_final: 0.8626 (mmm-85) REVERT: F 177 TYR cc_start: 0.9185 (t80) cc_final: 0.8471 (t80) REVERT: F 215 THR cc_start: 0.9492 (t) cc_final: 0.9183 (t) REVERT: F 225 GLU cc_start: 0.9196 (tt0) cc_final: 0.8983 (pt0) REVERT: G 46 ASP cc_start: 0.9225 (m-30) cc_final: 0.9004 (m-30) REVERT: G 47 TYR cc_start: 0.8976 (m-80) cc_final: 0.8709 (m-10) REVERT: G 96 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7369 (mtt90) REVERT: G 104 GLN cc_start: 0.8960 (mt0) cc_final: 0.7562 (tp40) REVERT: G 105 ARG cc_start: 0.8931 (tpt170) cc_final: 0.8517 (mmm-85) REVERT: G 142 TYR cc_start: 0.8132 (m-80) cc_final: 0.7863 (m-10) REVERT: G 177 TYR cc_start: 0.9284 (t80) cc_final: 0.8680 (t80) REVERT: G 229 PHE cc_start: 0.9292 (t80) cc_final: 0.8900 (t80) outliers start: 0 outliers final: 0 residues processed: 723 average time/residue: 0.2984 time to fit residues: 288.2642 Evaluate side-chains 484 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 246 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13265 Z= 0.317 Angle : 0.700 9.154 17976 Z= 0.361 Chirality : 0.040 0.127 2051 Planarity : 0.005 0.043 2212 Dihedral : 4.836 31.823 1890 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 5.83 % Allowed : 21.17 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.23), residues: 1575 helix: 1.78 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -1.65 (0.39), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 62 HIS 0.002 0.001 HIS E 220 PHE 0.017 0.001 PHE G 212 TYR 0.014 0.002 TYR C 142 ARG 0.009 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 504 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8787 (tt0) REVERT: A 49 TYR cc_start: 0.8902 (t80) cc_final: 0.8683 (t80) REVERT: A 71 ASN cc_start: 0.8562 (t0) cc_final: 0.8237 (t0) REVERT: A 96 ARG cc_start: 0.8332 (mtp180) cc_final: 0.8042 (mtt180) REVERT: A 104 GLN cc_start: 0.8928 (mt0) cc_final: 0.7797 (tp40) REVERT: A 105 ARG cc_start: 0.8915 (tpt170) cc_final: 0.8609 (mmm-85) REVERT: B 40 THR cc_start: 0.9668 (OUTLIER) cc_final: 0.9342 (p) REVERT: B 96 ARG cc_start: 0.8365 (mtp180) cc_final: 0.8093 (mtt180) REVERT: B 104 GLN cc_start: 0.9010 (mt0) cc_final: 0.7884 (tp40) REVERT: B 105 ARG cc_start: 0.8983 (tpt170) cc_final: 0.8738 (mmm-85) REVERT: B 119 MET cc_start: 0.8400 (mmm) cc_final: 0.8113 (mmp) REVERT: B 122 LYS cc_start: 0.9426 (mmtp) cc_final: 0.9184 (mmmm) REVERT: B 148 LYS cc_start: 0.9514 (mmmt) cc_final: 0.9308 (mmmt) REVERT: B 152 LYS cc_start: 0.9519 (mttt) cc_final: 0.9289 (mppt) REVERT: B 179 ARG cc_start: 0.9079 (mmm-85) cc_final: 0.8546 (ttm-80) REVERT: B 233 CYS cc_start: 0.8695 (m) cc_final: 0.8389 (m) REVERT: C 26 MET cc_start: 0.7871 (mmp) cc_final: 0.7666 (mmp) REVERT: C 96 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8052 (mtt180) REVERT: C 104 GLN cc_start: 0.9061 (mt0) cc_final: 0.7919 (tp40) REVERT: C 120 ASP cc_start: 0.8266 (t70) cc_final: 0.8053 (t0) REVERT: C 152 LYS cc_start: 0.9533 (mttt) cc_final: 0.9239 (mppt) REVERT: C 177 TYR cc_start: 0.8987 (t80) cc_final: 0.8738 (t80) REVERT: C 179 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8602 (mtp85) REVERT: C 221 TYR cc_start: 0.9185 (t80) cc_final: 0.8982 (t80) REVERT: C 233 CYS cc_start: 0.8972 (m) cc_final: 0.8702 (m) REVERT: D 32 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8634 (tp40) REVERT: D 47 TYR cc_start: 0.9007 (m-80) cc_final: 0.8614 (m-80) REVERT: D 68 TYR cc_start: 0.8555 (m-80) cc_final: 0.8221 (t80) REVERT: D 71 ASN cc_start: 0.8784 (t0) cc_final: 0.8387 (t0) REVERT: D 96 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8202 (mtt180) REVERT: D 104 GLN cc_start: 0.8923 (mt0) cc_final: 0.7769 (tp40) REVERT: D 105 ARG cc_start: 0.9052 (tpt170) cc_final: 0.8749 (mmm-85) REVERT: D 120 ASP cc_start: 0.8718 (t0) cc_final: 0.8352 (t0) REVERT: E 47 TYR cc_start: 0.9020 (m-80) cc_final: 0.8667 (m-80) REVERT: E 71 ASN cc_start: 0.8525 (t0) cc_final: 0.8174 (t0) REVERT: E 96 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8112 (mtt180) REVERT: E 102 MET cc_start: 0.9326 (ttm) cc_final: 0.9092 (ttm) REVERT: E 104 GLN cc_start: 0.8989 (mt0) cc_final: 0.7903 (tp40) REVERT: E 120 ASP cc_start: 0.8477 (t0) cc_final: 0.8077 (t0) REVERT: E 152 LYS cc_start: 0.9525 (mttt) cc_final: 0.9257 (mppt) REVERT: E 216 LYS cc_start: 0.9580 (mmmm) cc_final: 0.9230 (mmmm) REVERT: F 96 ARG cc_start: 0.8407 (mtp180) cc_final: 0.8025 (mtt90) REVERT: F 104 GLN cc_start: 0.9027 (mt0) cc_final: 0.7957 (tp40) REVERT: F 105 ARG cc_start: 0.8975 (tpt170) cc_final: 0.8705 (mmm-85) REVERT: F 179 ARG cc_start: 0.9083 (mmm-85) cc_final: 0.8550 (mtp85) REVERT: G 40 THR cc_start: 0.9656 (OUTLIER) cc_final: 0.9320 (p) REVERT: G 71 ASN cc_start: 0.8631 (t0) cc_final: 0.8375 (t0) REVERT: G 95 LEU cc_start: 0.9366 (mt) cc_final: 0.9120 (pt) REVERT: G 96 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7672 (mtt180) REVERT: G 104 GLN cc_start: 0.8938 (mt0) cc_final: 0.7656 (tp40) REVERT: G 105 ARG cc_start: 0.8967 (tpt170) cc_final: 0.8688 (mmm-85) REVERT: G 120 ASP cc_start: 0.8479 (t0) cc_final: 0.8080 (t0) REVERT: G 122 LYS cc_start: 0.9465 (mmtp) cc_final: 0.9208 (mmtp) REVERT: G 152 LYS cc_start: 0.9536 (mttt) cc_final: 0.9269 (mppt) REVERT: G 246 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8415 (mp10) outliers start: 78 outliers final: 55 residues processed: 534 average time/residue: 0.3157 time to fit residues: 225.1352 Evaluate side-chains 494 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 437 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13265 Z= 0.315 Angle : 0.669 8.302 17976 Z= 0.341 Chirality : 0.039 0.133 2051 Planarity : 0.005 0.058 2212 Dihedral : 4.407 26.311 1890 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.76 % Allowed : 22.81 % Favored : 71.43 % 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: 2.24 (0.23), residues: 1575 helix: 2.21 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -1.20 (0.40), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 62 HIS 0.002 0.001 HIS A 220 PHE 0.015 0.001 PHE G 229 TYR 0.017 0.002 TYR G 47 ARG 0.006 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 466 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9005 (m-80) cc_final: 0.8682 (m-80) REVERT: A 49 TYR cc_start: 0.8897 (t80) cc_final: 0.8653 (t80) REVERT: A 71 ASN cc_start: 0.8528 (t0) cc_final: 0.8195 (t0) REVERT: A 96 ARG cc_start: 0.8429 (mtp180) cc_final: 0.8041 (mtt180) REVERT: A 104 GLN cc_start: 0.8955 (mt0) cc_final: 0.7807 (tp40) REVERT: A 105 ARG cc_start: 0.8917 (tpt170) cc_final: 0.8594 (mmm-85) REVERT: A 120 ASP cc_start: 0.8558 (t0) cc_final: 0.8269 (t0) REVERT: B 32 GLN cc_start: 0.8891 (tt0) cc_final: 0.8553 (tt0) REVERT: B 96 ARG cc_start: 0.8438 (mtp180) cc_final: 0.8070 (mtt180) REVERT: B 104 GLN cc_start: 0.9030 (mt0) cc_final: 0.7860 (tp40) REVERT: B 152 LYS cc_start: 0.9528 (mttt) cc_final: 0.9296 (mppt) REVERT: B 233 CYS cc_start: 0.8798 (m) cc_final: 0.8556 (m) REVERT: C 32 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8331 (tp40) REVERT: C 96 ARG cc_start: 0.8473 (mtp180) cc_final: 0.8124 (mtt180) REVERT: C 104 GLN cc_start: 0.9088 (mt0) cc_final: 0.7908 (tm-30) REVERT: C 152 LYS cc_start: 0.9532 (mttt) cc_final: 0.9262 (mppt) REVERT: C 177 TYR cc_start: 0.8987 (t80) cc_final: 0.8716 (t80) REVERT: C 201 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8418 (tpt-90) REVERT: C 216 LYS cc_start: 0.9550 (mmmm) cc_final: 0.9157 (mmtp) REVERT: C 226 ARG cc_start: 0.8710 (mmp-170) cc_final: 0.8137 (mmp-170) REVERT: C 233 CYS cc_start: 0.8967 (m) cc_final: 0.8749 (m) REVERT: D 32 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8606 (tp40) REVERT: D 68 TYR cc_start: 0.8528 (m-80) cc_final: 0.8252 (t80) REVERT: D 71 ASN cc_start: 0.8776 (t0) cc_final: 0.8447 (t0) REVERT: D 96 ARG cc_start: 0.8504 (mtp180) cc_final: 0.8181 (mtt180) REVERT: D 104 GLN cc_start: 0.8935 (mt0) cc_final: 0.7836 (tp40) REVERT: D 105 ARG cc_start: 0.9078 (tpt170) cc_final: 0.8652 (mmm-85) REVERT: D 108 ILE cc_start: 0.9436 (mm) cc_final: 0.9178 (mp) REVERT: D 120 ASP cc_start: 0.8650 (t0) cc_final: 0.8218 (t0) REVERT: D 177 TYR cc_start: 0.8916 (t80) cc_final: 0.8709 (t80) REVERT: E 47 TYR cc_start: 0.9029 (m-80) cc_final: 0.8646 (m-80) REVERT: E 71 ASN cc_start: 0.8549 (t0) cc_final: 0.8317 (t0) REVERT: E 96 ARG cc_start: 0.8369 (mtp180) cc_final: 0.8085 (mtt180) REVERT: E 104 GLN cc_start: 0.8977 (mt0) cc_final: 0.7866 (tm-30) REVERT: E 120 ASP cc_start: 0.8432 (t0) cc_final: 0.7875 (t0) REVERT: E 148 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9342 (mmmt) REVERT: E 152 LYS cc_start: 0.9547 (mttt) cc_final: 0.9258 (mppt) REVERT: E 214 LYS cc_start: 0.9765 (mmtp) cc_final: 0.9547 (mmtt) REVERT: E 216 LYS cc_start: 0.9582 (mmmm) cc_final: 0.9222 (mmtp) REVERT: E 226 ARG cc_start: 0.8849 (mmp-170) cc_final: 0.8238 (mmp80) REVERT: F 96 ARG cc_start: 0.8455 (mtp180) cc_final: 0.8013 (mtt90) REVERT: F 104 GLN cc_start: 0.9034 (mt0) cc_final: 0.7942 (tp40) REVERT: F 105 ARG cc_start: 0.8991 (tpt170) cc_final: 0.8700 (mmm-85) REVERT: F 179 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8724 (mtp85) REVERT: F 216 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9217 (mmmm) REVERT: F 223 ASP cc_start: 0.9666 (t0) cc_final: 0.9463 (t0) REVERT: G 38 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8322 (tp30) REVERT: G 71 ASN cc_start: 0.8641 (t0) cc_final: 0.8407 (t0) REVERT: G 95 LEU cc_start: 0.9400 (mt) cc_final: 0.9192 (pt) REVERT: G 96 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7751 (mtt180) REVERT: G 104 GLN cc_start: 0.8947 (mt0) cc_final: 0.7623 (tp40) REVERT: G 105 ARG cc_start: 0.8994 (tpt170) cc_final: 0.8645 (mmm-85) REVERT: G 120 ASP cc_start: 0.8409 (t0) cc_final: 0.7980 (t0) REVERT: G 148 LYS cc_start: 0.9603 (mmmt) cc_final: 0.9313 (mmmt) REVERT: G 152 LYS cc_start: 0.9556 (mttt) cc_final: 0.9281 (mppt) REVERT: G 246 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8607 (mp10) outliers start: 77 outliers final: 58 residues processed: 501 average time/residue: 0.3060 time to fit residues: 209.1842 Evaluate side-chains 497 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 439 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 146 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.0770 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 50.0000 chunk 98 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13265 Z= 0.192 Angle : 0.627 8.610 17976 Z= 0.315 Chirality : 0.038 0.182 2051 Planarity : 0.005 0.048 2212 Dihedral : 3.841 17.633 1890 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.81 % Allowed : 25.06 % Favored : 71.13 % 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: 2.30 (0.22), residues: 1575 helix: 2.36 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -1.86 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 62 HIS 0.001 0.000 HIS G 236 PHE 0.020 0.001 PHE F 137 TYR 0.014 0.001 TYR D 217 ARG 0.006 0.001 ARG G 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 466 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8647 (tp40) REVERT: A 47 TYR cc_start: 0.8938 (m-80) cc_final: 0.8615 (m-80) REVERT: A 71 ASN cc_start: 0.8501 (t0) cc_final: 0.8154 (t0) REVERT: A 96 ARG cc_start: 0.8318 (mtp180) cc_final: 0.7979 (mtt180) REVERT: A 104 GLN cc_start: 0.8918 (mt0) cc_final: 0.7681 (tp40) REVERT: A 105 ARG cc_start: 0.8904 (tpt170) cc_final: 0.8579 (mmm-85) REVERT: A 120 ASP cc_start: 0.8506 (t0) cc_final: 0.8018 (t0) REVERT: A 122 LYS cc_start: 0.9364 (mmmt) cc_final: 0.9031 (mmmm) REVERT: B 32 GLN cc_start: 0.8878 (tt0) cc_final: 0.8614 (tt0) REVERT: B 96 ARG cc_start: 0.8344 (mtp180) cc_final: 0.7974 (mtt180) REVERT: B 104 GLN cc_start: 0.8982 (mt0) cc_final: 0.7647 (tp40) REVERT: B 105 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8697 (mmm-85) REVERT: B 223 ASP cc_start: 0.9449 (t0) cc_final: 0.9241 (t0) REVERT: B 233 CYS cc_start: 0.8841 (m) cc_final: 0.8609 (m) REVERT: C 26 MET cc_start: 0.7924 (mmp) cc_final: 0.7714 (mmp) REVERT: C 96 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7976 (mtt180) REVERT: C 104 GLN cc_start: 0.9023 (mt0) cc_final: 0.7887 (tm-30) REVERT: C 226 ARG cc_start: 0.8811 (mmp-170) cc_final: 0.8175 (mmp-170) REVERT: C 233 CYS cc_start: 0.8972 (m) cc_final: 0.8743 (m) REVERT: D 71 ASN cc_start: 0.8733 (t0) cc_final: 0.8308 (t0) REVERT: D 96 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8036 (mtt180) REVERT: D 104 GLN cc_start: 0.8876 (mt0) cc_final: 0.7722 (tp40) REVERT: D 105 ARG cc_start: 0.9028 (tpt170) cc_final: 0.8778 (mmm-85) REVERT: D 120 ASP cc_start: 0.8512 (t0) cc_final: 0.7870 (t0) REVERT: D 177 TYR cc_start: 0.8817 (t80) cc_final: 0.8602 (t80) REVERT: D 223 ASP cc_start: 0.9415 (t0) cc_final: 0.9174 (t0) REVERT: D 226 ARG cc_start: 0.9186 (ttp80) cc_final: 0.8968 (ttp80) REVERT: E 40 THR cc_start: 0.9708 (OUTLIER) cc_final: 0.9484 (p) REVERT: E 47 TYR cc_start: 0.8979 (m-80) cc_final: 0.8607 (m-80) REVERT: E 71 ASN cc_start: 0.8481 (t0) cc_final: 0.8137 (t0) REVERT: E 96 ARG cc_start: 0.8285 (mtp180) cc_final: 0.7989 (mtt180) REVERT: E 104 GLN cc_start: 0.8948 (mt0) cc_final: 0.7715 (tm-30) REVERT: E 120 ASP cc_start: 0.8307 (t0) cc_final: 0.7639 (t0) REVERT: E 152 LYS cc_start: 0.9558 (mttt) cc_final: 0.9331 (mttt) REVERT: E 226 ARG cc_start: 0.8910 (mmp-170) cc_final: 0.8291 (mmp80) REVERT: E 233 CYS cc_start: 0.8903 (m) cc_final: 0.8692 (m) REVERT: F 32 GLN cc_start: 0.9000 (tp40) cc_final: 0.8698 (tt0) REVERT: F 96 ARG cc_start: 0.8346 (mtp180) cc_final: 0.7928 (mtt180) REVERT: F 104 GLN cc_start: 0.8897 (mt0) cc_final: 0.7781 (tp40) REVERT: F 105 ARG cc_start: 0.8961 (tpt170) cc_final: 0.8678 (mmm-85) REVERT: F 179 ARG cc_start: 0.8967 (mmm-85) cc_final: 0.8682 (mtp85) REVERT: F 216 LYS cc_start: 0.9448 (mmmm) cc_final: 0.9165 (mmmm) REVERT: F 233 CYS cc_start: 0.9025 (m) cc_final: 0.8817 (m) REVERT: G 28 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8773 (mm) REVERT: G 71 ASN cc_start: 0.8612 (t0) cc_final: 0.8259 (t0) REVERT: G 96 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7684 (mtt180) REVERT: G 104 GLN cc_start: 0.8908 (mt0) cc_final: 0.7579 (tp40) REVERT: G 105 ARG cc_start: 0.8976 (tpt170) cc_final: 0.8691 (mmm-85) REVERT: G 120 ASP cc_start: 0.8256 (t0) cc_final: 0.7792 (t0) REVERT: G 148 LYS cc_start: 0.9611 (mmmt) cc_final: 0.9304 (mmmt) REVERT: G 152 LYS cc_start: 0.9548 (mttt) cc_final: 0.9277 (mppt) REVERT: G 201 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8504 (tpp80) REVERT: G 233 CYS cc_start: 0.8607 (m) cc_final: 0.8382 (m) REVERT: G 246 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8708 (mp10) outliers start: 51 outliers final: 33 residues processed: 488 average time/residue: 0.2650 time to fit residues: 178.1887 Evaluate side-chains 483 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 447 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 0 optimal weight: 60.0000 chunk 79 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13265 Z= 0.250 Angle : 0.611 8.320 17976 Z= 0.311 Chirality : 0.039 0.152 2051 Planarity : 0.004 0.050 2212 Dihedral : 3.705 17.030 1890 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.64 % Allowed : 26.03 % Favored : 69.33 % 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: 2.42 (0.22), residues: 1575 helix: 2.41 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -1.65 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 62 HIS 0.002 0.001 HIS E 236 PHE 0.012 0.001 PHE B 124 TYR 0.014 0.001 TYR B 34 ARG 0.007 0.001 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 444 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8692 (tp40) REVERT: A 47 TYR cc_start: 0.8971 (m-80) cc_final: 0.8768 (m-10) REVERT: A 71 ASN cc_start: 0.8495 (t0) cc_final: 0.8111 (t0) REVERT: A 83 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7087 (mtm110) REVERT: A 96 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8096 (mtt180) REVERT: A 104 GLN cc_start: 0.8961 (mt0) cc_final: 0.7663 (tp40) REVERT: A 105 ARG cc_start: 0.8926 (tpt170) cc_final: 0.8595 (mmm-85) REVERT: A 120 ASP cc_start: 0.8607 (t0) cc_final: 0.8121 (t0) REVERT: B 47 TYR cc_start: 0.9021 (m-80) cc_final: 0.8804 (m-10) REVERT: B 96 ARG cc_start: 0.8361 (mtp180) cc_final: 0.8054 (mtt180) REVERT: B 104 GLN cc_start: 0.9013 (mt0) cc_final: 0.7675 (tp40) REVERT: B 233 CYS cc_start: 0.8859 (m) cc_final: 0.8641 (m) REVERT: C 26 MET cc_start: 0.8031 (mmp) cc_final: 0.7824 (mmp) REVERT: C 96 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8020 (mtt180) REVERT: C 104 GLN cc_start: 0.9067 (mt0) cc_final: 0.7951 (tm-30) REVERT: C 226 ARG cc_start: 0.8868 (mmp-170) cc_final: 0.8282 (mmp-170) REVERT: C 233 CYS cc_start: 0.8996 (m) cc_final: 0.8773 (m) REVERT: D 32 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8600 (tp40) REVERT: D 71 ASN cc_start: 0.8702 (t0) cc_final: 0.8360 (t0) REVERT: D 96 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8121 (mtt180) REVERT: D 104 GLN cc_start: 0.8922 (mt0) cc_final: 0.7811 (tp40) REVERT: D 105 ARG cc_start: 0.9040 (tpt170) cc_final: 0.8689 (mmm-85) REVERT: D 108 ILE cc_start: 0.9412 (mm) cc_final: 0.9186 (mp) REVERT: D 120 ASP cc_start: 0.8410 (t0) cc_final: 0.7824 (t0) REVERT: D 223 ASP cc_start: 0.9408 (t0) cc_final: 0.9192 (t0) REVERT: D 226 ARG cc_start: 0.9151 (ttp80) cc_final: 0.8930 (ttp80) REVERT: E 32 GLN cc_start: 0.8898 (mt0) cc_final: 0.8372 (tt0) REVERT: E 40 THR cc_start: 0.9695 (OUTLIER) cc_final: 0.9444 (p) REVERT: E 71 ASN cc_start: 0.8598 (t0) cc_final: 0.8368 (t0) REVERT: E 96 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8026 (mtt180) REVERT: E 104 GLN cc_start: 0.8962 (mt0) cc_final: 0.7810 (tm-30) REVERT: E 120 ASP cc_start: 0.8399 (t0) cc_final: 0.7722 (t0) REVERT: E 152 LYS cc_start: 0.9589 (mttt) cc_final: 0.9360 (mttt) REVERT: E 209 GLN cc_start: 0.8921 (pm20) cc_final: 0.8707 (pm20) REVERT: E 226 ARG cc_start: 0.8919 (mmp-170) cc_final: 0.8326 (mmp80) REVERT: E 233 CYS cc_start: 0.8911 (m) cc_final: 0.8697 (m) REVERT: F 96 ARG cc_start: 0.8433 (mtp180) cc_final: 0.8020 (mtt90) REVERT: F 104 GLN cc_start: 0.8925 (mt0) cc_final: 0.7699 (tp40) REVERT: F 105 ARG cc_start: 0.8985 (tpt170) cc_final: 0.8634 (mmm-85) REVERT: F 179 ARG cc_start: 0.8967 (mmm-85) cc_final: 0.8531 (tpp80) REVERT: F 216 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9125 (mmmm) REVERT: F 223 ASP cc_start: 0.9617 (t0) cc_final: 0.9262 (t0) REVERT: F 233 CYS cc_start: 0.9035 (m) cc_final: 0.8821 (m) REVERT: G 71 ASN cc_start: 0.8468 (t0) cc_final: 0.8165 (t0) REVERT: G 96 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7889 (mtt180) REVERT: G 104 GLN cc_start: 0.8945 (mt0) cc_final: 0.7715 (tp40) REVERT: G 105 ARG cc_start: 0.9006 (tpt170) cc_final: 0.8715 (mmm-85) REVERT: G 120 ASP cc_start: 0.8376 (t0) cc_final: 0.7874 (t0) REVERT: G 148 LYS cc_start: 0.9652 (mmmt) cc_final: 0.9324 (mmmt) REVERT: G 152 LYS cc_start: 0.9555 (mttt) cc_final: 0.9273 (mppt) REVERT: G 201 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8512 (tpp80) REVERT: G 233 CYS cc_start: 0.8717 (m) cc_final: 0.8490 (m) outliers start: 62 outliers final: 45 residues processed: 468 average time/residue: 0.2722 time to fit residues: 174.6533 Evaluate side-chains 487 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 439 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 0.0570 chunk 155 optimal weight: 0.6980 chunk 129 optimal weight: 0.0370 chunk 72 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 150 optimal weight: 7.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13265 Z= 0.176 Angle : 0.600 8.371 17976 Z= 0.304 Chirality : 0.038 0.163 2051 Planarity : 0.005 0.049 2212 Dihedral : 3.502 17.211 1890 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.99 % Allowed : 27.23 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.22), residues: 1575 helix: 2.57 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -1.59 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 62 HIS 0.001 0.000 HIS E 236 PHE 0.012 0.001 PHE B 137 TYR 0.014 0.001 TYR A 49 ARG 0.007 0.001 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 476 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8600 (tp40) REVERT: A 71 ASN cc_start: 0.8474 (t0) cc_final: 0.8017 (t0) REVERT: A 83 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6997 (mtm110) REVERT: A 96 ARG cc_start: 0.8360 (mtp180) cc_final: 0.8109 (mtt180) REVERT: A 104 GLN cc_start: 0.8923 (mt0) cc_final: 0.7664 (tp40) REVERT: A 105 ARG cc_start: 0.8888 (tpt170) cc_final: 0.8585 (mmm-85) REVERT: A 120 ASP cc_start: 0.8449 (t0) cc_final: 0.7838 (t0) REVERT: A 122 LYS cc_start: 0.9361 (mmmt) cc_final: 0.9081 (mttm) REVERT: B 96 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7981 (mtp180) REVERT: B 104 GLN cc_start: 0.8967 (mt0) cc_final: 0.7563 (tp40) REVERT: B 233 CYS cc_start: 0.8842 (m) cc_final: 0.8609 (m) REVERT: C 26 MET cc_start: 0.7907 (mmp) cc_final: 0.7597 (mmp) REVERT: C 96 ARG cc_start: 0.8358 (mtp180) cc_final: 0.7943 (mtt180) REVERT: C 104 GLN cc_start: 0.9023 (mt0) cc_final: 0.7939 (tm-30) REVERT: C 226 ARG cc_start: 0.8862 (mmp-170) cc_final: 0.8272 (mmp-170) REVERT: C 233 CYS cc_start: 0.9016 (m) cc_final: 0.8786 (m) REVERT: D 32 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8540 (tp40) REVERT: D 71 ASN cc_start: 0.8797 (t0) cc_final: 0.8479 (t0) REVERT: D 96 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8000 (mtp180) REVERT: D 104 GLN cc_start: 0.8845 (mt0) cc_final: 0.7784 (tm-30) REVERT: D 105 ARG cc_start: 0.9027 (tpt170) cc_final: 0.8632 (mmm-85) REVERT: D 108 ILE cc_start: 0.9397 (mm) cc_final: 0.9158 (mp) REVERT: D 120 ASP cc_start: 0.8221 (t0) cc_final: 0.7552 (t0) REVERT: E 32 GLN cc_start: 0.8890 (mt0) cc_final: 0.8263 (tt0) REVERT: E 71 ASN cc_start: 0.8611 (t0) cc_final: 0.8376 (t0) REVERT: E 96 ARG cc_start: 0.8334 (mtp180) cc_final: 0.7975 (mtt180) REVERT: E 104 GLN cc_start: 0.8936 (mt0) cc_final: 0.7632 (tm-30) REVERT: E 120 ASP cc_start: 0.8291 (t0) cc_final: 0.7681 (t0) REVERT: E 152 LYS cc_start: 0.9572 (mttt) cc_final: 0.9290 (mttt) REVERT: E 209 GLN cc_start: 0.8881 (pm20) cc_final: 0.8664 (pm20) REVERT: E 226 ARG cc_start: 0.8936 (mmp-170) cc_final: 0.8340 (mmp-170) REVERT: E 233 CYS cc_start: 0.8959 (m) cc_final: 0.8742 (m) REVERT: F 96 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8022 (mtp180) REVERT: F 104 GLN cc_start: 0.8897 (mt0) cc_final: 0.7686 (tp40) REVERT: F 105 ARG cc_start: 0.8979 (tpt170) cc_final: 0.8664 (mmm-85) REVERT: F 233 CYS cc_start: 0.9070 (m) cc_final: 0.8864 (m) REVERT: G 71 ASN cc_start: 0.8389 (t0) cc_final: 0.8065 (t0) REVERT: G 96 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7744 (mtt180) REVERT: G 104 GLN cc_start: 0.8895 (mt0) cc_final: 0.7489 (tp40) REVERT: G 105 ARG cc_start: 0.8965 (tpt170) cc_final: 0.8667 (mmm-85) REVERT: G 120 ASP cc_start: 0.8215 (t0) cc_final: 0.7678 (t0) REVERT: G 148 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9330 (mmmt) REVERT: G 152 LYS cc_start: 0.9546 (mttt) cc_final: 0.9245 (mppt) REVERT: G 160 LYS cc_start: 0.9314 (ttmm) cc_final: 0.9024 (ttmm) REVERT: G 201 ARG cc_start: 0.8697 (tpp80) cc_final: 0.8456 (tpp80) REVERT: G 233 CYS cc_start: 0.8696 (m) cc_final: 0.8464 (m) REVERT: G 246 GLN cc_start: 0.8256 (mp10) cc_final: 0.7835 (mp10) outliers start: 40 outliers final: 29 residues processed: 494 average time/residue: 0.2613 time to fit residues: 179.0089 Evaluate side-chains 489 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 458 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13265 Z= 0.207 Angle : 0.598 8.060 17976 Z= 0.305 Chirality : 0.039 0.173 2051 Planarity : 0.004 0.047 2212 Dihedral : 3.419 16.673 1890 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.59 % Allowed : 28.50 % Favored : 67.91 % 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: 2.71 (0.22), residues: 1575 helix: 2.60 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 62 HIS 0.002 0.000 HIS C 236 PHE 0.013 0.001 PHE F 124 TYR 0.017 0.001 TYR D 97 ARG 0.010 0.001 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 451 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8656 (tp40) REVERT: A 38 GLU cc_start: 0.8289 (tp30) cc_final: 0.7717 (tp30) REVERT: A 71 ASN cc_start: 0.8448 (t0) cc_final: 0.7995 (t0) REVERT: A 96 ARG cc_start: 0.8372 (mtp180) cc_final: 0.8085 (mtt180) REVERT: A 104 GLN cc_start: 0.8939 (mt0) cc_final: 0.7647 (tp40) REVERT: A 105 ARG cc_start: 0.8905 (tpt170) cc_final: 0.8600 (mmm-85) REVERT: A 120 ASP cc_start: 0.8428 (t0) cc_final: 0.7853 (t0) REVERT: A 122 LYS cc_start: 0.9373 (mmmt) cc_final: 0.9086 (mttm) REVERT: A 209 GLN cc_start: 0.8952 (pm20) cc_final: 0.8734 (pm20) REVERT: B 32 GLN cc_start: 0.8887 (tt0) cc_final: 0.8603 (tt0) REVERT: B 47 TYR cc_start: 0.8989 (m-80) cc_final: 0.8773 (m-10) REVERT: B 96 ARG cc_start: 0.8342 (mtp180) cc_final: 0.7973 (mtt180) REVERT: B 104 GLN cc_start: 0.8970 (mt0) cc_final: 0.7649 (tp40) REVERT: B 233 CYS cc_start: 0.8874 (m) cc_final: 0.8649 (m) REVERT: C 96 ARG cc_start: 0.8390 (mtp180) cc_final: 0.7967 (mtt180) REVERT: C 104 GLN cc_start: 0.9034 (mt0) cc_final: 0.7932 (tm-30) REVERT: C 226 ARG cc_start: 0.8887 (mmp-170) cc_final: 0.8317 (mmp-170) REVERT: C 233 CYS cc_start: 0.9001 (m) cc_final: 0.8787 (m) REVERT: D 32 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8531 (tp40) REVERT: D 71 ASN cc_start: 0.8819 (t0) cc_final: 0.8473 (t0) REVERT: D 83 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6314 (tmt170) REVERT: D 96 ARG cc_start: 0.8389 (mtp180) cc_final: 0.8038 (mtp180) REVERT: D 104 GLN cc_start: 0.8898 (mt0) cc_final: 0.7791 (tm-30) REVERT: D 105 ARG cc_start: 0.9032 (tpt170) cc_final: 0.8650 (mmm-85) REVERT: D 108 ILE cc_start: 0.9399 (mm) cc_final: 0.9154 (mp) REVERT: D 120 ASP cc_start: 0.8297 (t0) cc_final: 0.7624 (t0) REVERT: E 32 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8350 (tt0) REVERT: E 71 ASN cc_start: 0.8531 (t0) cc_final: 0.8242 (t0) REVERT: E 96 ARG cc_start: 0.8432 (mtp180) cc_final: 0.8011 (mtt180) REVERT: E 104 GLN cc_start: 0.8947 (mt0) cc_final: 0.7644 (tm-30) REVERT: E 120 ASP cc_start: 0.8330 (t0) cc_final: 0.7615 (t0) REVERT: E 152 LYS cc_start: 0.9576 (mttt) cc_final: 0.9312 (mttt) REVERT: E 209 GLN cc_start: 0.8900 (pm20) cc_final: 0.8693 (pm20) REVERT: E 226 ARG cc_start: 0.8953 (mmp-170) cc_final: 0.8364 (mmp-170) REVERT: F 96 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8033 (mtt180) REVERT: F 104 GLN cc_start: 0.8887 (mt0) cc_final: 0.7862 (tp40) REVERT: F 105 ARG cc_start: 0.8979 (tpt170) cc_final: 0.8736 (mmm-85) REVERT: F 223 ASP cc_start: 0.9626 (t0) cc_final: 0.9370 (t0) REVERT: G 32 GLN cc_start: 0.8973 (tt0) cc_final: 0.8706 (tt0) REVERT: G 71 ASN cc_start: 0.8361 (t0) cc_final: 0.8071 (t0) REVERT: G 96 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7808 (mtt180) REVERT: G 104 GLN cc_start: 0.8918 (mt0) cc_final: 0.7503 (tp40) REVERT: G 105 ARG cc_start: 0.9010 (tpt170) cc_final: 0.8703 (mmm-85) REVERT: G 120 ASP cc_start: 0.8286 (t0) cc_final: 0.7738 (t0) REVERT: G 148 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9351 (mmmt) REVERT: G 152 LYS cc_start: 0.9549 (mttt) cc_final: 0.9249 (mppt) REVERT: G 216 LYS cc_start: 0.9639 (tptt) cc_final: 0.9374 (mmmm) REVERT: G 233 CYS cc_start: 0.8740 (m) cc_final: 0.8503 (m) REVERT: G 246 GLN cc_start: 0.8335 (mp10) cc_final: 0.7851 (mp10) outliers start: 48 outliers final: 37 residues processed: 472 average time/residue: 0.2632 time to fit residues: 171.0757 Evaluate side-chains 484 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 445 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 105 optimal weight: 0.0870 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13265 Z= 0.374 Angle : 0.658 7.918 17976 Z= 0.342 Chirality : 0.041 0.165 2051 Planarity : 0.005 0.048 2212 Dihedral : 3.752 16.724 1890 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.79 % Allowed : 27.52 % Favored : 67.69 % 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: 2.58 (0.22), residues: 1575 helix: 2.48 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.50 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 62 HIS 0.003 0.001 HIS B 220 PHE 0.020 0.001 PHE D 124 TYR 0.018 0.002 TYR D 34 ARG 0.009 0.001 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 414 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8590 (t0) cc_final: 0.8124 (t0) REVERT: A 96 ARG cc_start: 0.8440 (mtp180) cc_final: 0.8176 (mtt180) REVERT: A 104 GLN cc_start: 0.8993 (mt0) cc_final: 0.7660 (tp40) REVERT: A 105 ARG cc_start: 0.8961 (tpt170) cc_final: 0.8639 (mmm-85) REVERT: A 120 ASP cc_start: 0.8687 (t0) cc_final: 0.8226 (t0) REVERT: A 122 LYS cc_start: 0.9429 (mmmt) cc_final: 0.9138 (mttm) REVERT: A 209 GLN cc_start: 0.9009 (pm20) cc_final: 0.8803 (pm20) REVERT: B 68 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 96 ARG cc_start: 0.8468 (mtp180) cc_final: 0.8060 (mtt180) REVERT: B 104 GLN cc_start: 0.9088 (mt0) cc_final: 0.7815 (tm-30) REVERT: B 233 CYS cc_start: 0.8886 (m) cc_final: 0.8665 (m) REVERT: C 26 MET cc_start: 0.8044 (mmp) cc_final: 0.7822 (mmp) REVERT: C 96 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8083 (mtt180) REVERT: C 104 GLN cc_start: 0.9082 (mt0) cc_final: 0.7916 (tm-30) REVERT: C 226 ARG cc_start: 0.8907 (mmp-170) cc_final: 0.8334 (mmp-170) REVERT: D 32 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8600 (tp40) REVERT: D 68 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8230 (t80) REVERT: D 71 ASN cc_start: 0.8755 (t0) cc_final: 0.8446 (t0) REVERT: D 96 ARG cc_start: 0.8543 (mtp180) cc_final: 0.8133 (mtp180) REVERT: D 104 GLN cc_start: 0.9002 (mt0) cc_final: 0.7894 (tm-30) REVERT: D 105 ARG cc_start: 0.9067 (tpt170) cc_final: 0.8733 (mmm-85) REVERT: D 108 ILE cc_start: 0.9448 (mm) cc_final: 0.9209 (mp) REVERT: D 120 ASP cc_start: 0.8567 (t0) cc_final: 0.7993 (t0) REVERT: E 71 ASN cc_start: 0.8701 (t0) cc_final: 0.8439 (t0) REVERT: E 96 ARG cc_start: 0.8559 (mtp180) cc_final: 0.8179 (mtt180) REVERT: E 104 GLN cc_start: 0.9037 (mt0) cc_final: 0.7827 (tm-30) REVERT: E 120 ASP cc_start: 0.8505 (t0) cc_final: 0.7929 (t0) REVERT: E 152 LYS cc_start: 0.9594 (mttt) cc_final: 0.9373 (mttt) REVERT: E 226 ARG cc_start: 0.8962 (mmp-170) cc_final: 0.8377 (mmp-170) REVERT: F 96 ARG cc_start: 0.8577 (mtp180) cc_final: 0.8208 (mtt90) REVERT: F 104 GLN cc_start: 0.9000 (mt0) cc_final: 0.8035 (tp40) REVERT: F 105 ARG cc_start: 0.9012 (tpt170) cc_final: 0.8778 (mmm-85) REVERT: F 120 ASP cc_start: 0.8391 (t0) cc_final: 0.8166 (t0) REVERT: G 32 GLN cc_start: 0.8940 (tt0) cc_final: 0.8677 (tt0) REVERT: G 71 ASN cc_start: 0.8456 (t0) cc_final: 0.8144 (t0) REVERT: G 96 ARG cc_start: 0.8376 (mtp180) cc_final: 0.7987 (mtt180) REVERT: G 104 GLN cc_start: 0.8988 (mt0) cc_final: 0.7864 (tp40) REVERT: G 105 ARG cc_start: 0.9047 (tpt170) cc_final: 0.8741 (mmm-85) REVERT: G 120 ASP cc_start: 0.8501 (t0) cc_final: 0.7910 (t0) REVERT: G 148 LYS cc_start: 0.9651 (mmmt) cc_final: 0.9351 (mmmt) REVERT: G 152 LYS cc_start: 0.9562 (mttt) cc_final: 0.9270 (mppt) REVERT: G 216 LYS cc_start: 0.9638 (tptt) cc_final: 0.9374 (mmmm) REVERT: G 233 CYS cc_start: 0.8811 (m) cc_final: 0.8595 (m) REVERT: G 246 GLN cc_start: 0.8292 (mp10) cc_final: 0.7790 (mp10) outliers start: 64 outliers final: 48 residues processed: 440 average time/residue: 0.2801 time to fit residues: 168.6225 Evaluate side-chains 456 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 406 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 130 optimal weight: 0.0050 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13265 Z= 0.202 Angle : 0.640 9.374 17976 Z= 0.324 Chirality : 0.040 0.193 2051 Planarity : 0.005 0.055 2212 Dihedral : 3.534 17.276 1890 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.84 % Allowed : 30.07 % Favored : 67.09 % 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: 2.78 (0.22), residues: 1575 helix: 2.61 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 62 HIS 0.002 0.000 HIS G 236 PHE 0.014 0.001 PHE D 124 TYR 0.017 0.001 TYR C 221 ARG 0.012 0.001 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 439 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8351 (tp30) cc_final: 0.7845 (tp30) REVERT: A 71 ASN cc_start: 0.8576 (t0) cc_final: 0.8192 (t0) REVERT: A 96 ARG cc_start: 0.8411 (mtp180) cc_final: 0.8142 (mtt180) REVERT: A 104 GLN cc_start: 0.8964 (mt0) cc_final: 0.7670 (tp40) REVERT: A 105 ARG cc_start: 0.8919 (tpt170) cc_final: 0.8589 (mmm-85) REVERT: A 120 ASP cc_start: 0.8543 (t0) cc_final: 0.8106 (t0) REVERT: A 122 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9118 (mttm) REVERT: B 32 GLN cc_start: 0.8863 (tt0) cc_final: 0.8624 (tt0) REVERT: B 96 ARG cc_start: 0.8376 (mtp180) cc_final: 0.7941 (mtp180) REVERT: B 104 GLN cc_start: 0.8958 (mt0) cc_final: 0.7880 (tm-30) REVERT: B 105 ARG cc_start: 0.8828 (mmt90) cc_final: 0.8410 (mmm-85) REVERT: B 233 CYS cc_start: 0.8979 (m) cc_final: 0.8764 (m) REVERT: C 26 MET cc_start: 0.7983 (mmp) cc_final: 0.7726 (mmp) REVERT: C 32 GLN cc_start: 0.8984 (tp40) cc_final: 0.8550 (tp40) REVERT: C 96 ARG cc_start: 0.8359 (mtp180) cc_final: 0.7988 (mtt180) REVERT: C 104 GLN cc_start: 0.9024 (mt0) cc_final: 0.7909 (tm-30) REVERT: C 216 LYS cc_start: 0.9391 (mmmm) cc_final: 0.9119 (mmtp) REVERT: C 226 ARG cc_start: 0.8946 (mmp-170) cc_final: 0.8374 (mmp-170) REVERT: D 32 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8509 (tp40) REVERT: D 68 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7985 (t80) REVERT: D 71 ASN cc_start: 0.8817 (t0) cc_final: 0.8560 (t0) REVERT: D 96 ARG cc_start: 0.8429 (mtp180) cc_final: 0.8129 (mtp180) REVERT: D 104 GLN cc_start: 0.8935 (mt0) cc_final: 0.7843 (tm-30) REVERT: D 105 ARG cc_start: 0.9027 (tpt170) cc_final: 0.8684 (mmm-85) REVERT: D 108 ILE cc_start: 0.9411 (mm) cc_final: 0.9175 (mp) REVERT: D 120 ASP cc_start: 0.8345 (t0) cc_final: 0.7679 (t0) REVERT: E 71 ASN cc_start: 0.8734 (t0) cc_final: 0.8469 (t0) REVERT: E 96 ARG cc_start: 0.8464 (mtp180) cc_final: 0.8105 (mtt180) REVERT: E 104 GLN cc_start: 0.8933 (mt0) cc_final: 0.7880 (tm-30) REVERT: E 120 ASP cc_start: 0.8283 (t0) cc_final: 0.7631 (t0) REVERT: E 152 LYS cc_start: 0.9574 (mttt) cc_final: 0.9296 (mttt) REVERT: E 226 ARG cc_start: 0.8966 (mmp-170) cc_final: 0.8362 (mmp-170) REVERT: F 96 ARG cc_start: 0.8491 (mtp180) cc_final: 0.8045 (mtp180) REVERT: F 104 GLN cc_start: 0.8913 (mt0) cc_final: 0.7932 (tm-30) REVERT: F 105 ARG cc_start: 0.9004 (tpt170) cc_final: 0.8744 (mmm-85) REVERT: F 191 MET cc_start: 0.9393 (tpp) cc_final: 0.9068 (mmm) REVERT: G 71 ASN cc_start: 0.8427 (t0) cc_final: 0.8139 (t0) REVERT: G 96 ARG cc_start: 0.8248 (mtp180) cc_final: 0.7947 (mtt180) REVERT: G 104 GLN cc_start: 0.8943 (mt0) cc_final: 0.7590 (tp40) REVERT: G 105 ARG cc_start: 0.9021 (tpt170) cc_final: 0.8713 (mmm-85) REVERT: G 120 ASP cc_start: 0.8250 (t0) cc_final: 0.7803 (t0) REVERT: G 148 LYS cc_start: 0.9641 (mmmt) cc_final: 0.9361 (mmmt) REVERT: G 152 LYS cc_start: 0.9557 (mttt) cc_final: 0.9252 (mppt) REVERT: G 179 ARG cc_start: 0.8973 (mtp85) cc_final: 0.8718 (mtp85) REVERT: G 216 LYS cc_start: 0.9632 (tptt) cc_final: 0.9386 (mmmm) REVERT: G 233 CYS cc_start: 0.8826 (m) cc_final: 0.8602 (m) REVERT: G 246 GLN cc_start: 0.8222 (mp-120) cc_final: 0.7666 (mp10) outliers start: 38 outliers final: 31 residues processed: 457 average time/residue: 0.2765 time to fit residues: 173.1529 Evaluate side-chains 458 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 426 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 160 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13265 Z= 0.198 Angle : 0.655 10.403 17976 Z= 0.331 Chirality : 0.040 0.198 2051 Planarity : 0.004 0.051 2212 Dihedral : 3.418 16.392 1890 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.54 % Allowed : 31.11 % Favored : 66.34 % 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: 2.82 (0.22), residues: 1575 helix: 2.64 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.32 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 62 HIS 0.001 0.000 HIS G 236 PHE 0.013 0.001 PHE D 124 TYR 0.017 0.001 TYR A 49 ARG 0.011 0.001 ARG D 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 443 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8336 (tp30) cc_final: 0.7860 (tp30) REVERT: A 71 ASN cc_start: 0.8590 (t0) cc_final: 0.8142 (t0) REVERT: A 96 ARG cc_start: 0.8396 (mtp180) cc_final: 0.8101 (mtt180) REVERT: A 104 GLN cc_start: 0.8939 (mt0) cc_final: 0.7654 (tp40) REVERT: A 105 ARG cc_start: 0.8904 (tpt170) cc_final: 0.8578 (mmm-85) REVERT: A 120 ASP cc_start: 0.8467 (t0) cc_final: 0.7820 (t0) REVERT: A 122 LYS cc_start: 0.9393 (mmmt) cc_final: 0.9117 (mttm) REVERT: A 209 GLN cc_start: 0.9003 (pm20) cc_final: 0.8767 (pm20) REVERT: B 96 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7903 (mtp180) REVERT: B 104 GLN cc_start: 0.8961 (mt0) cc_final: 0.7897 (tm-30) REVERT: B 233 CYS cc_start: 0.8960 (m) cc_final: 0.8726 (m) REVERT: C 26 MET cc_start: 0.7930 (mmp) cc_final: 0.7654 (mmp) REVERT: C 32 GLN cc_start: 0.8989 (tp40) cc_final: 0.8547 (tp40) REVERT: C 96 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7976 (mtt180) REVERT: C 104 GLN cc_start: 0.8988 (mt0) cc_final: 0.7859 (tm-30) REVERT: C 216 LYS cc_start: 0.9387 (mmmm) cc_final: 0.9059 (mmtp) REVERT: C 226 ARG cc_start: 0.8939 (mmp-170) cc_final: 0.8373 (mmp-170) REVERT: D 71 ASN cc_start: 0.8718 (t0) cc_final: 0.8428 (t0) REVERT: D 96 ARG cc_start: 0.8443 (mtp180) cc_final: 0.8092 (mtp180) REVERT: D 104 GLN cc_start: 0.8913 (mt0) cc_final: 0.7739 (tm-30) REVERT: D 105 ARG cc_start: 0.9002 (tpt170) cc_final: 0.8697 (mmm-85) REVERT: D 120 ASP cc_start: 0.8193 (t0) cc_final: 0.7547 (t0) REVERT: E 71 ASN cc_start: 0.8689 (t0) cc_final: 0.8453 (t0) REVERT: E 96 ARG cc_start: 0.8432 (mtp180) cc_final: 0.8066 (mtt180) REVERT: E 104 GLN cc_start: 0.8939 (mt0) cc_final: 0.7834 (tm-30) REVERT: E 119 MET cc_start: 0.8875 (mmp) cc_final: 0.8616 (mmm) REVERT: E 120 ASP cc_start: 0.8228 (t0) cc_final: 0.7580 (t0) REVERT: E 152 LYS cc_start: 0.9567 (mttt) cc_final: 0.9291 (mttt) REVERT: E 226 ARG cc_start: 0.8970 (mmp-170) cc_final: 0.8366 (mmp-170) REVERT: F 96 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8017 (mtp180) REVERT: F 104 GLN cc_start: 0.8862 (mt0) cc_final: 0.7855 (tm-30) REVERT: F 105 ARG cc_start: 0.8984 (tpt170) cc_final: 0.8641 (mmm-85) REVERT: F 191 MET cc_start: 0.9401 (tpp) cc_final: 0.9102 (mmm) REVERT: F 223 ASP cc_start: 0.9640 (t0) cc_final: 0.9338 (t0) REVERT: G 71 ASN cc_start: 0.8460 (t0) cc_final: 0.8058 (t0) REVERT: G 96 ARG cc_start: 0.8247 (mtp180) cc_final: 0.7920 (mtt180) REVERT: G 104 GLN cc_start: 0.8909 (mt0) cc_final: 0.7508 (tp40) REVERT: G 105 ARG cc_start: 0.9016 (tpt170) cc_final: 0.8706 (mmm-85) REVERT: G 120 ASP cc_start: 0.8166 (t0) cc_final: 0.7674 (t0) REVERT: G 148 LYS cc_start: 0.9587 (mmmt) cc_final: 0.9377 (mmmt) REVERT: G 152 LYS cc_start: 0.9545 (mttt) cc_final: 0.9230 (mppt) REVERT: G 179 ARG cc_start: 0.8947 (mtp85) cc_final: 0.8679 (mtp85) REVERT: G 216 LYS cc_start: 0.9626 (tptt) cc_final: 0.9405 (mmmm) REVERT: G 233 CYS cc_start: 0.8817 (m) cc_final: 0.8587 (m) REVERT: G 246 GLN cc_start: 0.8273 (mp-120) cc_final: 0.7775 (mp10) outliers start: 34 outliers final: 30 residues processed: 457 average time/residue: 0.2731 time to fit residues: 172.5265 Evaluate side-chains 466 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 436 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 127 optimal weight: 0.0000 chunk 53 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 92 optimal weight: 50.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 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 = 0.3737 r_free = 0.3737 target = 0.116790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.084136 restraints weight = 31857.912| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.98 r_work: 0.2955 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13265 Z= 0.207 Angle : 0.650 8.843 17976 Z= 0.330 Chirality : 0.040 0.187 2051 Planarity : 0.004 0.048 2212 Dihedral : 3.388 16.381 1890 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.24 % Allowed : 31.94 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.22), residues: 1575 helix: 2.68 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 62 HIS 0.001 0.000 HIS E 236 PHE 0.014 0.001 PHE D 124 TYR 0.018 0.001 TYR C 221 ARG 0.012 0.001 ARG G 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3808.93 seconds wall clock time: 68 minutes 27.28 seconds (4107.28 seconds total)