Starting phenix.real_space_refine on Fri Mar 15 03:43:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsd_30831/03_2024/7dsd_30831.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsd_30831/03_2024/7dsd_30831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsd_30831/03_2024/7dsd_30831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsd_30831/03_2024/7dsd_30831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsd_30831/03_2024/7dsd_30831.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsd_30831/03_2024/7dsd_30831.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 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 91 5.16 5 C 6874 2.51 5 N 1694 2.21 5 O 1883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 83": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F ARG 176": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 83": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G ARG 176": "NH1" <-> "NH2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10542 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 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: 5.62, per 1000 atoms: 0.53 Number of scatterers: 10542 At special positions: 0 Unit cell: (112.554, 111.54, 92.274, 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 91 16.00 O 1883 8.00 N 1694 7.00 C 6874 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: 3.90 Conformation dependent library (CDL) restraints added in 1.9 seconds 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2590 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 70.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 47 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.766A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 15 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 47 through 70 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 47 through 70 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.627A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 107 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.766A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 47 through 70 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 107 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS D 156 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 15 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 47 through 70 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 removed outlier: 3.589A pdb=" N ALA E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 15 Processing helix chain 'F' and resid 25 through 36 Processing helix chain 'F' and resid 47 through 70 Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS F 156 " --> pdb=" O LYS F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 removed outlier: 3.589A pdb=" N ALA F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 15 Processing helix chain 'G' and resid 25 through 36 Processing helix chain 'G' and resid 47 through 70 Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.627A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 107 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS G 156 " --> pdb=" O LYS G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1935 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: 2.49 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3231 1.34 - 1.46: 2370 1.46 - 1.58: 5039 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 10780 Sorted by residual: bond pdb=" C1 NAG F1001 " pdb=" O5 NAG F1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG D1001 " pdb=" O5 NAG D1001 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 10775 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.85: 350 106.85 - 113.65: 6006 113.65 - 120.45: 4279 120.45 - 127.25: 3883 127.25 - 134.05: 119 Bond angle restraints: 14637 Sorted by residual: angle pdb=" N ALA B 93 " pdb=" CA ALA B 93 " pdb=" C ALA B 93 " ideal model delta sigma weight residual 110.44 115.35 -4.91 1.20e+00 6.94e-01 1.68e+01 angle pdb=" N ALA E 93 " pdb=" CA ALA E 93 " pdb=" C ALA E 93 " ideal model delta sigma weight residual 110.44 115.34 -4.90 1.20e+00 6.94e-01 1.66e+01 angle pdb=" N ALA A 93 " pdb=" CA ALA A 93 " pdb=" C ALA A 93 " ideal model delta sigma weight residual 110.44 115.33 -4.89 1.20e+00 6.94e-01 1.66e+01 angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 110.44 115.31 -4.87 1.20e+00 6.94e-01 1.65e+01 angle pdb=" N ALA C 93 " pdb=" CA ALA C 93 " pdb=" C ALA C 93 " ideal model delta sigma weight residual 110.44 115.31 -4.87 1.20e+00 6.94e-01 1.65e+01 ... (remaining 14632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.45: 5912 11.45 - 22.91: 430 22.91 - 34.36: 119 34.36 - 45.81: 35 45.81 - 57.27: 56 Dihedral angle restraints: 6552 sinusoidal: 2576 harmonic: 3976 Sorted by residual: dihedral pdb=" CA ALA B 93 " pdb=" C ALA B 93 " pdb=" N VAL B 94 " pdb=" CA VAL B 94 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ALA E 93 " pdb=" C ALA E 93 " pdb=" N VAL E 94 " pdb=" CA VAL E 94 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ALA A 93 " pdb=" C ALA A 93 " pdb=" N VAL A 94 " pdb=" CA VAL A 94 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 6549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 892 0.024 - 0.048: 496 0.048 - 0.073: 180 0.073 - 0.097: 82 0.097 - 0.121: 58 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" C PRO C 60 " pdb=" CB PRO C 60 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA PRO B 60 " pdb=" N PRO B 60 " pdb=" C PRO B 60 " pdb=" CB PRO B 60 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA PRO D 60 " pdb=" N PRO D 60 " pdb=" C PRO D 60 " pdb=" CB PRO D 60 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 1705 not shown) Planarity restraints: 1813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " 0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO E 60 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 59 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO G 60 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 60 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.023 5.00e-02 4.00e+02 ... (remaining 1810 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3381 2.84 - 3.36: 10475 3.36 - 3.87: 16450 3.87 - 4.39: 18303 4.39 - 4.90: 31894 Nonbonded interactions: 80503 Sorted by model distance: nonbonded pdb=" OH TYR G 68 " pdb=" OG1 THR G 103 " model vdw 2.326 2.440 nonbonded pdb=" OH TYR A 68 " pdb=" OG1 THR A 103 " model vdw 2.326 2.440 nonbonded pdb=" OH TYR E 68 " pdb=" OG1 THR E 103 " model vdw 2.326 2.440 nonbonded pdb=" OH TYR B 68 " pdb=" OG1 THR B 103 " model vdw 2.326 2.440 nonbonded pdb=" OH TYR F 68 " pdb=" OG1 THR F 103 " model vdw 2.327 2.440 ... (remaining 80498 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: 1.100 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: 4.190 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 28.850 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10780 Z= 0.282 Angle : 0.636 5.746 14637 Z= 0.384 Chirality : 0.039 0.121 1708 Planarity : 0.004 0.040 1806 Dihedral : 10.556 57.267 3920 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1309 helix: 0.09 (0.16), residues: 931 sheet: None (None), residues: 0 loop : -2.62 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 81 HIS 0.001 0.000 HIS B 166 PHE 0.008 0.001 PHE G 63 TYR 0.007 0.001 TYR E 34 ARG 0.003 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 1.150 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 26 MET cc_start: 0.7741 (mmm) cc_final: 0.7531 (mmp) REVERT: A 71 ASN cc_start: 0.8868 (t0) cc_final: 0.8270 (t0) REVERT: A 74 ILE cc_start: 0.8273 (pt) cc_final: 0.8051 (tp) REVERT: A 96 ARG cc_start: 0.7451 (mtp180) cc_final: 0.7189 (mmt180) REVERT: A 120 ASP cc_start: 0.8254 (t70) cc_final: 0.7622 (t0) REVERT: A 133 ASP cc_start: 0.9094 (t0) cc_final: 0.8852 (t0) REVERT: A 142 TYR cc_start: 0.8896 (m-80) cc_final: 0.8629 (m-80) REVERT: A 152 LYS cc_start: 0.9271 (mttt) cc_final: 0.8975 (mppt) REVERT: A 167 GLU cc_start: 0.8757 (mp0) cc_final: 0.8319 (pm20) REVERT: B 26 MET cc_start: 0.7740 (mmm) cc_final: 0.7363 (mmp) REVERT: B 71 ASN cc_start: 0.8670 (t0) cc_final: 0.8256 (t0) REVERT: B 81 TRP cc_start: 0.6649 (m100) cc_final: 0.6434 (t60) REVERT: B 96 ARG cc_start: 0.7419 (mtp180) cc_final: 0.7116 (mtt180) REVERT: B 105 ARG cc_start: 0.8551 (mpt180) cc_final: 0.8318 (mmt-90) REVERT: B 120 ASP cc_start: 0.8198 (t70) cc_final: 0.7423 (t70) REVERT: B 142 TYR cc_start: 0.8859 (m-80) cc_final: 0.8654 (m-80) REVERT: B 164 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8524 (pp20) REVERT: B 165 GLU cc_start: 0.8827 (mp0) cc_final: 0.8486 (mp0) REVERT: B 167 GLU cc_start: 0.8707 (mp0) cc_final: 0.8286 (pm20) REVERT: C 26 MET cc_start: 0.7933 (mmm) cc_final: 0.7681 (mmp) REVERT: C 71 ASN cc_start: 0.8836 (t0) cc_final: 0.8348 (t0) REVERT: C 74 ILE cc_start: 0.8233 (pt) cc_final: 0.7995 (tp) REVERT: C 82 LYS cc_start: 0.8921 (tttt) cc_final: 0.8717 (tppt) REVERT: C 96 ARG cc_start: 0.7553 (mtp180) cc_final: 0.7286 (mtt180) REVERT: C 120 ASP cc_start: 0.8174 (t70) cc_final: 0.7622 (t0) REVERT: C 133 ASP cc_start: 0.9083 (t0) cc_final: 0.8861 (t0) REVERT: C 142 TYR cc_start: 0.8896 (m-80) cc_final: 0.8477 (m-80) REVERT: C 165 GLU cc_start: 0.8851 (mp0) cc_final: 0.8068 (mp0) REVERT: C 167 GLU cc_start: 0.8709 (mp0) cc_final: 0.8393 (pm20) REVERT: D 26 MET cc_start: 0.7920 (mmm) cc_final: 0.7655 (mmp) REVERT: D 71 ASN cc_start: 0.8776 (t0) cc_final: 0.8249 (t0) REVERT: D 74 ILE cc_start: 0.8285 (pt) cc_final: 0.8068 (tp) REVERT: D 96 ARG cc_start: 0.7312 (mtp180) cc_final: 0.7055 (mmt180) REVERT: D 120 ASP cc_start: 0.8235 (t70) cc_final: 0.7863 (t0) REVERT: D 133 ASP cc_start: 0.9152 (t0) cc_final: 0.8903 (t0) REVERT: D 152 LYS cc_start: 0.9211 (mttt) cc_final: 0.8863 (mppt) REVERT: D 167 GLU cc_start: 0.8730 (mp0) cc_final: 0.8435 (pm20) REVERT: E 26 MET cc_start: 0.7733 (mmm) cc_final: 0.7519 (mmp) REVERT: E 71 ASN cc_start: 0.8864 (t0) cc_final: 0.8250 (t0) REVERT: E 74 ILE cc_start: 0.8268 (pt) cc_final: 0.8043 (tp) REVERT: E 82 LYS cc_start: 0.9007 (tttt) cc_final: 0.8754 (tppt) REVERT: E 96 ARG cc_start: 0.7391 (mtp180) cc_final: 0.7092 (mmt180) REVERT: E 120 ASP cc_start: 0.8217 (t70) cc_final: 0.7606 (t0) REVERT: E 165 GLU cc_start: 0.8813 (mp0) cc_final: 0.8246 (mp0) REVERT: E 167 GLU cc_start: 0.8748 (mp0) cc_final: 0.8379 (pm20) REVERT: F 26 MET cc_start: 0.7754 (mmm) cc_final: 0.7306 (mmp) REVERT: F 71 ASN cc_start: 0.8925 (t0) cc_final: 0.8438 (t0) REVERT: F 74 ILE cc_start: 0.8202 (pt) cc_final: 0.8001 (tp) REVERT: F 96 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7203 (mmt180) REVERT: F 105 ARG cc_start: 0.8644 (mpt180) cc_final: 0.8398 (mmt-90) REVERT: F 119 MET cc_start: 0.8683 (mmm) cc_final: 0.8357 (mmt) REVERT: F 120 ASP cc_start: 0.8188 (t70) cc_final: 0.7686 (t0) REVERT: F 165 GLU cc_start: 0.8839 (mp0) cc_final: 0.8298 (mp0) REVERT: F 167 GLU cc_start: 0.8704 (mp0) cc_final: 0.8206 (pm20) REVERT: G 26 MET cc_start: 0.7721 (mmm) cc_final: 0.7462 (mmp) REVERT: G 71 ASN cc_start: 0.8730 (t0) cc_final: 0.8091 (t0) REVERT: G 81 TRP cc_start: 0.6714 (m100) cc_final: 0.6438 (t60) REVERT: G 96 ARG cc_start: 0.7582 (mtp180) cc_final: 0.7325 (mmt180) REVERT: G 119 MET cc_start: 0.8640 (mmm) cc_final: 0.8227 (mmp) REVERT: G 120 ASP cc_start: 0.8218 (t70) cc_final: 0.7654 (t0) REVERT: G 133 ASP cc_start: 0.9138 (t0) cc_final: 0.8838 (t0) REVERT: G 152 LYS cc_start: 0.9208 (mttt) cc_final: 0.8896 (mttp) REVERT: G 164 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8691 (pp20) REVERT: G 165 GLU cc_start: 0.8889 (mp0) cc_final: 0.8345 (mp0) REVERT: G 167 GLU cc_start: 0.8748 (mp0) cc_final: 0.8381 (pm20) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 1.4873 time to fit residues: 618.9178 Evaluate side-chains 370 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 120 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 154 GLN B 71 ASN B 104 GLN B 154 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN D 71 ASN D 104 GLN D 154 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN E 154 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN F 154 GLN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 154 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10780 Z= 0.197 Angle : 0.593 5.665 14637 Z= 0.301 Chirality : 0.039 0.140 1708 Planarity : 0.005 0.037 1806 Dihedral : 4.255 21.729 1589 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.29 % Allowed : 16.96 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1309 helix: 1.43 (0.18), residues: 938 sheet: None (None), residues: 0 loop : -2.47 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 62 HIS 0.001 0.000 HIS F 166 PHE 0.005 0.001 PHE C 189 TYR 0.012 0.001 TYR A 47 ARG 0.007 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 383 time to evaluate : 1.170 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 26 MET cc_start: 0.7624 (mmm) cc_final: 0.7314 (mmp) REVERT: A 71 ASN cc_start: 0.8794 (t0) cc_final: 0.8332 (t0) REVERT: A 74 ILE cc_start: 0.8175 (pt) cc_final: 0.7925 (tp) REVERT: A 81 TRP cc_start: 0.7159 (t-100) cc_final: 0.6303 (t60) REVERT: A 96 ARG cc_start: 0.7364 (mtp180) cc_final: 0.7144 (mmt180) REVERT: A 152 LYS cc_start: 0.9249 (mttt) cc_final: 0.8969 (mppt) REVERT: A 167 GLU cc_start: 0.8571 (mp0) cc_final: 0.8183 (pm20) REVERT: B 26 MET cc_start: 0.7534 (mmm) cc_final: 0.7102 (mmp) REVERT: B 71 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.7973 (t0) REVERT: B 79 GLU cc_start: 0.9183 (tp30) cc_final: 0.8947 (tp30) REVERT: B 82 LYS cc_start: 0.9087 (tptt) cc_final: 0.8773 (tmmt) REVERT: B 96 ARG cc_start: 0.7304 (mtp180) cc_final: 0.7012 (mtt180) REVERT: B 105 ARG cc_start: 0.8549 (mpt180) cc_final: 0.8317 (mmt-90) REVERT: B 142 TYR cc_start: 0.8845 (m-80) cc_final: 0.8253 (m-80) REVERT: B 164 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8540 (pp20) REVERT: B 165 GLU cc_start: 0.8768 (mp0) cc_final: 0.8486 (mp0) REVERT: B 167 GLU cc_start: 0.8657 (mp0) cc_final: 0.8244 (pm20) REVERT: C 26 MET cc_start: 0.7631 (mmm) cc_final: 0.7321 (mmp) REVERT: C 40 THR cc_start: 0.8600 (t) cc_final: 0.8012 (p) REVERT: C 71 ASN cc_start: 0.8834 (t0) cc_final: 0.8422 (t0) REVERT: C 74 ILE cc_start: 0.8224 (pt) cc_final: 0.8002 (tp) REVERT: C 81 TRP cc_start: 0.6875 (t-100) cc_final: 0.6017 (t60) REVERT: C 96 ARG cc_start: 0.7348 (mtp180) cc_final: 0.7066 (mtt-85) REVERT: C 142 TYR cc_start: 0.8899 (m-80) cc_final: 0.8313 (m-80) REVERT: C 152 LYS cc_start: 0.9166 (mttt) cc_final: 0.8907 (mppt) REVERT: C 167 GLU cc_start: 0.8654 (mp0) cc_final: 0.8214 (pm20) REVERT: C 179 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7892 (ttp-110) REVERT: D 26 MET cc_start: 0.7625 (mmm) cc_final: 0.7335 (mmp) REVERT: D 68 TYR cc_start: 0.8047 (m-80) cc_final: 0.7258 (m-80) REVERT: D 71 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8039 (t0) REVERT: D 74 ILE cc_start: 0.8159 (pt) cc_final: 0.7954 (tp) REVERT: D 79 GLU cc_start: 0.9088 (tp30) cc_final: 0.8777 (tp30) REVERT: D 96 ARG cc_start: 0.7246 (mtp180) cc_final: 0.6993 (mmt180) REVERT: D 148 LYS cc_start: 0.9305 (mmpt) cc_final: 0.9079 (mmpt) REVERT: D 152 LYS cc_start: 0.9182 (mttt) cc_final: 0.8854 (mppt) REVERT: D 167 GLU cc_start: 0.8830 (mp0) cc_final: 0.8461 (pm20) REVERT: E 26 MET cc_start: 0.7558 (mmm) cc_final: 0.7275 (mmp) REVERT: E 71 ASN cc_start: 0.8900 (t0) cc_final: 0.8413 (t0) REVERT: E 74 ILE cc_start: 0.8161 (pt) cc_final: 0.7919 (tp) REVERT: E 81 TRP cc_start: 0.7360 (t-100) cc_final: 0.6387 (t60) REVERT: E 96 ARG cc_start: 0.7274 (mtp180) cc_final: 0.6992 (mmt180) REVERT: E 142 TYR cc_start: 0.8814 (m-10) cc_final: 0.8433 (m-10) REVERT: E 165 GLU cc_start: 0.8571 (mp0) cc_final: 0.8357 (mp0) REVERT: E 167 GLU cc_start: 0.8786 (mp0) cc_final: 0.8344 (pm20) REVERT: F 26 MET cc_start: 0.7604 (mmm) cc_final: 0.7116 (mmp) REVERT: F 40 THR cc_start: 0.8491 (t) cc_final: 0.7842 (p) REVERT: F 71 ASN cc_start: 0.8753 (t0) cc_final: 0.8204 (t0) REVERT: F 81 TRP cc_start: 0.7030 (t-100) cc_final: 0.6112 (t60) REVERT: F 96 ARG cc_start: 0.7202 (mtp180) cc_final: 0.6955 (mmt180) REVERT: F 105 ARG cc_start: 0.8670 (mpt180) cc_final: 0.8427 (mmt-90) REVERT: F 142 TYR cc_start: 0.8798 (m-80) cc_final: 0.8015 (m-80) REVERT: F 148 LYS cc_start: 0.9360 (mmpt) cc_final: 0.8931 (mmpt) REVERT: F 152 LYS cc_start: 0.9206 (mttt) cc_final: 0.8798 (mppt) REVERT: F 167 GLU cc_start: 0.8611 (mp0) cc_final: 0.8184 (pm20) REVERT: F 179 ARG cc_start: 0.8136 (ttm110) cc_final: 0.7809 (ttp-110) REVERT: G 26 MET cc_start: 0.7642 (mmm) cc_final: 0.7317 (mmp) REVERT: G 71 ASN cc_start: 0.8686 (t0) cc_final: 0.8019 (t0) REVERT: G 73 ASN cc_start: 0.8588 (m-40) cc_final: 0.8323 (m-40) REVERT: G 81 TRP cc_start: 0.6702 (m100) cc_final: 0.6419 (t60) REVERT: G 96 ARG cc_start: 0.7463 (mtp180) cc_final: 0.7214 (mmt180) REVERT: G 105 ARG cc_start: 0.8520 (mmt90) cc_final: 0.8206 (mmt-90) REVERT: G 119 MET cc_start: 0.8486 (mmm) cc_final: 0.8223 (mmp) REVERT: G 136 GLU cc_start: 0.8575 (pm20) cc_final: 0.8371 (pm20) REVERT: G 142 TYR cc_start: 0.8718 (m-10) cc_final: 0.8388 (m-10) REVERT: G 148 LYS cc_start: 0.9336 (mmpt) cc_final: 0.8798 (mmpt) REVERT: G 152 LYS cc_start: 0.9174 (mttt) cc_final: 0.8743 (mtmm) REVERT: G 164 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8714 (pp20) REVERT: G 165 GLU cc_start: 0.8854 (mp0) cc_final: 0.8366 (mp0) REVERT: G 167 GLU cc_start: 0.8836 (mp0) cc_final: 0.8465 (pm20) outliers start: 14 outliers final: 7 residues processed: 386 average time/residue: 1.4497 time to fit residues: 591.1466 Evaluate side-chains 386 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 377 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 35 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 0.0060 chunk 119 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 104 GLN D 104 GLN E 104 GLN G 71 ASN G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10780 Z= 0.193 Angle : 0.596 5.562 14637 Z= 0.301 Chirality : 0.039 0.137 1708 Planarity : 0.005 0.039 1806 Dihedral : 4.103 19.294 1589 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.03 % Allowed : 20.65 % Favored : 77.33 % 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: 1.55 (0.24), residues: 1309 helix: 2.00 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.39 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 62 HIS 0.001 0.000 HIS F 166 PHE 0.004 0.001 PHE G 189 TYR 0.009 0.001 TYR B 34 ARG 0.008 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 390 time to evaluate : 1.182 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: A 26 MET cc_start: 0.7631 (mmm) cc_final: 0.7355 (mmp) REVERT: A 71 ASN cc_start: 0.8793 (t0) cc_final: 0.8446 (t0) REVERT: A 74 ILE cc_start: 0.8226 (pt) cc_final: 0.7949 (tp) REVERT: A 81 TRP cc_start: 0.7171 (t-100) cc_final: 0.6391 (t60) REVERT: A 96 ARG cc_start: 0.7324 (mtp180) cc_final: 0.7117 (mmt180) REVERT: A 152 LYS cc_start: 0.9240 (mttt) cc_final: 0.8998 (mtmm) REVERT: A 167 GLU cc_start: 0.8670 (mp0) cc_final: 0.8299 (pm20) REVERT: A 169 ILE cc_start: 0.9087 (mt) cc_final: 0.8840 (tt) REVERT: B 26 MET cc_start: 0.7601 (mmm) cc_final: 0.7164 (mmp) REVERT: B 71 ASN cc_start: 0.8526 (t0) cc_final: 0.8152 (t0) REVERT: B 81 TRP cc_start: 0.7113 (t-100) cc_final: 0.6281 (t60) REVERT: B 96 ARG cc_start: 0.7271 (mtp180) cc_final: 0.6970 (mtt180) REVERT: B 105 ARG cc_start: 0.8534 (mpt180) cc_final: 0.8299 (mmt-90) REVERT: B 142 TYR cc_start: 0.8847 (m-80) cc_final: 0.8103 (m-80) REVERT: B 152 LYS cc_start: 0.9149 (mttt) cc_final: 0.8885 (mtmm) REVERT: B 165 GLU cc_start: 0.8731 (mp0) cc_final: 0.7832 (mp0) REVERT: B 167 GLU cc_start: 0.8661 (mp0) cc_final: 0.8259 (pm20) REVERT: C 26 MET cc_start: 0.7639 (mmm) cc_final: 0.7354 (mmp) REVERT: C 40 THR cc_start: 0.8724 (t) cc_final: 0.8227 (p) REVERT: C 71 ASN cc_start: 0.8837 (t0) cc_final: 0.8605 (t0) REVERT: C 74 ILE cc_start: 0.8192 (pt) cc_final: 0.7978 (tp) REVERT: C 81 TRP cc_start: 0.6928 (t-100) cc_final: 0.5993 (t60) REVERT: C 96 ARG cc_start: 0.7318 (mtp180) cc_final: 0.7039 (mmt180) REVERT: C 142 TYR cc_start: 0.8832 (m-80) cc_final: 0.8299 (m-80) REVERT: C 152 LYS cc_start: 0.9105 (mttt) cc_final: 0.8852 (mtmm) REVERT: C 167 GLU cc_start: 0.8592 (mp0) cc_final: 0.8198 (pm20) REVERT: D 26 MET cc_start: 0.7627 (mmm) cc_final: 0.7337 (mmp) REVERT: D 68 TYR cc_start: 0.8063 (m-80) cc_final: 0.7749 (m-80) REVERT: D 71 ASN cc_start: 0.8798 (t0) cc_final: 0.8298 (t0) REVERT: D 74 ILE cc_start: 0.8234 (pt) cc_final: 0.8007 (tp) REVERT: D 81 TRP cc_start: 0.7425 (t-100) cc_final: 0.6434 (t60) REVERT: D 96 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6968 (mmt180) REVERT: D 152 LYS cc_start: 0.9162 (mttt) cc_final: 0.8913 (mtmm) REVERT: D 167 GLU cc_start: 0.8851 (mp0) cc_final: 0.8482 (pm20) REVERT: D 169 ILE cc_start: 0.9039 (mt) cc_final: 0.8738 (tt) REVERT: E 26 MET cc_start: 0.7663 (mmm) cc_final: 0.7377 (mmp) REVERT: E 71 ASN cc_start: 0.8897 (t0) cc_final: 0.8536 (t0) REVERT: E 74 ILE cc_start: 0.8186 (pt) cc_final: 0.7912 (tp) REVERT: E 81 TRP cc_start: 0.7313 (t-100) cc_final: 0.6347 (t60) REVERT: E 96 ARG cc_start: 0.7212 (mtp180) cc_final: 0.6935 (mmt180) REVERT: E 142 TYR cc_start: 0.8777 (m-80) cc_final: 0.8560 (m-10) REVERT: E 143 GLN cc_start: 0.8371 (mm110) cc_final: 0.8124 (mm110) REVERT: E 148 LYS cc_start: 0.9277 (mmpt) cc_final: 0.8899 (mmpt) REVERT: E 149 GLU cc_start: 0.9248 (mp0) cc_final: 0.9016 (pm20) REVERT: E 152 LYS cc_start: 0.9150 (mttt) cc_final: 0.8777 (mtmm) REVERT: E 167 GLU cc_start: 0.8768 (mp0) cc_final: 0.8455 (pm20) REVERT: F 26 MET cc_start: 0.7563 (mmm) cc_final: 0.7098 (mmp) REVERT: F 40 THR cc_start: 0.8540 (t) cc_final: 0.7909 (p) REVERT: F 71 ASN cc_start: 0.8792 (t0) cc_final: 0.8473 (t0) REVERT: F 81 TRP cc_start: 0.7067 (t-100) cc_final: 0.6267 (t60) REVERT: F 96 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6867 (mmt180) REVERT: F 105 ARG cc_start: 0.8666 (mpt180) cc_final: 0.8415 (mmt-90) REVERT: F 142 TYR cc_start: 0.8690 (m-80) cc_final: 0.7963 (m-80) REVERT: F 152 LYS cc_start: 0.9171 (mttt) cc_final: 0.8898 (mtmm) REVERT: F 167 GLU cc_start: 0.8604 (mp0) cc_final: 0.8194 (pm20) REVERT: F 179 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7770 (ttp-110) REVERT: G 26 MET cc_start: 0.7727 (mmm) cc_final: 0.7438 (mmp) REVERT: G 71 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.7894 (t0) REVERT: G 81 TRP cc_start: 0.6732 (m100) cc_final: 0.6441 (t60) REVERT: G 96 ARG cc_start: 0.7349 (mtp180) cc_final: 0.7123 (mmt180) REVERT: G 105 ARG cc_start: 0.8525 (mmt90) cc_final: 0.8196 (mmt-90) REVERT: G 119 MET cc_start: 0.8391 (mmm) cc_final: 0.8111 (mmp) REVERT: G 148 LYS cc_start: 0.9344 (mmpt) cc_final: 0.9093 (mmpt) REVERT: G 149 GLU cc_start: 0.9370 (mp0) cc_final: 0.9168 (pm20) REVERT: G 152 LYS cc_start: 0.9132 (mttt) cc_final: 0.8785 (mtmm) REVERT: G 167 GLU cc_start: 0.8809 (mp0) cc_final: 0.8460 (pm20) outliers start: 22 outliers final: 8 residues processed: 397 average time/residue: 1.4093 time to fit residues: 593.7870 Evaluate side-chains 387 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 378 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 71 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 40.0000 chunk 81 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 128 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 0.0060 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 104 GLN D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10780 Z= 0.184 Angle : 0.593 5.476 14637 Z= 0.297 Chirality : 0.039 0.130 1708 Planarity : 0.004 0.040 1806 Dihedral : 3.838 17.631 1589 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.21 % Allowed : 21.66 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1309 helix: 2.13 (0.18), residues: 924 sheet: None (None), residues: 0 loop : -1.19 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 62 HIS 0.000 0.000 HIS E 166 PHE 0.004 0.001 PHE B 137 TYR 0.017 0.001 TYR D 49 ARG 0.008 0.000 ARG G 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 382 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7672 (mmm) cc_final: 0.7394 (mmp) REVERT: A 71 ASN cc_start: 0.8794 (t0) cc_final: 0.8417 (t0) REVERT: A 74 ILE cc_start: 0.8201 (pt) cc_final: 0.7937 (tp) REVERT: A 81 TRP cc_start: 0.7213 (t-100) cc_final: 0.6348 (t60) REVERT: A 96 ARG cc_start: 0.7312 (mtp180) cc_final: 0.7051 (mmt180) REVERT: A 142 TYR cc_start: 0.8829 (m-80) cc_final: 0.8573 (m-10) REVERT: A 152 LYS cc_start: 0.9187 (mttt) cc_final: 0.8945 (mppt) REVERT: A 167 GLU cc_start: 0.8706 (mp0) cc_final: 0.8416 (pm20) REVERT: A 169 ILE cc_start: 0.9075 (mt) cc_final: 0.8848 (tt) REVERT: B 26 MET cc_start: 0.7623 (mmm) cc_final: 0.7227 (mmp) REVERT: B 71 ASN cc_start: 0.8497 (t0) cc_final: 0.8009 (t0) REVERT: B 81 TRP cc_start: 0.7098 (t-100) cc_final: 0.6380 (t60) REVERT: B 96 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6922 (mtt180) REVERT: B 105 ARG cc_start: 0.8529 (mpt180) cc_final: 0.8290 (mmt-90) REVERT: B 142 TYR cc_start: 0.8645 (m-80) cc_final: 0.8224 (m-10) REVERT: B 143 GLN cc_start: 0.8603 (mm110) cc_final: 0.8385 (mm110) REVERT: B 152 LYS cc_start: 0.9118 (mttt) cc_final: 0.8837 (mtmm) REVERT: B 167 GLU cc_start: 0.8597 (mp0) cc_final: 0.8316 (pm20) REVERT: B 169 ILE cc_start: 0.9017 (mt) cc_final: 0.8749 (tt) REVERT: C 26 MET cc_start: 0.7741 (mmm) cc_final: 0.7428 (mmp) REVERT: C 40 THR cc_start: 0.8680 (t) cc_final: 0.8225 (p) REVERT: C 71 ASN cc_start: 0.8808 (t0) cc_final: 0.8563 (t0) REVERT: C 74 ILE cc_start: 0.8206 (pt) cc_final: 0.7988 (tp) REVERT: C 81 TRP cc_start: 0.7013 (t-100) cc_final: 0.6131 (t60) REVERT: C 96 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6946 (mmt-90) REVERT: C 142 TYR cc_start: 0.8867 (m-80) cc_final: 0.8279 (m-10) REVERT: C 152 LYS cc_start: 0.9069 (mttt) cc_final: 0.8825 (mppt) REVERT: C 167 GLU cc_start: 0.8629 (mp0) cc_final: 0.8276 (pm20) REVERT: C 169 ILE cc_start: 0.9000 (mt) cc_final: 0.8671 (tt) REVERT: D 26 MET cc_start: 0.7612 (mmm) cc_final: 0.7248 (mmp) REVERT: D 68 TYR cc_start: 0.8067 (m-80) cc_final: 0.7479 (m-80) REVERT: D 71 ASN cc_start: 0.8608 (t0) cc_final: 0.8166 (t0) REVERT: D 81 TRP cc_start: 0.7581 (t-100) cc_final: 0.6609 (t60) REVERT: D 96 ARG cc_start: 0.7159 (mtp180) cc_final: 0.6952 (mmt180) REVERT: D 152 LYS cc_start: 0.9111 (mttt) cc_final: 0.8841 (mppt) REVERT: D 167 GLU cc_start: 0.8836 (mp0) cc_final: 0.8496 (pm20) REVERT: D 169 ILE cc_start: 0.8992 (mt) cc_final: 0.8718 (tt) REVERT: E 26 MET cc_start: 0.7721 (mmm) cc_final: 0.7379 (mmp) REVERT: E 71 ASN cc_start: 0.8861 (t0) cc_final: 0.8468 (t0) REVERT: E 74 ILE cc_start: 0.8148 (pt) cc_final: 0.7921 (tp) REVERT: E 81 TRP cc_start: 0.7314 (t-100) cc_final: 0.6471 (t60) REVERT: E 82 LYS cc_start: 0.8866 (tmmt) cc_final: 0.8605 (ptmm) REVERT: E 96 ARG cc_start: 0.7181 (mtp180) cc_final: 0.6911 (mmt180) REVERT: E 143 GLN cc_start: 0.8709 (mm110) cc_final: 0.8465 (mm110) REVERT: E 148 LYS cc_start: 0.9200 (mmpt) cc_final: 0.8870 (mmpt) REVERT: E 149 GLU cc_start: 0.9211 (mp0) cc_final: 0.8974 (pm20) REVERT: E 152 LYS cc_start: 0.9152 (mttt) cc_final: 0.8783 (mtmm) REVERT: E 164 GLU cc_start: 0.8830 (pt0) cc_final: 0.8403 (pp20) REVERT: E 167 GLU cc_start: 0.8759 (mp0) cc_final: 0.8474 (pm20) REVERT: E 169 ILE cc_start: 0.8994 (mt) cc_final: 0.8690 (tt) REVERT: F 40 THR cc_start: 0.8535 (t) cc_final: 0.7954 (p) REVERT: F 71 ASN cc_start: 0.8707 (t0) cc_final: 0.8400 (t0) REVERT: F 73 ASN cc_start: 0.8716 (m-40) cc_final: 0.8341 (m-40) REVERT: F 81 TRP cc_start: 0.7034 (t-100) cc_final: 0.6252 (t60) REVERT: F 96 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6842 (mmt180) REVERT: F 105 ARG cc_start: 0.8658 (mpt180) cc_final: 0.8406 (mmt-90) REVERT: F 142 TYR cc_start: 0.8695 (m-80) cc_final: 0.7939 (m-80) REVERT: F 152 LYS cc_start: 0.9168 (mttt) cc_final: 0.8896 (mtmm) REVERT: F 167 GLU cc_start: 0.8631 (mp0) cc_final: 0.8288 (pm20) REVERT: F 169 ILE cc_start: 0.9078 (mt) cc_final: 0.8779 (tt) REVERT: G 26 MET cc_start: 0.7721 (mmm) cc_final: 0.7482 (mmp) REVERT: G 71 ASN cc_start: 0.8806 (t0) cc_final: 0.8140 (t0) REVERT: G 96 ARG cc_start: 0.7210 (mtp180) cc_final: 0.6991 (mmt180) REVERT: G 105 ARG cc_start: 0.8563 (mmt90) cc_final: 0.8214 (mmt-90) REVERT: G 119 MET cc_start: 0.8287 (mmm) cc_final: 0.7975 (mmp) REVERT: G 152 LYS cc_start: 0.9118 (mttt) cc_final: 0.8794 (mtmm) REVERT: G 164 GLU cc_start: 0.7622 (pm20) cc_final: 0.7417 (pm20) REVERT: G 167 GLU cc_start: 0.8824 (mp0) cc_final: 0.8516 (pm20) REVERT: G 169 ILE cc_start: 0.9079 (mt) cc_final: 0.8819 (tt) outliers start: 24 outliers final: 9 residues processed: 395 average time/residue: 1.3642 time to fit residues: 571.7889 Evaluate side-chains 383 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 374 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 65 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 71 ASN D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10780 Z= 0.283 Angle : 0.632 5.820 14637 Z= 0.320 Chirality : 0.041 0.126 1708 Planarity : 0.004 0.043 1806 Dihedral : 3.813 18.416 1589 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.78 % Allowed : 21.20 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1309 helix: 2.10 (0.18), residues: 924 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 81 HIS 0.001 0.000 HIS G 166 PHE 0.007 0.001 PHE G 99 TYR 0.020 0.001 TYR D 49 ARG 0.006 0.001 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 365 time to evaluate : 1.267 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: A 26 MET cc_start: 0.7737 (mmm) cc_final: 0.7458 (mmp) REVERT: A 32 GLN cc_start: 0.8756 (tp40) cc_final: 0.8177 (tm-30) REVERT: A 40 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8267 (p) REVERT: A 71 ASN cc_start: 0.8736 (t0) cc_final: 0.8342 (t0) REVERT: A 74 ILE cc_start: 0.8233 (pt) cc_final: 0.7972 (tp) REVERT: A 81 TRP cc_start: 0.7292 (t-100) cc_final: 0.6430 (t60) REVERT: A 152 LYS cc_start: 0.9216 (mttt) cc_final: 0.8948 (mppt) REVERT: A 167 GLU cc_start: 0.8707 (mp0) cc_final: 0.8417 (pm20) REVERT: B 26 MET cc_start: 0.7802 (mmm) cc_final: 0.7491 (mmp) REVERT: B 71 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7927 (t0) REVERT: B 81 TRP cc_start: 0.7132 (t-100) cc_final: 0.6386 (t60) REVERT: B 96 ARG cc_start: 0.7240 (mtp180) cc_final: 0.6909 (mmt180) REVERT: B 105 ARG cc_start: 0.8554 (mpt180) cc_final: 0.8317 (mmt-90) REVERT: B 142 TYR cc_start: 0.8847 (m-80) cc_final: 0.8353 (m-10) REVERT: B 143 GLN cc_start: 0.8756 (mm110) cc_final: 0.8487 (mm110) REVERT: B 148 LYS cc_start: 0.9356 (mmpt) cc_final: 0.9103 (mmpt) REVERT: B 152 LYS cc_start: 0.9133 (mttt) cc_final: 0.8846 (mtmm) REVERT: B 167 GLU cc_start: 0.8665 (mp0) cc_final: 0.8347 (pm20) REVERT: C 26 MET cc_start: 0.7844 (mmm) cc_final: 0.7569 (mmp) REVERT: C 40 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8177 (p) REVERT: C 71 ASN cc_start: 0.8745 (t0) cc_final: 0.8471 (t0) REVERT: C 81 TRP cc_start: 0.7227 (t-100) cc_final: 0.6358 (t60) REVERT: C 82 LYS cc_start: 0.9094 (tptt) cc_final: 0.8790 (tmmt) REVERT: C 96 ARG cc_start: 0.7328 (mtp180) cc_final: 0.7051 (mmt-90) REVERT: C 142 TYR cc_start: 0.8925 (m-80) cc_final: 0.8292 (m-10) REVERT: C 148 LYS cc_start: 0.9338 (mmpt) cc_final: 0.9093 (mmpt) REVERT: C 152 LYS cc_start: 0.9057 (mttt) cc_final: 0.8779 (mppt) REVERT: C 167 GLU cc_start: 0.8674 (mp0) cc_final: 0.8324 (pm20) REVERT: D 26 MET cc_start: 0.7836 (mmm) cc_final: 0.7435 (mmp) REVERT: D 40 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8126 (p) REVERT: D 71 ASN cc_start: 0.8662 (t0) cc_final: 0.8151 (t0) REVERT: D 81 TRP cc_start: 0.7493 (t-100) cc_final: 0.6590 (t60) REVERT: D 96 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6926 (mmt180) REVERT: D 148 LYS cc_start: 0.9342 (mmpt) cc_final: 0.9091 (mmpt) REVERT: D 152 LYS cc_start: 0.9135 (mttt) cc_final: 0.8865 (mppt) REVERT: D 167 GLU cc_start: 0.8856 (mp0) cc_final: 0.8523 (pm20) REVERT: E 26 MET cc_start: 0.7889 (mmm) cc_final: 0.7539 (mmp) REVERT: E 40 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8075 (p) REVERT: E 71 ASN cc_start: 0.8825 (t0) cc_final: 0.8438 (t0) REVERT: E 74 ILE cc_start: 0.8176 (pt) cc_final: 0.7971 (tp) REVERT: E 81 TRP cc_start: 0.7401 (t-100) cc_final: 0.6525 (t60) REVERT: E 96 ARG cc_start: 0.7303 (mtp180) cc_final: 0.7037 (mmt180) REVERT: E 143 GLN cc_start: 0.8845 (mm110) cc_final: 0.8535 (mm110) REVERT: E 148 LYS cc_start: 0.9182 (mmpt) cc_final: 0.8730 (mmpt) REVERT: E 149 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8906 (pm20) REVERT: E 152 LYS cc_start: 0.9176 (mttt) cc_final: 0.8783 (mtmm) REVERT: E 164 GLU cc_start: 0.8865 (pt0) cc_final: 0.8454 (pp20) REVERT: E 167 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: F 40 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.7896 (p) REVERT: F 71 ASN cc_start: 0.8754 (t0) cc_final: 0.8461 (t0) REVERT: F 73 ASN cc_start: 0.8635 (m-40) cc_final: 0.8398 (m-40) REVERT: F 81 TRP cc_start: 0.7103 (t-100) cc_final: 0.6316 (t60) REVERT: F 96 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6874 (mmt180) REVERT: F 105 ARG cc_start: 0.8653 (mpt180) cc_final: 0.8401 (mmt-90) REVERT: F 142 TYR cc_start: 0.8719 (m-80) cc_final: 0.7887 (m-80) REVERT: F 148 LYS cc_start: 0.9325 (mmpt) cc_final: 0.8810 (mmpt) REVERT: F 152 LYS cc_start: 0.9161 (mttt) cc_final: 0.8780 (mppt) REVERT: F 167 GLU cc_start: 0.8671 (mp0) cc_final: 0.8309 (pm20) REVERT: F 179 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7953 (ttp-110) REVERT: G 26 MET cc_start: 0.7835 (mmm) cc_final: 0.7631 (mmp) REVERT: G 71 ASN cc_start: 0.8555 (t0) cc_final: 0.7672 (t0) REVERT: G 96 ARG cc_start: 0.7209 (mtp180) cc_final: 0.6995 (mmt180) REVERT: G 105 ARG cc_start: 0.8521 (mmt90) cc_final: 0.8186 (mmt-90) REVERT: G 119 MET cc_start: 0.8342 (mmm) cc_final: 0.8014 (mmp) REVERT: G 143 GLN cc_start: 0.8502 (mm110) cc_final: 0.8299 (mm110) REVERT: G 148 LYS cc_start: 0.9371 (mmpt) cc_final: 0.8888 (mmpt) REVERT: G 152 LYS cc_start: 0.9142 (mttt) cc_final: 0.8777 (mtmm) REVERT: G 167 GLU cc_start: 0.8845 (mp0) cc_final: 0.8525 (pm20) outliers start: 41 outliers final: 17 residues processed: 377 average time/residue: 1.4508 time to fit residues: 578.6493 Evaluate side-chains 384 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 359 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 199 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 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 199 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 104 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10780 Z= 0.215 Angle : 0.617 6.219 14637 Z= 0.312 Chirality : 0.040 0.137 1708 Planarity : 0.004 0.043 1806 Dihedral : 3.786 16.573 1589 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.04 % Allowed : 22.21 % Favored : 74.75 % 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: 1.93 (0.25), residues: 1309 helix: 2.25 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.17 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 81 HIS 0.000 0.000 HIS B 166 PHE 0.004 0.001 PHE G 99 TYR 0.011 0.001 TYR F 34 ARG 0.007 0.000 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 368 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7717 (mmm) cc_final: 0.7425 (mmp) REVERT: A 32 GLN cc_start: 0.8732 (tp40) cc_final: 0.8163 (tm-30) REVERT: A 40 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8238 (p) REVERT: A 71 ASN cc_start: 0.8700 (t0) cc_final: 0.8239 (t0) REVERT: A 74 ILE cc_start: 0.8320 (pt) cc_final: 0.8039 (tp) REVERT: A 81 TRP cc_start: 0.7234 (t-100) cc_final: 0.6348 (t60) REVERT: A 122 LYS cc_start: 0.8539 (mttm) cc_final: 0.8322 (mttm) REVERT: A 152 LYS cc_start: 0.9192 (mttt) cc_final: 0.8929 (mppt) REVERT: A 167 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: A 169 ILE cc_start: 0.9092 (mt) cc_final: 0.8802 (tt) REVERT: A 199 LEU cc_start: 0.8899 (tp) cc_final: 0.8605 (tt) REVERT: B 26 MET cc_start: 0.7753 (mmm) cc_final: 0.7476 (mmp) REVERT: B 40 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8094 (p) REVERT: B 71 ASN cc_start: 0.8489 (t0) cc_final: 0.7885 (t0) REVERT: B 81 TRP cc_start: 0.7168 (t-100) cc_final: 0.6380 (t60) REVERT: B 96 ARG cc_start: 0.7314 (mtp180) cc_final: 0.6978 (mmt180) REVERT: B 142 TYR cc_start: 0.8844 (m-80) cc_final: 0.8395 (m-10) REVERT: B 148 LYS cc_start: 0.9317 (mmpt) cc_final: 0.8787 (mmpt) REVERT: B 149 GLU cc_start: 0.9210 (pm20) cc_final: 0.8930 (pm20) REVERT: B 152 LYS cc_start: 0.9124 (mttt) cc_final: 0.8713 (mppt) REVERT: B 167 GLU cc_start: 0.8593 (mp0) cc_final: 0.8301 (pm20) REVERT: C 26 MET cc_start: 0.7709 (mmm) cc_final: 0.7420 (mmp) REVERT: C 40 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.7995 (p) REVERT: C 71 ASN cc_start: 0.8700 (t0) cc_final: 0.8299 (t0) REVERT: C 81 TRP cc_start: 0.7253 (t-100) cc_final: 0.6411 (t60) REVERT: C 96 ARG cc_start: 0.7265 (mtp180) cc_final: 0.6955 (mmt-90) REVERT: C 142 TYR cc_start: 0.8777 (m-80) cc_final: 0.8129 (m-10) REVERT: C 148 LYS cc_start: 0.9326 (mmpt) cc_final: 0.9120 (mmpt) REVERT: C 152 LYS cc_start: 0.9039 (mttt) cc_final: 0.8767 (mppt) REVERT: C 167 GLU cc_start: 0.8647 (mp0) cc_final: 0.8339 (pm20) REVERT: D 26 MET cc_start: 0.7788 (mmm) cc_final: 0.7360 (mmp) REVERT: D 40 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8094 (p) REVERT: D 71 ASN cc_start: 0.8642 (t0) cc_final: 0.8105 (t0) REVERT: D 81 TRP cc_start: 0.7460 (t-100) cc_final: 0.6597 (t60) REVERT: D 96 ARG cc_start: 0.7108 (mtp180) cc_final: 0.6892 (mmt180) REVERT: D 148 LYS cc_start: 0.9296 (mmpt) cc_final: 0.9064 (mmpt) REVERT: D 152 LYS cc_start: 0.9113 (mttt) cc_final: 0.8824 (mppt) REVERT: D 167 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: E 26 MET cc_start: 0.7881 (mmm) cc_final: 0.7527 (mmp) REVERT: E 40 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.7995 (p) REVERT: E 71 ASN cc_start: 0.8817 (t0) cc_final: 0.8410 (t0) REVERT: E 74 ILE cc_start: 0.8226 (pt) cc_final: 0.8004 (tp) REVERT: E 81 TRP cc_start: 0.7336 (t-100) cc_final: 0.6523 (t60) REVERT: E 96 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6884 (mtt180) REVERT: E 122 LYS cc_start: 0.8336 (mttp) cc_final: 0.8036 (mtmm) REVERT: E 143 GLN cc_start: 0.8934 (mm110) cc_final: 0.8590 (mm110) REVERT: E 164 GLU cc_start: 0.8872 (pt0) cc_final: 0.8462 (pp20) REVERT: E 167 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: F 40 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.7808 (p) REVERT: F 71 ASN cc_start: 0.8717 (t0) cc_final: 0.8438 (t0) REVERT: F 73 ASN cc_start: 0.8594 (m-40) cc_final: 0.8340 (m-40) REVERT: F 81 TRP cc_start: 0.7208 (t-100) cc_final: 0.6387 (t60) REVERT: F 96 ARG cc_start: 0.7163 (mtp180) cc_final: 0.6893 (mmt180) REVERT: F 105 ARG cc_start: 0.8660 (mpt180) cc_final: 0.8407 (mmt-90) REVERT: F 142 TYR cc_start: 0.8748 (m-80) cc_final: 0.8038 (m-80) REVERT: F 148 LYS cc_start: 0.9313 (mmpt) cc_final: 0.9089 (mmpt) REVERT: F 152 LYS cc_start: 0.9143 (mttt) cc_final: 0.8844 (mppt) REVERT: F 167 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: G 26 MET cc_start: 0.7787 (mmm) cc_final: 0.7509 (mmp) REVERT: G 71 ASN cc_start: 0.8502 (t0) cc_final: 0.7810 (t0) REVERT: G 119 MET cc_start: 0.8291 (mmm) cc_final: 0.7944 (mmp) REVERT: G 122 LYS cc_start: 0.8632 (mttm) cc_final: 0.8053 (mtmm) REVERT: G 143 GLN cc_start: 0.8545 (mm110) cc_final: 0.8325 (mm110) REVERT: G 167 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8548 (pm20) outliers start: 33 outliers final: 10 residues processed: 377 average time/residue: 1.4172 time to fit residues: 565.4949 Evaluate side-chains 385 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 364 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10780 Z= 0.211 Angle : 0.635 6.735 14637 Z= 0.319 Chirality : 0.039 0.144 1708 Planarity : 0.004 0.043 1806 Dihedral : 3.654 16.674 1589 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.30 % Allowed : 23.87 % Favored : 73.82 % 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: 2.00 (0.25), residues: 1309 helix: 2.32 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.18 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 81 HIS 0.001 0.000 HIS F 166 PHE 0.004 0.001 PHE G 99 TYR 0.011 0.001 TYR B 34 ARG 0.009 0.001 ARG F 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 374 time to evaluate : 1.267 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: symmetry clash REVERT: A 26 MET cc_start: 0.7828 (mmm) cc_final: 0.7547 (mmp) REVERT: A 40 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 71 ASN cc_start: 0.8678 (t0) cc_final: 0.8230 (t0) REVERT: A 74 ILE cc_start: 0.8262 (pt) cc_final: 0.7937 (tp) REVERT: A 81 TRP cc_start: 0.7282 (t-100) cc_final: 0.6381 (t60) REVERT: A 122 LYS cc_start: 0.8572 (mttm) cc_final: 0.8330 (mttm) REVERT: A 152 LYS cc_start: 0.9177 (mttt) cc_final: 0.8897 (mppt) REVERT: A 167 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: A 169 ILE cc_start: 0.9059 (mt) cc_final: 0.8818 (tt) REVERT: A 199 LEU cc_start: 0.8888 (tp) cc_final: 0.8601 (tt) REVERT: B 26 MET cc_start: 0.7739 (mmm) cc_final: 0.7510 (mmp) REVERT: B 40 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8111 (p) REVERT: B 71 ASN cc_start: 0.8383 (t0) cc_final: 0.7873 (t0) REVERT: B 81 TRP cc_start: 0.7182 (t-100) cc_final: 0.6379 (t60) REVERT: B 96 ARG cc_start: 0.7289 (mtp180) cc_final: 0.6950 (mmt180) REVERT: B 142 TYR cc_start: 0.8864 (m-80) cc_final: 0.8250 (m-10) REVERT: B 143 GLN cc_start: 0.9004 (mm110) cc_final: 0.8629 (mm110) REVERT: B 167 GLU cc_start: 0.8577 (mp0) cc_final: 0.8312 (pm20) REVERT: C 26 MET cc_start: 0.7782 (mmm) cc_final: 0.7412 (mmp) REVERT: C 40 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8071 (p) REVERT: C 71 ASN cc_start: 0.8694 (t0) cc_final: 0.8295 (t0) REVERT: C 81 TRP cc_start: 0.7193 (t-100) cc_final: 0.6405 (t60) REVERT: C 142 TYR cc_start: 0.8599 (m-80) cc_final: 0.8094 (m-10) REVERT: C 152 LYS cc_start: 0.9033 (mttt) cc_final: 0.8678 (mtmm) REVERT: C 167 GLU cc_start: 0.8638 (mp0) cc_final: 0.8374 (pm20) REVERT: D 26 MET cc_start: 0.7811 (mmm) cc_final: 0.7246 (mmp) REVERT: D 40 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8190 (p) REVERT: D 47 TYR cc_start: 0.8674 (m-80) cc_final: 0.8453 (m-10) REVERT: D 68 TYR cc_start: 0.7935 (m-80) cc_final: 0.6984 (m-80) REVERT: D 71 ASN cc_start: 0.8610 (t0) cc_final: 0.8058 (t0) REVERT: D 81 TRP cc_start: 0.7442 (t-100) cc_final: 0.6603 (t60) REVERT: D 152 LYS cc_start: 0.9113 (mttt) cc_final: 0.8875 (mtmm) REVERT: D 167 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: D 169 ILE cc_start: 0.8981 (mt) cc_final: 0.8672 (tt) REVERT: E 26 MET cc_start: 0.7901 (mmm) cc_final: 0.7556 (mmp) REVERT: E 40 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8105 (p) REVERT: E 71 ASN cc_start: 0.8779 (t0) cc_final: 0.8385 (t0) REVERT: E 74 ILE cc_start: 0.8222 (pt) cc_final: 0.8000 (tp) REVERT: E 81 TRP cc_start: 0.7405 (t-100) cc_final: 0.6636 (t60) REVERT: E 122 LYS cc_start: 0.8325 (mttp) cc_final: 0.8020 (mtmm) REVERT: E 143 GLN cc_start: 0.9005 (mm110) cc_final: 0.8683 (mm110) REVERT: E 149 GLU cc_start: 0.9179 (pm20) cc_final: 0.8895 (pm20) REVERT: E 152 LYS cc_start: 0.9171 (mttt) cc_final: 0.8784 (mtmm) REVERT: E 164 GLU cc_start: 0.8899 (pt0) cc_final: 0.8584 (pm20) REVERT: E 165 GLU cc_start: 0.8827 (mp0) cc_final: 0.8385 (mp0) REVERT: E 167 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: F 40 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.7917 (p) REVERT: F 71 ASN cc_start: 0.8695 (t0) cc_final: 0.8408 (t0) REVERT: F 73 ASN cc_start: 0.8568 (m-40) cc_final: 0.8306 (m-40) REVERT: F 81 TRP cc_start: 0.7201 (t-100) cc_final: 0.6344 (t60) REVERT: F 105 ARG cc_start: 0.8646 (mpt180) cc_final: 0.8392 (mmt-90) REVERT: F 142 TYR cc_start: 0.8702 (m-80) cc_final: 0.7936 (m-80) REVERT: F 152 LYS cc_start: 0.9137 (mttt) cc_final: 0.8866 (mtmm) REVERT: F 167 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: F 169 ILE cc_start: 0.9019 (mt) cc_final: 0.8695 (tt) REVERT: F 179 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7920 (mtp-110) REVERT: G 26 MET cc_start: 0.7778 (mmm) cc_final: 0.7519 (mmp) REVERT: G 71 ASN cc_start: 0.8630 (t0) cc_final: 0.8036 (t0) REVERT: G 119 MET cc_start: 0.8276 (mmm) cc_final: 0.7966 (mmp) REVERT: G 122 LYS cc_start: 0.8617 (mttm) cc_final: 0.8267 (mtmm) REVERT: G 143 GLN cc_start: 0.8574 (mm110) cc_final: 0.8365 (mm110) REVERT: G 167 GLU cc_start: 0.8849 (mp0) cc_final: 0.8554 (pm20) outliers start: 25 outliers final: 11 residues processed: 381 average time/residue: 1.4391 time to fit residues: 580.4591 Evaluate side-chains 387 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 366 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 40 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10780 Z= 0.230 Angle : 0.681 7.471 14637 Z= 0.340 Chirality : 0.040 0.133 1708 Planarity : 0.005 0.043 1806 Dihedral : 3.612 16.499 1589 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.40 % Allowed : 24.88 % Favored : 72.72 % 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: 1.95 (0.25), residues: 1309 helix: 2.29 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.22 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP G 81 HIS 0.000 0.000 HIS A 166 PHE 0.005 0.001 PHE G 99 TYR 0.011 0.001 TYR B 34 ARG 0.013 0.001 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 361 time to evaluate : 1.289 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: 0.8746 (tp40) cc_final: 0.8176 (tm-30) REVERT: A 40 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8382 (p) REVERT: A 71 ASN cc_start: 0.8615 (t0) cc_final: 0.8185 (t0) REVERT: A 74 ILE cc_start: 0.8249 (pt) cc_final: 0.7953 (tp) REVERT: A 81 TRP cc_start: 0.7307 (t-100) cc_final: 0.6452 (t60) REVERT: A 152 LYS cc_start: 0.9177 (mttt) cc_final: 0.8930 (mtmm) REVERT: A 167 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: A 169 ILE cc_start: 0.9038 (mt) cc_final: 0.8801 (tt) REVERT: A 199 LEU cc_start: 0.8924 (tp) cc_final: 0.8632 (tt) REVERT: B 40 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8109 (p) REVERT: B 71 ASN cc_start: 0.8549 (t0) cc_final: 0.8086 (t0) REVERT: B 81 TRP cc_start: 0.7186 (t-100) cc_final: 0.6376 (t60) REVERT: B 96 ARG cc_start: 0.7235 (mtp180) cc_final: 0.6920 (mmt180) REVERT: B 102 MET cc_start: 0.8767 (ttp) cc_final: 0.8540 (ttm) REVERT: B 142 TYR cc_start: 0.8844 (m-80) cc_final: 0.8308 (m-10) REVERT: B 143 GLN cc_start: 0.9027 (mm110) cc_final: 0.8687 (mm110) REVERT: B 167 GLU cc_start: 0.8575 (mp0) cc_final: 0.8312 (pm20) REVERT: C 26 MET cc_start: 0.7786 (mmm) cc_final: 0.7427 (mmp) REVERT: C 40 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8087 (p) REVERT: C 71 ASN cc_start: 0.8671 (t0) cc_final: 0.8257 (t0) REVERT: C 81 TRP cc_start: 0.7154 (t-100) cc_final: 0.6406 (t60) REVERT: C 96 ARG cc_start: 0.7196 (mtp180) cc_final: 0.6849 (mmt-90) REVERT: C 152 LYS cc_start: 0.9047 (mttt) cc_final: 0.8711 (mtmm) REVERT: C 167 GLU cc_start: 0.8665 (mp0) cc_final: 0.8407 (pm20) REVERT: D 26 MET cc_start: 0.7891 (mmm) cc_final: 0.7392 (mmp) REVERT: D 40 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8218 (p) REVERT: D 47 TYR cc_start: 0.8677 (m-80) cc_final: 0.8452 (m-10) REVERT: D 71 ASN cc_start: 0.8635 (t0) cc_final: 0.8049 (t0) REVERT: D 81 TRP cc_start: 0.7493 (t-100) cc_final: 0.6760 (t60) REVERT: D 152 LYS cc_start: 0.9109 (mttt) cc_final: 0.8889 (mtmm) REVERT: D 167 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8546 (pm20) REVERT: D 169 ILE cc_start: 0.8974 (mt) cc_final: 0.8658 (tt) REVERT: E 40 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8124 (p) REVERT: E 71 ASN cc_start: 0.8772 (t0) cc_final: 0.8369 (t0) REVERT: E 74 ILE cc_start: 0.8199 (pt) cc_final: 0.7978 (tp) REVERT: E 81 TRP cc_start: 0.7413 (t-100) cc_final: 0.6743 (t60) REVERT: E 83 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8204 (mtm110) REVERT: E 96 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6884 (mmt180) REVERT: E 143 GLN cc_start: 0.9056 (mm110) cc_final: 0.8751 (mm110) REVERT: E 149 GLU cc_start: 0.9172 (pm20) cc_final: 0.8880 (pm20) REVERT: E 152 LYS cc_start: 0.9171 (mttt) cc_final: 0.8781 (mtmm) REVERT: E 164 GLU cc_start: 0.8897 (pt0) cc_final: 0.8547 (pm20) REVERT: E 167 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8500 (pm20) REVERT: F 40 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.7821 (p) REVERT: F 71 ASN cc_start: 0.8676 (t0) cc_final: 0.8382 (t0) REVERT: F 73 ASN cc_start: 0.8580 (m-40) cc_final: 0.8301 (m-40) REVERT: F 81 TRP cc_start: 0.7238 (t-100) cc_final: 0.6367 (t60) REVERT: F 105 ARG cc_start: 0.8678 (mpt180) cc_final: 0.8442 (mmt-90) REVERT: F 142 TYR cc_start: 0.8631 (m-80) cc_final: 0.8040 (m-80) REVERT: F 152 LYS cc_start: 0.9142 (mttt) cc_final: 0.8865 (mtmm) REVERT: F 167 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: F 169 ILE cc_start: 0.9019 (mt) cc_final: 0.8694 (tt) REVERT: F 179 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7918 (mtp-110) REVERT: G 26 MET cc_start: 0.7830 (mmm) cc_final: 0.7592 (mmp) REVERT: G 71 ASN cc_start: 0.8509 (t0) cc_final: 0.7769 (t0) REVERT: G 119 MET cc_start: 0.8289 (mmm) cc_final: 0.7980 (mmp) REVERT: G 122 LYS cc_start: 0.8595 (mttm) cc_final: 0.8264 (mtmm) REVERT: G 143 GLN cc_start: 0.8611 (mm110) cc_final: 0.8346 (mm110) REVERT: G 152 LYS cc_start: 0.9127 (mttt) cc_final: 0.8732 (mtmm) REVERT: G 167 GLU cc_start: 0.8864 (mp0) cc_final: 0.8571 (pm20) outliers start: 26 outliers final: 10 residues processed: 369 average time/residue: 1.4166 time to fit residues: 553.5154 Evaluate side-chains 376 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 356 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 161 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10780 Z= 0.225 Angle : 0.712 7.644 14637 Z= 0.352 Chirality : 0.039 0.162 1708 Planarity : 0.005 0.043 1806 Dihedral : 3.560 16.167 1589 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.84 % Allowed : 26.18 % Favored : 71.98 % 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: 1.99 (0.25), residues: 1309 helix: 2.32 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.22 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 81 HIS 0.000 0.000 HIS F 166 PHE 0.004 0.001 PHE G 189 TYR 0.010 0.001 TYR G 142 ARG 0.008 0.001 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 361 time to evaluate : 1.173 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 40 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 71 ASN cc_start: 0.8602 (t0) cc_final: 0.8203 (t0) REVERT: A 74 ILE cc_start: 0.8263 (pt) cc_final: 0.7964 (tp) REVERT: A 81 TRP cc_start: 0.7290 (t-100) cc_final: 0.6448 (t60) REVERT: A 122 LYS cc_start: 0.8547 (mttm) cc_final: 0.8300 (mtmt) REVERT: A 152 LYS cc_start: 0.9165 (mttt) cc_final: 0.8910 (mtmm) REVERT: A 167 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: A 169 ILE cc_start: 0.9023 (mt) cc_final: 0.8804 (tt) REVERT: A 199 LEU cc_start: 0.8917 (tp) cc_final: 0.8634 (tt) REVERT: B 40 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8117 (p) REVERT: B 71 ASN cc_start: 0.8563 (t0) cc_final: 0.8086 (t0) REVERT: B 81 TRP cc_start: 0.7200 (t-100) cc_final: 0.6328 (t60) REVERT: B 96 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6897 (mtt-85) REVERT: B 142 TYR cc_start: 0.8829 (m-80) cc_final: 0.8349 (m-10) REVERT: B 143 GLN cc_start: 0.9083 (mm110) cc_final: 0.8730 (mm110) REVERT: B 152 LYS cc_start: 0.9114 (mttt) cc_final: 0.8702 (mtmm) REVERT: B 167 GLU cc_start: 0.8579 (mp0) cc_final: 0.8333 (pm20) REVERT: C 26 MET cc_start: 0.7822 (mmm) cc_final: 0.7481 (mmp) REVERT: C 40 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8078 (p) REVERT: C 71 ASN cc_start: 0.8640 (t0) cc_final: 0.8242 (t0) REVERT: C 81 TRP cc_start: 0.7151 (t-100) cc_final: 0.6494 (t60) REVERT: C 82 LYS cc_start: 0.9006 (tptt) cc_final: 0.8761 (tptt) REVERT: C 96 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6867 (mmt180) REVERT: C 152 LYS cc_start: 0.9041 (mttt) cc_final: 0.8705 (mtmm) REVERT: C 160 LYS cc_start: 0.9201 (mtpp) cc_final: 0.8959 (ttmm) REVERT: C 167 GLU cc_start: 0.8674 (mp0) cc_final: 0.8414 (pm20) REVERT: D 26 MET cc_start: 0.7924 (mmm) cc_final: 0.7446 (mmp) REVERT: D 40 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8243 (p) REVERT: D 47 TYR cc_start: 0.8652 (m-80) cc_final: 0.8428 (m-10) REVERT: D 68 TYR cc_start: 0.7913 (m-80) cc_final: 0.6963 (m-80) REVERT: D 71 ASN cc_start: 0.8583 (t0) cc_final: 0.8071 (t0) REVERT: D 81 TRP cc_start: 0.7372 (t-100) cc_final: 0.6643 (t60) REVERT: D 152 LYS cc_start: 0.9092 (mttt) cc_final: 0.8845 (mtmm) REVERT: D 167 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8546 (pm20) REVERT: D 169 ILE cc_start: 0.8963 (mt) cc_final: 0.8654 (tt) REVERT: E 40 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8127 (p) REVERT: E 71 ASN cc_start: 0.8744 (t0) cc_final: 0.8338 (t0) REVERT: E 74 ILE cc_start: 0.8244 (pt) cc_final: 0.8013 (tp) REVERT: E 81 TRP cc_start: 0.7318 (t-100) cc_final: 0.6659 (t60) REVERT: E 96 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6877 (mmt180) REVERT: E 143 GLN cc_start: 0.9087 (mm110) cc_final: 0.8775 (mm110) REVERT: E 149 GLU cc_start: 0.9173 (pm20) cc_final: 0.8878 (pm20) REVERT: E 152 LYS cc_start: 0.9166 (mttt) cc_final: 0.8773 (mtmm) REVERT: E 164 GLU cc_start: 0.8886 (pt0) cc_final: 0.8626 (pm20) REVERT: E 165 GLU cc_start: 0.8802 (mp0) cc_final: 0.8241 (mp0) REVERT: E 167 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: E 169 ILE cc_start: 0.8994 (mt) cc_final: 0.8648 (tt) REVERT: F 40 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.7924 (p) REVERT: F 71 ASN cc_start: 0.8671 (t0) cc_final: 0.8366 (t0) REVERT: F 73 ASN cc_start: 0.8501 (m-40) cc_final: 0.8211 (m-40) REVERT: F 81 TRP cc_start: 0.7332 (t-100) cc_final: 0.6430 (t60) REVERT: F 105 ARG cc_start: 0.8680 (mpt180) cc_final: 0.8442 (mmt-90) REVERT: F 122 LYS cc_start: 0.8547 (mttm) cc_final: 0.8345 (mttp) REVERT: F 142 TYR cc_start: 0.8599 (m-80) cc_final: 0.8042 (m-80) REVERT: F 152 LYS cc_start: 0.9136 (mttt) cc_final: 0.8853 (mtmm) REVERT: F 167 GLU cc_start: 0.8645 (mp0) cc_final: 0.8338 (pm20) REVERT: F 169 ILE cc_start: 0.9029 (mt) cc_final: 0.8714 (tt) REVERT: F 179 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7903 (mtp-110) REVERT: G 26 MET cc_start: 0.7796 (mmm) cc_final: 0.7570 (mmp) REVERT: G 71 ASN cc_start: 0.8590 (t0) cc_final: 0.8050 (t0) REVERT: G 119 MET cc_start: 0.8266 (mmm) cc_final: 0.7958 (mmp) REVERT: G 122 LYS cc_start: 0.8583 (mttm) cc_final: 0.8259 (mtmm) REVERT: G 143 GLN cc_start: 0.8643 (mm110) cc_final: 0.8362 (mm110) REVERT: G 152 LYS cc_start: 0.9116 (mttt) cc_final: 0.8727 (mtmm) REVERT: G 167 GLU cc_start: 0.8905 (mp0) cc_final: 0.8618 (pm20) REVERT: G 169 ILE cc_start: 0.9037 (mt) cc_final: 0.8741 (tt) REVERT: G 199 LEU cc_start: 0.8923 (tp) cc_final: 0.8628 (tt) outliers start: 20 outliers final: 7 residues processed: 369 average time/residue: 1.4190 time to fit residues: 554.7233 Evaluate side-chains 373 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 357 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain G residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10780 Z= 0.260 Angle : 0.748 9.226 14637 Z= 0.372 Chirality : 0.041 0.181 1708 Planarity : 0.005 0.044 1806 Dihedral : 3.712 17.414 1589 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.84 % Allowed : 27.19 % Favored : 70.97 % 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: 1.97 (0.25), residues: 1309 helix: 2.28 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.15 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 81 HIS 0.001 0.000 HIS B 166 PHE 0.006 0.001 PHE C 189 TYR 0.013 0.001 TYR B 34 ARG 0.010 0.001 ARG C 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 349 time to evaluate : 1.066 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 40 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8277 (p) REVERT: A 71 ASN cc_start: 0.8587 (t0) cc_final: 0.8214 (t0) REVERT: A 74 ILE cc_start: 0.8303 (pt) cc_final: 0.7989 (tp) REVERT: A 81 TRP cc_start: 0.7348 (t-100) cc_final: 0.6512 (t60) REVERT: A 122 LYS cc_start: 0.8562 (mttm) cc_final: 0.8305 (mtmt) REVERT: A 152 LYS cc_start: 0.9176 (mttt) cc_final: 0.8919 (mtmm) REVERT: A 167 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: A 169 ILE cc_start: 0.9092 (mt) cc_final: 0.8824 (tt) REVERT: A 199 LEU cc_start: 0.8928 (tp) cc_final: 0.8648 (tt) REVERT: B 70 MET cc_start: 0.8628 (mtm) cc_final: 0.8311 (mtp) REVERT: B 71 ASN cc_start: 0.8561 (t0) cc_final: 0.8182 (t0) REVERT: B 81 TRP cc_start: 0.7212 (t-100) cc_final: 0.6328 (t60) REVERT: B 96 ARG cc_start: 0.7249 (mtp180) cc_final: 0.6920 (mtt-85) REVERT: B 142 TYR cc_start: 0.8832 (m-80) cc_final: 0.8326 (m-10) REVERT: B 143 GLN cc_start: 0.9105 (mm110) cc_final: 0.8731 (mm110) REVERT: B 152 LYS cc_start: 0.9146 (mttt) cc_final: 0.8751 (mtmm) REVERT: B 167 GLU cc_start: 0.8594 (mp0) cc_final: 0.8330 (pm20) REVERT: C 26 MET cc_start: 0.7870 (mmm) cc_final: 0.7555 (mmp) REVERT: C 40 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8057 (p) REVERT: C 71 ASN cc_start: 0.8653 (t0) cc_final: 0.8234 (t0) REVERT: C 81 TRP cc_start: 0.7159 (t-100) cc_final: 0.6532 (t60) REVERT: C 82 LYS cc_start: 0.9007 (tptt) cc_final: 0.8780 (tptt) REVERT: C 96 ARG cc_start: 0.7238 (mtp180) cc_final: 0.6938 (mmt180) REVERT: C 152 LYS cc_start: 0.9085 (mttt) cc_final: 0.8747 (mtmm) REVERT: C 160 LYS cc_start: 0.9215 (mtpp) cc_final: 0.8983 (ttmm) REVERT: C 167 GLU cc_start: 0.8723 (mp0) cc_final: 0.8435 (pm20) REVERT: D 26 MET cc_start: 0.7967 (mmm) cc_final: 0.7501 (mmp) REVERT: D 40 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8254 (p) REVERT: D 47 TYR cc_start: 0.8671 (m-80) cc_final: 0.8454 (m-10) REVERT: D 71 ASN cc_start: 0.8734 (t0) cc_final: 0.8168 (t0) REVERT: D 81 TRP cc_start: 0.7532 (t-100) cc_final: 0.6773 (t60) REVERT: D 152 LYS cc_start: 0.9124 (mttt) cc_final: 0.8890 (mtmm) REVERT: D 167 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: D 169 ILE cc_start: 0.8991 (mt) cc_final: 0.8658 (tt) REVERT: E 40 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8038 (p) REVERT: E 71 ASN cc_start: 0.8712 (t0) cc_final: 0.8291 (t0) REVERT: E 74 ILE cc_start: 0.8236 (pt) cc_final: 0.7979 (tp) REVERT: E 81 TRP cc_start: 0.7314 (t-100) cc_final: 0.6620 (t60) REVERT: E 96 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6948 (mmt180) REVERT: E 143 GLN cc_start: 0.9101 (mm110) cc_final: 0.8786 (mm110) REVERT: E 149 GLU cc_start: 0.9152 (pm20) cc_final: 0.8853 (pm20) REVERT: E 152 LYS cc_start: 0.9201 (mttt) cc_final: 0.8810 (mtmm) REVERT: E 164 GLU cc_start: 0.8911 (pt0) cc_final: 0.8640 (pm20) REVERT: E 165 GLU cc_start: 0.8820 (mp0) cc_final: 0.8257 (mp0) REVERT: E 167 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: F 40 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.7858 (p) REVERT: F 71 ASN cc_start: 0.8659 (t0) cc_final: 0.8372 (t0) REVERT: F 73 ASN cc_start: 0.8503 (m-40) cc_final: 0.8249 (m-40) REVERT: F 81 TRP cc_start: 0.7321 (t-100) cc_final: 0.6501 (t60) REVERT: F 105 ARG cc_start: 0.8686 (mpt180) cc_final: 0.8450 (mmt-90) REVERT: F 122 LYS cc_start: 0.8577 (mttm) cc_final: 0.8363 (mttp) REVERT: F 142 TYR cc_start: 0.8565 (m-80) cc_final: 0.7984 (m-80) REVERT: F 152 LYS cc_start: 0.9141 (mttt) cc_final: 0.8775 (mtmm) REVERT: F 167 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: F 179 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7908 (mtp-110) REVERT: G 71 ASN cc_start: 0.8467 (t0) cc_final: 0.7775 (t0) REVERT: G 119 MET cc_start: 0.8288 (mmm) cc_final: 0.7983 (mmp) REVERT: G 122 LYS cc_start: 0.8602 (mttm) cc_final: 0.8260 (mtmm) REVERT: G 143 GLN cc_start: 0.8762 (mm110) cc_final: 0.8528 (mm110) REVERT: G 167 GLU cc_start: 0.8760 (mp0) cc_final: 0.8493 (pm20) REVERT: G 199 LEU cc_start: 0.8969 (tp) cc_final: 0.8670 (tt) outliers start: 20 outliers final: 10 residues processed: 357 average time/residue: 1.4305 time to fit residues: 540.7650 Evaluate side-chains 366 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 347 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 72 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 50.0000 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075188 restraints weight = 19511.729| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.37 r_work: 0.2770 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10780 Z= 0.241 Angle : 0.746 8.881 14637 Z= 0.370 Chirality : 0.040 0.158 1708 Planarity : 0.005 0.044 1806 Dihedral : 3.640 16.736 1589 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.38 % Allowed : 27.83 % Favored : 70.78 % 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: 2.00 (0.25), residues: 1309 helix: 2.32 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.19 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 81 HIS 0.001 0.000 HIS C 166 PHE 0.004 0.001 PHE G 99 TYR 0.011 0.001 TYR B 34 ARG 0.010 0.001 ARG C 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7334.41 seconds wall clock time: 127 minutes 55.10 seconds (7675.10 seconds total)