Starting phenix.real_space_refine on Sat Jul 20 19:05:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsc_30830/07_2024/7dsc_30830.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsc_30830/07_2024/7dsc_30830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsc_30830/07_2024/7dsc_30830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsc_30830/07_2024/7dsc_30830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsc_30830/07_2024/7dsc_30830.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsc_30830/07_2024/7dsc_30830.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 104 5.16 5 C 7736 2.51 5 N 1888 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" 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 ARG 83": "NH1" <-> "NH2" Residue "B GLU 140": "OE1" <-> "OE2" 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 ARG 83": "NH1" <-> "NH2" Residue "C GLU 140": "OE1" <-> "OE2" 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 ARG 83": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" 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 ARG 83": "NH1" <-> "NH2" Residue "E GLU 140": "OE1" <-> "OE2" 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 ARG 83": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" 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 ARG 83": "NH1" <-> "NH2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G ARG 176": "NH1" <-> "NH2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H ARG 171": "NH1" <-> "NH2" Residue "H ARG 176": "NH1" <-> "NH2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "H ARG 201": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11848 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 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 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.57, per 1000 atoms: 0.64 Number of scatterers: 11848 At special positions: 0 Unit cell: (124.722, 124.722, 88.218, 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 104 16.00 O 2120 8.00 N 1888 7.00 C 7736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, 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 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 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 " " NAG H1001 " - " ASN H 139 " Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 2.1 seconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 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: 3.629A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 Processing helix chain 'B' and resid 6 through 18 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: 3.628A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.036A pdb=" N LYS B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 Processing helix chain 'C' and resid 6 through 18 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: 3.629A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 107 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 Processing helix chain 'D' and resid 6 through 18 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: 3.629A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 107 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 Processing helix chain 'E' and resid 6 through 18 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: 3.629A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 107 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 Processing helix chain 'F' and resid 6 through 18 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: 3.628A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 107 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.036A pdb=" N LYS F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE F 153 " --> pdb=" O GLU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 Processing helix chain 'G' and resid 6 through 18 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: 3.629A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 107 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE G 153 " --> pdb=" O GLU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 25 through 36 Processing helix chain 'H' and resid 47 through 70 Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 107 Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 129 Processing helix chain 'H' and resid 146 through 156 removed outlier: 4.036A pdb=" N LYS H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE H 153 " --> pdb=" O GLU H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 204 809 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 5.39 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: 3624 1.34 - 1.46: 2598 1.46 - 1.58: 5738 1.58 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 12120 Sorted by residual: 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 1.97e+00 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 1.97e+00 bond pdb=" C1 NAG H1001 " pdb=" O5 NAG H1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+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 1.94e+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 1.94e+00 ... (remaining 12115 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 432 107.14 - 113.85: 6827 113.85 - 120.56: 5143 120.56 - 127.28: 3934 127.28 - 133.99: 136 Bond angle restraints: 16472 Sorted by residual: angle pdb=" N VAL H 58 " pdb=" CA VAL H 58 " pdb=" C VAL H 58 " ideal model delta sigma weight residual 108.88 113.31 -4.43 2.16e+00 2.14e-01 4.21e+00 angle pdb=" N VAL E 58 " pdb=" CA VAL E 58 " pdb=" C VAL E 58 " ideal model delta sigma weight residual 108.88 113.27 -4.39 2.16e+00 2.14e-01 4.13e+00 angle pdb=" N VAL A 58 " pdb=" CA VAL A 58 " pdb=" C VAL A 58 " ideal model delta sigma weight residual 108.88 113.27 -4.39 2.16e+00 2.14e-01 4.13e+00 angle pdb=" N VAL C 58 " pdb=" CA VAL C 58 " pdb=" C VAL C 58 " ideal model delta sigma weight residual 108.88 113.27 -4.39 2.16e+00 2.14e-01 4.13e+00 angle pdb=" N VAL G 58 " pdb=" CA VAL G 58 " pdb=" C VAL G 58 " ideal model delta sigma weight residual 108.88 113.27 -4.39 2.16e+00 2.14e-01 4.13e+00 ... (remaining 16467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.98: 6520 13.98 - 27.96: 560 27.96 - 41.94: 200 41.94 - 55.93: 64 55.93 - 69.91: 8 Dihedral angle restraints: 7352 sinusoidal: 2840 harmonic: 4512 Sorted by residual: dihedral pdb=" CB CYS H 43 " pdb=" SG CYS H 43 " pdb=" SG CYS H 159 " pdb=" CB CYS H 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.88 -26.88 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 159 " pdb=" CB CYS F 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.87 -26.87 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS B 43 " pdb=" SG CYS B 43 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.87 -26.87 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 7349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1284 0.036 - 0.071: 501 0.071 - 0.107: 116 0.107 - 0.142: 27 0.142 - 0.178: 8 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB VAL B 58 " pdb=" CA VAL B 58 " pdb=" CG1 VAL B 58 " pdb=" CG2 VAL B 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CB VAL E 58 " pdb=" CA VAL E 58 " pdb=" CG1 VAL E 58 " pdb=" CG2 VAL E 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 1933 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 59 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO F 60 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 59 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO B 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.026 5.00e-02 4.00e+02 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3552 2.82 - 3.34: 11795 3.34 - 3.86: 19114 3.86 - 4.38: 20138 4.38 - 4.90: 36138 Nonbonded interactions: 90737 Sorted by model distance: nonbonded pdb=" OH TYR G 68 " pdb=" OG1 THR G 103 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR H 68 " pdb=" OG1 THR H 103 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR A 68 " pdb=" OG1 THR A 103 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR E 68 " pdb=" OG1 THR E 103 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR C 68 " pdb=" OG1 THR C 103 " model vdw 2.300 2.440 ... (remaining 90732 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' selection = chain 'H' } 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 group one per residue 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.710 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 0.039 12120 Z= 0.252 Angle : 0.563 5.363 16472 Z= 0.321 Chirality : 0.040 0.178 1936 Planarity : 0.004 0.046 2024 Dihedral : 12.770 69.908 4360 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 17.22 % Favored : 82.78 % 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: -0.35 (0.21), residues: 1480 helix: 0.64 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.98 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 62 HIS 0.001 0.000 HIS F 166 PHE 0.007 0.001 PHE D 64 TYR 0.008 0.001 TYR H 177 ARG 0.002 0.000 ARG F 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 1.313 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 95 LEU cc_start: 0.8749 (mt) cc_final: 0.8504 (tp) REVERT: A 134 LEU cc_start: 0.7989 (mt) cc_final: 0.7573 (mt) REVERT: A 159 CYS cc_start: 0.4649 (m) cc_final: 0.4133 (m) REVERT: B 26 MET cc_start: 0.7042 (mmm) cc_final: 0.6798 (mmm) REVERT: B 95 LEU cc_start: 0.8719 (mt) cc_final: 0.8514 (tp) REVERT: B 134 LEU cc_start: 0.7898 (mt) cc_final: 0.7489 (mt) REVERT: B 185 CYS cc_start: 0.9068 (m) cc_final: 0.8527 (m) REVERT: C 95 LEU cc_start: 0.8748 (mt) cc_final: 0.8503 (tp) REVERT: C 134 LEU cc_start: 0.7986 (mt) cc_final: 0.7572 (mt) REVERT: C 159 CYS cc_start: 0.4643 (m) cc_final: 0.4129 (m) REVERT: D 26 MET cc_start: 0.7038 (mmm) cc_final: 0.6790 (mmm) REVERT: D 95 LEU cc_start: 0.8718 (mt) cc_final: 0.8515 (tp) REVERT: D 134 LEU cc_start: 0.7891 (mt) cc_final: 0.7481 (mt) REVERT: D 185 CYS cc_start: 0.9068 (m) cc_final: 0.8525 (m) REVERT: E 95 LEU cc_start: 0.8742 (mt) cc_final: 0.8497 (tp) REVERT: E 134 LEU cc_start: 0.7989 (mt) cc_final: 0.7576 (mt) REVERT: E 159 CYS cc_start: 0.4646 (m) cc_final: 0.4129 (m) REVERT: F 26 MET cc_start: 0.7039 (mmm) cc_final: 0.6794 (mmm) REVERT: F 95 LEU cc_start: 0.8721 (mt) cc_final: 0.8516 (tp) REVERT: F 134 LEU cc_start: 0.7892 (mt) cc_final: 0.7485 (mt) REVERT: F 185 CYS cc_start: 0.9068 (m) cc_final: 0.8532 (m) REVERT: G 95 LEU cc_start: 0.8743 (mt) cc_final: 0.8497 (tp) REVERT: G 134 LEU cc_start: 0.7993 (mt) cc_final: 0.7581 (mt) REVERT: G 159 CYS cc_start: 0.4648 (m) cc_final: 0.4129 (m) REVERT: H 26 MET cc_start: 0.7041 (mmm) cc_final: 0.6798 (mmm) REVERT: H 95 LEU cc_start: 0.8722 (mt) cc_final: 0.8517 (tp) REVERT: H 134 LEU cc_start: 0.7899 (mt) cc_final: 0.7489 (mt) REVERT: H 185 CYS cc_start: 0.9065 (m) cc_final: 0.8529 (m) outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.2313 time to fit residues: 221.7132 Evaluate side-chains 510 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12120 Z= 0.209 Angle : 0.691 6.942 16472 Z= 0.351 Chirality : 0.041 0.164 1936 Planarity : 0.005 0.050 2024 Dihedral : 4.698 22.619 1792 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.55 % Allowed : 25.41 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1480 helix: 1.82 (0.16), residues: 1112 sheet: None (None), residues: 0 loop : -2.37 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 62 HIS 0.001 0.000 HIS G 166 PHE 0.022 0.002 PHE G 99 TYR 0.022 0.002 TYR B 51 ARG 0.007 0.001 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 560 time to evaluate : 1.385 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: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8848 (mt) cc_final: 0.8541 (tp) REVERT: A 142 TYR cc_start: 0.6345 (m-80) cc_final: 0.5901 (m-80) REVERT: A 170 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8694 (t) REVERT: B 71 ASN cc_start: 0.8549 (m-40) cc_final: 0.7580 (t0) REVERT: B 95 LEU cc_start: 0.8869 (mt) cc_final: 0.8606 (tp) REVERT: B 170 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8715 (t) REVERT: B 185 CYS cc_start: 0.8965 (m) cc_final: 0.8401 (m) REVERT: C 95 LEU cc_start: 0.8854 (mt) cc_final: 0.8545 (tp) REVERT: C 142 TYR cc_start: 0.6343 (m-80) cc_final: 0.5900 (m-80) REVERT: C 170 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8697 (t) REVERT: D 71 ASN cc_start: 0.8550 (m-40) cc_final: 0.7582 (t0) REVERT: D 95 LEU cc_start: 0.8889 (mt) cc_final: 0.8633 (tp) REVERT: D 170 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8720 (t) REVERT: D 185 CYS cc_start: 0.8964 (m) cc_final: 0.8401 (m) REVERT: E 95 LEU cc_start: 0.8850 (mt) cc_final: 0.8542 (tp) REVERT: E 142 TYR cc_start: 0.6344 (m-80) cc_final: 0.5899 (m-80) REVERT: E 170 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8700 (t) REVERT: F 71 ASN cc_start: 0.8551 (m-40) cc_final: 0.7586 (t0) REVERT: F 95 LEU cc_start: 0.8871 (mt) cc_final: 0.8609 (tp) REVERT: F 170 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8718 (t) REVERT: F 185 CYS cc_start: 0.8965 (m) cc_final: 0.8399 (m) REVERT: G 95 LEU cc_start: 0.8845 (mt) cc_final: 0.8537 (tp) REVERT: G 142 TYR cc_start: 0.6342 (m-80) cc_final: 0.5901 (m-80) REVERT: G 170 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8718 (t) REVERT: H 71 ASN cc_start: 0.8531 (m-40) cc_final: 0.7544 (t0) REVERT: H 95 LEU cc_start: 0.8887 (mt) cc_final: 0.8629 (tp) REVERT: H 170 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8711 (t) REVERT: H 185 CYS cc_start: 0.8968 (m) cc_final: 0.8405 (m) outliers start: 55 outliers final: 38 residues processed: 588 average time/residue: 0.2614 time to fit residues: 217.2257 Evaluate side-chains 560 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 514 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 50.0000 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 50.0000 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12120 Z= 0.203 Angle : 0.654 6.443 16472 Z= 0.330 Chirality : 0.041 0.169 1936 Planarity : 0.005 0.053 2024 Dihedral : 4.079 19.912 1792 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.72 % Allowed : 23.92 % Favored : 71.36 % 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: 1.58 (0.22), residues: 1480 helix: 1.99 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.14 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 62 HIS 0.002 0.001 HIS C 166 PHE 0.024 0.001 PHE H 99 TYR 0.021 0.001 TYR B 142 ARG 0.004 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 527 time to evaluate : 1.385 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: 0.6946 (mmm) cc_final: 0.6644 (mmm) REVERT: A 95 LEU cc_start: 0.8818 (mt) cc_final: 0.8558 (tp) REVERT: A 170 SER cc_start: 0.9087 (OUTLIER) cc_final: 0.8742 (t) REVERT: B 95 LEU cc_start: 0.8830 (mt) cc_final: 0.8555 (tp) REVERT: B 156 LYS cc_start: 0.7729 (mttt) cc_final: 0.7528 (mtpt) REVERT: B 170 SER cc_start: 0.9087 (t) cc_final: 0.8765 (t) REVERT: B 185 CYS cc_start: 0.8908 (m) cc_final: 0.8393 (m) REVERT: C 26 MET cc_start: 0.6944 (mmm) cc_final: 0.6646 (mmm) REVERT: C 95 LEU cc_start: 0.8820 (mt) cc_final: 0.8561 (tp) REVERT: C 170 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8743 (t) REVERT: D 95 LEU cc_start: 0.8831 (mt) cc_final: 0.8557 (tp) REVERT: D 156 LYS cc_start: 0.7732 (mttt) cc_final: 0.7513 (mtpt) REVERT: D 165 GLU cc_start: 0.7550 (mp0) cc_final: 0.7172 (mp0) REVERT: D 170 SER cc_start: 0.9088 (t) cc_final: 0.8768 (t) REVERT: D 185 CYS cc_start: 0.8892 (m) cc_final: 0.8380 (m) REVERT: E 26 MET cc_start: 0.6943 (mmm) cc_final: 0.6643 (mmm) REVERT: E 95 LEU cc_start: 0.8819 (mt) cc_final: 0.8556 (tp) REVERT: E 170 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8744 (t) REVERT: F 95 LEU cc_start: 0.8826 (mt) cc_final: 0.8552 (tp) REVERT: F 156 LYS cc_start: 0.7731 (mttt) cc_final: 0.7500 (mtpt) REVERT: F 165 GLU cc_start: 0.7549 (mp0) cc_final: 0.7148 (mp0) REVERT: F 170 SER cc_start: 0.9083 (t) cc_final: 0.8794 (t) REVERT: F 185 CYS cc_start: 0.8909 (m) cc_final: 0.8400 (m) REVERT: G 26 MET cc_start: 0.6942 (mmm) cc_final: 0.6643 (mmm) REVERT: G 95 LEU cc_start: 0.8814 (mt) cc_final: 0.8555 (tp) REVERT: G 170 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8744 (t) REVERT: H 95 LEU cc_start: 0.8825 (mt) cc_final: 0.8552 (tp) REVERT: H 156 LYS cc_start: 0.7727 (mttt) cc_final: 0.7499 (mtpt) REVERT: H 165 GLU cc_start: 0.7555 (mp0) cc_final: 0.7158 (mp0) REVERT: H 170 SER cc_start: 0.9076 (t) cc_final: 0.8788 (t) REVERT: H 185 CYS cc_start: 0.8909 (m) cc_final: 0.8395 (m) outliers start: 57 outliers final: 48 residues processed: 556 average time/residue: 0.2119 time to fit residues: 169.1306 Evaluate side-chains 539 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 487 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 185 CYS Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12120 Z= 0.190 Angle : 0.661 8.938 16472 Z= 0.334 Chirality : 0.041 0.172 1936 Planarity : 0.005 0.053 2024 Dihedral : 4.022 18.103 1792 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 6.21 % Allowed : 24.83 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1480 helix: 2.08 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -2.13 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 62 HIS 0.001 0.000 HIS B 166 PHE 0.024 0.001 PHE D 99 TYR 0.016 0.001 TYR A 142 ARG 0.003 0.000 ARG F 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 509 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.6897 (mmm) cc_final: 0.6549 (mmm) REVERT: A 68 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: A 95 LEU cc_start: 0.8741 (mt) cc_final: 0.8468 (tp) REVERT: A 160 LYS cc_start: 0.7363 (tppt) cc_final: 0.6948 (tppt) REVERT: A 170 SER cc_start: 0.9104 (t) cc_final: 0.8751 (t) REVERT: B 95 LEU cc_start: 0.8791 (mt) cc_final: 0.8526 (tp) REVERT: B 156 LYS cc_start: 0.7756 (mttt) cc_final: 0.7498 (mtpt) REVERT: B 165 GLU cc_start: 0.7562 (mp0) cc_final: 0.7275 (mp0) REVERT: B 170 SER cc_start: 0.9085 (t) cc_final: 0.8757 (t) REVERT: B 185 CYS cc_start: 0.8839 (m) cc_final: 0.8359 (m) REVERT: C 26 MET cc_start: 0.6901 (mmm) cc_final: 0.6549 (mmm) REVERT: C 68 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6619 (m-80) REVERT: C 95 LEU cc_start: 0.8743 (mt) cc_final: 0.8468 (tp) REVERT: C 160 LYS cc_start: 0.7365 (tppt) cc_final: 0.6948 (tppt) REVERT: C 170 SER cc_start: 0.9104 (t) cc_final: 0.8751 (t) REVERT: D 95 LEU cc_start: 0.8791 (mt) cc_final: 0.8525 (tp) REVERT: D 156 LYS cc_start: 0.7757 (mttt) cc_final: 0.7515 (mtpt) REVERT: D 170 SER cc_start: 0.9088 (t) cc_final: 0.8762 (t) REVERT: D 185 CYS cc_start: 0.8831 (m) cc_final: 0.8375 (m) REVERT: E 26 MET cc_start: 0.6901 (mmm) cc_final: 0.6552 (mmm) REVERT: E 68 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: E 95 LEU cc_start: 0.8745 (mt) cc_final: 0.8468 (tp) REVERT: E 160 LYS cc_start: 0.7367 (tppt) cc_final: 0.6964 (tppt) REVERT: E 170 SER cc_start: 0.9105 (t) cc_final: 0.8750 (t) REVERT: F 95 LEU cc_start: 0.8786 (mt) cc_final: 0.8522 (tp) REVERT: F 156 LYS cc_start: 0.7751 (mttt) cc_final: 0.7504 (mtpt) REVERT: F 170 SER cc_start: 0.9066 (t) cc_final: 0.8743 (t) REVERT: F 185 CYS cc_start: 0.8837 (m) cc_final: 0.8363 (m) REVERT: G 26 MET cc_start: 0.6898 (mmm) cc_final: 0.6547 (mmm) REVERT: G 68 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6619 (m-80) REVERT: G 95 LEU cc_start: 0.8743 (mt) cc_final: 0.8467 (tp) REVERT: G 160 LYS cc_start: 0.7364 (tppt) cc_final: 0.6948 (tppt) REVERT: G 170 SER cc_start: 0.9104 (t) cc_final: 0.8750 (t) REVERT: H 95 LEU cc_start: 0.8783 (mt) cc_final: 0.8520 (tp) REVERT: H 156 LYS cc_start: 0.7750 (mttt) cc_final: 0.7503 (mtpt) REVERT: H 170 SER cc_start: 0.9062 (t) cc_final: 0.8796 (t) REVERT: H 185 CYS cc_start: 0.8840 (m) cc_final: 0.8369 (m) outliers start: 75 outliers final: 57 residues processed: 553 average time/residue: 0.2203 time to fit residues: 175.7668 Evaluate side-chains 549 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 488 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12120 Z= 0.213 Angle : 0.691 11.890 16472 Z= 0.344 Chirality : 0.042 0.168 1936 Planarity : 0.005 0.054 2024 Dihedral : 4.083 17.377 1792 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 6.62 % Allowed : 25.99 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.22), residues: 1480 helix: 2.18 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -1.84 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 62 HIS 0.001 0.001 HIS F 166 PHE 0.017 0.001 PHE D 99 TYR 0.015 0.001 TYR A 142 ARG 0.005 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 495 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.6908 (mmm) cc_final: 0.6532 (mmm) REVERT: A 68 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: A 95 LEU cc_start: 0.8690 (mt) cc_final: 0.8436 (tp) REVERT: A 102 MET cc_start: 0.8597 (tpp) cc_final: 0.8292 (tpp) REVERT: A 104 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6471 (mp-120) REVERT: A 160 LYS cc_start: 0.7498 (tppt) cc_final: 0.7114 (tppt) REVERT: A 170 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8770 (t) REVERT: B 95 LEU cc_start: 0.8756 (mt) cc_final: 0.8500 (tp) REVERT: B 102 MET cc_start: 0.8627 (tpp) cc_final: 0.8304 (tpp) REVERT: B 156 LYS cc_start: 0.7795 (mttt) cc_final: 0.7545 (mtpt) REVERT: B 165 GLU cc_start: 0.7649 (mp0) cc_final: 0.7376 (mp0) REVERT: B 170 SER cc_start: 0.9141 (t) cc_final: 0.8830 (t) REVERT: B 185 CYS cc_start: 0.8839 (m) cc_final: 0.8390 (m) REVERT: C 26 MET cc_start: 0.6909 (mmm) cc_final: 0.6535 (mmm) REVERT: C 68 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: C 95 LEU cc_start: 0.8690 (mt) cc_final: 0.8437 (tp) REVERT: C 102 MET cc_start: 0.8591 (tpp) cc_final: 0.8289 (tpp) REVERT: C 104 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6472 (mp-120) REVERT: C 160 LYS cc_start: 0.7498 (tppt) cc_final: 0.7113 (tppt) REVERT: C 170 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8767 (t) REVERT: D 95 LEU cc_start: 0.8754 (mt) cc_final: 0.8499 (tp) REVERT: D 102 MET cc_start: 0.8623 (tpp) cc_final: 0.8305 (tpp) REVERT: D 156 LYS cc_start: 0.7793 (mttt) cc_final: 0.7569 (mtpt) REVERT: D 165 GLU cc_start: 0.7601 (mp0) cc_final: 0.7182 (mp0) REVERT: D 170 SER cc_start: 0.9130 (t) cc_final: 0.8817 (t) REVERT: D 185 CYS cc_start: 0.8831 (m) cc_final: 0.8388 (m) REVERT: E 26 MET cc_start: 0.6887 (mmm) cc_final: 0.6510 (mmm) REVERT: E 68 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: E 95 LEU cc_start: 0.8693 (mt) cc_final: 0.8437 (tp) REVERT: E 102 MET cc_start: 0.8591 (tpp) cc_final: 0.8313 (tpp) REVERT: E 104 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6472 (mp-120) REVERT: E 160 LYS cc_start: 0.7510 (tppt) cc_final: 0.7140 (tppt) REVERT: E 170 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8764 (t) REVERT: F 95 LEU cc_start: 0.8748 (mt) cc_final: 0.8493 (tp) REVERT: F 102 MET cc_start: 0.8625 (tpp) cc_final: 0.8306 (tpp) REVERT: F 156 LYS cc_start: 0.7783 (mttt) cc_final: 0.7564 (mtpt) REVERT: F 165 GLU cc_start: 0.7618 (mp0) cc_final: 0.7193 (mp0) REVERT: F 170 SER cc_start: 0.9111 (t) cc_final: 0.8794 (t) REVERT: F 185 CYS cc_start: 0.8835 (m) cc_final: 0.8391 (m) REVERT: G 26 MET cc_start: 0.6906 (mmm) cc_final: 0.6529 (mmm) REVERT: G 68 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: G 95 LEU cc_start: 0.8689 (mt) cc_final: 0.8436 (tp) REVERT: G 102 MET cc_start: 0.8595 (tpp) cc_final: 0.8287 (tpp) REVERT: G 104 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6472 (mp-120) REVERT: G 160 LYS cc_start: 0.7484 (tppt) cc_final: 0.7096 (tppt) REVERT: G 170 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8764 (t) REVERT: H 95 LEU cc_start: 0.8750 (mt) cc_final: 0.8494 (tp) REVERT: H 102 MET cc_start: 0.8611 (tpp) cc_final: 0.8305 (tpp) REVERT: H 156 LYS cc_start: 0.7784 (mttt) cc_final: 0.7565 (mtpt) REVERT: H 165 GLU cc_start: 0.7623 (mp0) cc_final: 0.7200 (mp0) REVERT: H 170 SER cc_start: 0.9105 (t) cc_final: 0.8788 (t) REVERT: H 185 CYS cc_start: 0.8837 (m) cc_final: 0.8395 (m) outliers start: 80 outliers final: 59 residues processed: 537 average time/residue: 0.2172 time to fit residues: 169.4929 Evaluate side-chains 551 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 480 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12120 Z= 0.204 Angle : 0.718 13.900 16472 Z= 0.351 Chirality : 0.043 0.158 1936 Planarity : 0.005 0.055 2024 Dihedral : 4.113 18.546 1792 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.22 % Allowed : 28.23 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.22), residues: 1480 helix: 2.18 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -1.81 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 62 HIS 0.000 0.000 HIS D 166 PHE 0.024 0.001 PHE H 99 TYR 0.013 0.001 TYR H 142 ARG 0.005 0.001 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 503 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: A 95 LEU cc_start: 0.8718 (mt) cc_final: 0.8419 (tp) REVERT: A 102 MET cc_start: 0.8616 (tpp) cc_final: 0.8408 (tpp) REVERT: A 160 LYS cc_start: 0.7492 (tppt) cc_final: 0.7120 (tppt) REVERT: A 165 GLU cc_start: 0.7868 (mp0) cc_final: 0.7660 (pm20) REVERT: A 167 GLU cc_start: 0.7956 (pp20) cc_final: 0.7569 (pp20) REVERT: A 170 SER cc_start: 0.9105 (t) cc_final: 0.8775 (t) REVERT: B 66 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8497 (tt) REVERT: B 68 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: B 95 LEU cc_start: 0.8827 (mt) cc_final: 0.8534 (tt) REVERT: B 170 SER cc_start: 0.9147 (t) cc_final: 0.8838 (t) REVERT: B 185 CYS cc_start: 0.8854 (m) cc_final: 0.8462 (m) REVERT: C 68 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: C 95 LEU cc_start: 0.8717 (mt) cc_final: 0.8420 (tp) REVERT: C 102 MET cc_start: 0.8612 (tpp) cc_final: 0.8403 (tpp) REVERT: C 160 LYS cc_start: 0.7493 (tppt) cc_final: 0.7127 (tppt) REVERT: C 165 GLU cc_start: 0.7868 (mp0) cc_final: 0.7658 (pm20) REVERT: C 167 GLU cc_start: 0.7954 (pp20) cc_final: 0.7568 (pp20) REVERT: C 170 SER cc_start: 0.9103 (t) cc_final: 0.8775 (t) REVERT: D 68 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6288 (m-80) REVERT: D 95 LEU cc_start: 0.8824 (mt) cc_final: 0.8534 (tt) REVERT: D 156 LYS cc_start: 0.7801 (mttt) cc_final: 0.7567 (mtpt) REVERT: D 165 GLU cc_start: 0.7650 (mp0) cc_final: 0.7322 (mp0) REVERT: D 170 SER cc_start: 0.9150 (t) cc_final: 0.8841 (t) REVERT: D 185 CYS cc_start: 0.8852 (m) cc_final: 0.8452 (m) REVERT: E 68 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: E 95 LEU cc_start: 0.8721 (mt) cc_final: 0.8422 (tp) REVERT: E 102 MET cc_start: 0.8610 (tpp) cc_final: 0.8400 (tpp) REVERT: E 170 SER cc_start: 0.9117 (t) cc_final: 0.8781 (t) REVERT: F 66 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8515 (tt) REVERT: F 68 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: F 95 LEU cc_start: 0.8764 (mt) cc_final: 0.8500 (tt) REVERT: F 156 LYS cc_start: 0.7808 (mttt) cc_final: 0.7584 (mtpt) REVERT: F 165 GLU cc_start: 0.7642 (mp0) cc_final: 0.7330 (mp0) REVERT: F 170 SER cc_start: 0.9117 (t) cc_final: 0.8856 (t) REVERT: F 185 CYS cc_start: 0.8843 (m) cc_final: 0.8455 (m) REVERT: G 68 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: G 95 LEU cc_start: 0.8717 (mt) cc_final: 0.8417 (tp) REVERT: G 102 MET cc_start: 0.8614 (tpp) cc_final: 0.8400 (tpp) REVERT: G 160 LYS cc_start: 0.7527 (tppt) cc_final: 0.7157 (tppt) REVERT: G 165 GLU cc_start: 0.7845 (mp0) cc_final: 0.7636 (pm20) REVERT: G 167 GLU cc_start: 0.7957 (pp20) cc_final: 0.7573 (pp20) REVERT: G 170 SER cc_start: 0.9097 (t) cc_final: 0.8768 (t) REVERT: H 68 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6316 (m-80) REVERT: H 95 LEU cc_start: 0.8767 (mt) cc_final: 0.8503 (tt) REVERT: H 140 GLU cc_start: 0.6239 (pm20) cc_final: 0.5403 (pm20) REVERT: H 143 GLN cc_start: 0.6750 (mm-40) cc_final: 0.6484 (pp30) REVERT: H 156 LYS cc_start: 0.7811 (mttt) cc_final: 0.7582 (mtpt) REVERT: H 165 GLU cc_start: 0.7648 (mp0) cc_final: 0.7328 (mp0) REVERT: H 170 SER cc_start: 0.9102 (t) cc_final: 0.8847 (t) REVERT: H 185 CYS cc_start: 0.8847 (m) cc_final: 0.8454 (m) outliers start: 63 outliers final: 50 residues processed: 531 average time/residue: 0.2099 time to fit residues: 161.0005 Evaluate side-chains 539 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 479 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.0050 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12120 Z= 0.192 Angle : 0.746 14.063 16472 Z= 0.357 Chirality : 0.043 0.167 1936 Planarity : 0.005 0.055 2024 Dihedral : 4.064 17.648 1792 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.30 % Allowed : 27.65 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.22), residues: 1480 helix: 2.28 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -1.86 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 62 HIS 0.000 0.000 HIS E 166 PHE 0.020 0.001 PHE B 99 TYR 0.018 0.001 TYR E 142 ARG 0.004 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 496 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: A 95 LEU cc_start: 0.8727 (mt) cc_final: 0.8443 (tp) REVERT: A 102 MET cc_start: 0.8611 (tpp) cc_final: 0.8242 (tpp) REVERT: A 160 LYS cc_start: 0.7532 (tppt) cc_final: 0.7204 (tppt) REVERT: A 165 GLU cc_start: 0.7850 (mp0) cc_final: 0.7629 (pm20) REVERT: A 167 GLU cc_start: 0.8049 (pp20) cc_final: 0.7801 (pp20) REVERT: A 170 SER cc_start: 0.9133 (t) cc_final: 0.8787 (t) REVERT: B 68 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6382 (m-80) REVERT: B 95 LEU cc_start: 0.8812 (mt) cc_final: 0.8509 (tt) REVERT: B 104 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7896 (mp10) REVERT: B 170 SER cc_start: 0.9135 (t) cc_final: 0.8821 (t) REVERT: B 185 CYS cc_start: 0.8849 (m) cc_final: 0.8466 (m) REVERT: C 68 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: C 95 LEU cc_start: 0.8727 (mt) cc_final: 0.8441 (tp) REVERT: C 102 MET cc_start: 0.8605 (tpp) cc_final: 0.8244 (tpp) REVERT: C 119 MET cc_start: 0.7941 (mmp) cc_final: 0.7662 (mmt) REVERT: C 160 LYS cc_start: 0.7534 (tppt) cc_final: 0.7204 (tppt) REVERT: C 165 GLU cc_start: 0.7849 (mp0) cc_final: 0.7627 (pm20) REVERT: C 170 SER cc_start: 0.9128 (t) cc_final: 0.8786 (t) REVERT: D 68 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: D 95 LEU cc_start: 0.8809 (mt) cc_final: 0.8504 (tt) REVERT: D 104 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7821 (mp10) REVERT: D 170 SER cc_start: 0.9141 (t) cc_final: 0.8829 (t) REVERT: D 185 CYS cc_start: 0.8849 (m) cc_final: 0.8461 (m) REVERT: E 68 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: E 95 LEU cc_start: 0.8731 (mt) cc_final: 0.8439 (tp) REVERT: E 102 MET cc_start: 0.8597 (tpp) cc_final: 0.8216 (tpp) REVERT: E 156 LYS cc_start: 0.7780 (mttt) cc_final: 0.7487 (mtpt) REVERT: E 170 SER cc_start: 0.9135 (t) cc_final: 0.8785 (t) REVERT: F 68 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6371 (m-80) REVERT: F 95 LEU cc_start: 0.8803 (mt) cc_final: 0.8505 (tt) REVERT: F 104 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7826 (mp10) REVERT: F 156 LYS cc_start: 0.7751 (mttt) cc_final: 0.7549 (mtpt) REVERT: F 170 SER cc_start: 0.9120 (t) cc_final: 0.8841 (t) REVERT: F 185 CYS cc_start: 0.8838 (m) cc_final: 0.8441 (m) REVERT: G 68 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: G 95 LEU cc_start: 0.8727 (mt) cc_final: 0.8440 (tp) REVERT: G 102 MET cc_start: 0.8611 (tpp) cc_final: 0.8237 (tpp) REVERT: G 119 MET cc_start: 0.7968 (mmp) cc_final: 0.7686 (mmt) REVERT: G 160 LYS cc_start: 0.7533 (tppt) cc_final: 0.7205 (tppt) REVERT: G 165 GLU cc_start: 0.7849 (mp0) cc_final: 0.7636 (pm20) REVERT: G 170 SER cc_start: 0.9122 (t) cc_final: 0.8778 (t) REVERT: H 68 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: H 95 LEU cc_start: 0.8805 (mt) cc_final: 0.8502 (tt) REVERT: H 170 SER cc_start: 0.9105 (t) cc_final: 0.8824 (t) REVERT: H 185 CYS cc_start: 0.8842 (m) cc_final: 0.8447 (m) outliers start: 64 outliers final: 50 residues processed: 525 average time/residue: 0.2147 time to fit residues: 161.6332 Evaluate side-chains 540 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 482 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 30.0000 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 133 optimal weight: 50.0000 chunk 140 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 C 104 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 71 ASN H 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12120 Z= 0.224 Angle : 0.780 13.888 16472 Z= 0.375 Chirality : 0.043 0.157 1936 Planarity : 0.005 0.056 2024 Dihedral : 4.223 23.074 1792 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.87 % Allowed : 26.57 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.22), residues: 1480 helix: 2.30 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.23 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 62 HIS 0.001 0.000 HIS C 166 PHE 0.011 0.001 PHE D 163 TYR 0.015 0.001 TYR C 142 ARG 0.004 0.001 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 487 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: A 95 LEU cc_start: 0.8718 (mt) cc_final: 0.8421 (tp) REVERT: A 102 MET cc_start: 0.8516 (tpp) cc_final: 0.8106 (tpp) REVERT: A 119 MET cc_start: 0.7948 (mmp) cc_final: 0.7590 (mmt) REVERT: A 160 LYS cc_start: 0.7559 (tppt) cc_final: 0.7332 (tppt) REVERT: A 165 GLU cc_start: 0.7832 (mp0) cc_final: 0.7631 (pm20) REVERT: A 167 GLU cc_start: 0.8002 (pp20) cc_final: 0.7078 (pp20) REVERT: A 170 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8813 (t) REVERT: B 32 GLN cc_start: 0.8601 (tp40) cc_final: 0.7797 (tm-30) REVERT: B 68 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: B 95 LEU cc_start: 0.8783 (mt) cc_final: 0.8462 (tt) REVERT: B 170 SER cc_start: 0.9145 (t) cc_final: 0.8838 (t) REVERT: B 185 CYS cc_start: 0.8822 (m) cc_final: 0.8383 (m) REVERT: C 68 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: C 95 LEU cc_start: 0.8719 (mt) cc_final: 0.8418 (tp) REVERT: C 102 MET cc_start: 0.8515 (tpp) cc_final: 0.8109 (tpp) REVERT: C 119 MET cc_start: 0.7957 (mmp) cc_final: 0.7710 (mmt) REVERT: C 160 LYS cc_start: 0.7550 (tppt) cc_final: 0.7322 (tppt) REVERT: C 167 GLU cc_start: 0.7976 (pp20) cc_final: 0.7053 (pp20) REVERT: C 170 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8829 (t) REVERT: D 68 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: D 95 LEU cc_start: 0.8780 (mt) cc_final: 0.8463 (tt) REVERT: D 103 THR cc_start: 0.8674 (m) cc_final: 0.8456 (p) REVERT: D 162 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8359 (pt) REVERT: D 170 SER cc_start: 0.9146 (t) cc_final: 0.8836 (t) REVERT: D 185 CYS cc_start: 0.8826 (m) cc_final: 0.8380 (m) REVERT: E 68 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: E 95 LEU cc_start: 0.8721 (mt) cc_final: 0.8422 (tp) REVERT: E 102 MET cc_start: 0.8522 (tpp) cc_final: 0.8108 (tpp) REVERT: E 119 MET cc_start: 0.7960 (mmp) cc_final: 0.7699 (mmt) REVERT: E 142 TYR cc_start: 0.6706 (m-80) cc_final: 0.6469 (m-80) REVERT: E 156 LYS cc_start: 0.7948 (mttt) cc_final: 0.7659 (mtpt) REVERT: E 167 GLU cc_start: 0.8130 (pp20) cc_final: 0.7277 (pp20) REVERT: E 170 SER cc_start: 0.9191 (t) cc_final: 0.8870 (t) REVERT: F 68 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: F 95 LEU cc_start: 0.8779 (mt) cc_final: 0.8454 (tt) REVERT: F 170 SER cc_start: 0.9159 (t) cc_final: 0.8820 (t) REVERT: F 185 CYS cc_start: 0.8823 (m) cc_final: 0.8386 (m) REVERT: G 68 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: G 95 LEU cc_start: 0.8720 (mt) cc_final: 0.8420 (tp) REVERT: G 102 MET cc_start: 0.8516 (tpp) cc_final: 0.8103 (tpp) REVERT: G 119 MET cc_start: 0.7982 (mmp) cc_final: 0.7724 (mmt) REVERT: G 160 LYS cc_start: 0.7548 (tppt) cc_final: 0.7259 (tppt) REVERT: G 167 GLU cc_start: 0.7978 (pp20) cc_final: 0.7051 (pp20) REVERT: G 170 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8809 (t) REVERT: H 32 GLN cc_start: 0.8619 (tp40) cc_final: 0.7804 (tm-30) REVERT: H 68 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: H 95 LEU cc_start: 0.8777 (mt) cc_final: 0.8455 (tt) REVERT: H 170 SER cc_start: 0.9140 (t) cc_final: 0.8808 (t) REVERT: H 185 CYS cc_start: 0.8825 (m) cc_final: 0.8387 (m) outliers start: 83 outliers final: 60 residues processed: 523 average time/residue: 0.2067 time to fit residues: 156.4020 Evaluate side-chains 546 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 474 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 0.0770 chunk 82 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 144 optimal weight: 0.9980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN B 104 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12120 Z= 0.204 Angle : 0.792 14.871 16472 Z= 0.375 Chirality : 0.042 0.169 1936 Planarity : 0.005 0.055 2024 Dihedral : 4.197 27.408 1792 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.88 % Allowed : 28.64 % Favored : 66.47 % 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: 2.03 (0.22), residues: 1480 helix: 2.37 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.17 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 62 HIS 0.001 0.000 HIS F 166 PHE 0.030 0.001 PHE D 99 TYR 0.014 0.001 TYR H 51 ARG 0.004 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 481 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: A 95 LEU cc_start: 0.8702 (mt) cc_final: 0.8417 (tp) REVERT: A 102 MET cc_start: 0.8552 (tpp) cc_final: 0.8166 (tpp) REVERT: A 160 LYS cc_start: 0.7574 (tppt) cc_final: 0.7363 (tppt) REVERT: A 167 GLU cc_start: 0.7889 (pp20) cc_final: 0.7309 (pp20) REVERT: A 170 SER cc_start: 0.9133 (t) cc_final: 0.8784 (t) REVERT: B 68 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: B 95 LEU cc_start: 0.8758 (mt) cc_final: 0.8433 (tt) REVERT: B 102 MET cc_start: 0.8566 (tpp) cc_final: 0.8167 (tpp) REVERT: B 103 THR cc_start: 0.8609 (m) cc_final: 0.8406 (p) REVERT: B 170 SER cc_start: 0.9112 (t) cc_final: 0.8792 (t) REVERT: B 185 CYS cc_start: 0.8876 (m) cc_final: 0.8462 (m) REVERT: C 68 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: C 95 LEU cc_start: 0.8701 (mt) cc_final: 0.8415 (tp) REVERT: C 102 MET cc_start: 0.8555 (tpp) cc_final: 0.8167 (tpp) REVERT: C 160 LYS cc_start: 0.7616 (tppt) cc_final: 0.7408 (tppt) REVERT: C 167 GLU cc_start: 0.7885 (pp20) cc_final: 0.7362 (pp20) REVERT: C 170 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8825 (t) REVERT: D 68 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6291 (m-80) REVERT: D 95 LEU cc_start: 0.8757 (mt) cc_final: 0.8434 (tt) REVERT: D 170 SER cc_start: 0.9130 (t) cc_final: 0.8807 (t) REVERT: D 185 CYS cc_start: 0.8869 (m) cc_final: 0.8451 (m) REVERT: E 68 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: E 95 LEU cc_start: 0.8707 (mt) cc_final: 0.8419 (tp) REVERT: E 102 MET cc_start: 0.8534 (tpp) cc_final: 0.8149 (tpp) REVERT: E 119 MET cc_start: 0.7886 (mmp) cc_final: 0.7666 (mmt) REVERT: E 156 LYS cc_start: 0.7944 (mttt) cc_final: 0.7690 (mtpt) REVERT: E 170 SER cc_start: 0.9179 (t) cc_final: 0.8857 (t) REVERT: F 68 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6299 (m-80) REVERT: F 95 LEU cc_start: 0.8767 (mt) cc_final: 0.8436 (tt) REVERT: F 170 SER cc_start: 0.9140 (t) cc_final: 0.8817 (t) REVERT: F 185 CYS cc_start: 0.8864 (m) cc_final: 0.8449 (m) REVERT: G 68 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: G 95 LEU cc_start: 0.8702 (mt) cc_final: 0.8416 (tp) REVERT: G 102 MET cc_start: 0.8548 (tpp) cc_final: 0.8165 (tpp) REVERT: G 119 MET cc_start: 0.8011 (mmp) cc_final: 0.7702 (mmt) REVERT: G 160 LYS cc_start: 0.7570 (tppt) cc_final: 0.7368 (tppt) REVERT: G 167 GLU cc_start: 0.7887 (pp20) cc_final: 0.7368 (pp20) REVERT: G 170 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8784 (t) REVERT: H 68 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: H 95 LEU cc_start: 0.8755 (mt) cc_final: 0.8436 (tt) REVERT: H 140 GLU cc_start: 0.5964 (pm20) cc_final: 0.5757 (pm20) REVERT: H 170 SER cc_start: 0.9119 (t) cc_final: 0.8802 (t) REVERT: H 185 CYS cc_start: 0.8871 (m) cc_final: 0.8454 (m) outliers start: 59 outliers final: 44 residues processed: 513 average time/residue: 0.2097 time to fit residues: 155.5279 Evaluate side-chains 524 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 470 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 0.0970 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 0.2980 chunk 12 optimal weight: 0.0070 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 50.0000 chunk 128 optimal weight: 0.0980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12120 Z= 0.205 Angle : 0.848 15.286 16472 Z= 0.388 Chirality : 0.043 0.160 1936 Planarity : 0.005 0.054 2024 Dihedral : 4.182 29.543 1792 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.48 % Allowed : 30.30 % Favored : 66.23 % 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 (0.23), residues: 1480 helix: 2.30 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -2.31 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 62 HIS 0.002 0.000 HIS E 166 PHE 0.009 0.001 PHE B 163 TYR 0.021 0.001 TYR H 51 ARG 0.006 0.000 ARG E 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 488 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: A 95 LEU cc_start: 0.8684 (mt) cc_final: 0.8399 (tp) REVERT: A 102 MET cc_start: 0.8525 (tpp) cc_final: 0.8107 (tpp) REVERT: A 167 GLU cc_start: 0.7883 (pp20) cc_final: 0.7439 (pp20) REVERT: A 170 SER cc_start: 0.9140 (t) cc_final: 0.8801 (t) REVERT: B 68 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: B 95 LEU cc_start: 0.8748 (mt) cc_final: 0.8412 (tt) REVERT: B 102 MET cc_start: 0.8595 (tpp) cc_final: 0.8232 (tpp) REVERT: B 140 GLU cc_start: 0.6087 (pm20) cc_final: 0.5840 (pm20) REVERT: B 170 SER cc_start: 0.9076 (t) cc_final: 0.8806 (t) REVERT: B 185 CYS cc_start: 0.8855 (m) cc_final: 0.8181 (m) REVERT: C 68 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: C 95 LEU cc_start: 0.8680 (mt) cc_final: 0.8396 (tp) REVERT: C 102 MET cc_start: 0.8519 (tpp) cc_final: 0.8103 (tpp) REVERT: C 160 LYS cc_start: 0.7649 (tppt) cc_final: 0.7445 (tppt) REVERT: C 167 GLU cc_start: 0.7814 (pp20) cc_final: 0.7514 (pp20) REVERT: C 170 SER cc_start: 0.9144 (t) cc_final: 0.8803 (t) REVERT: D 68 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6278 (m-80) REVERT: D 95 LEU cc_start: 0.8767 (mt) cc_final: 0.8428 (tt) REVERT: D 170 SER cc_start: 0.9094 (t) cc_final: 0.8822 (t) REVERT: D 185 CYS cc_start: 0.8872 (m) cc_final: 0.8221 (m) REVERT: E 68 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: E 95 LEU cc_start: 0.8684 (mt) cc_final: 0.8399 (tp) REVERT: E 102 MET cc_start: 0.8525 (tpp) cc_final: 0.8106 (tpp) REVERT: E 156 LYS cc_start: 0.7906 (mttt) cc_final: 0.7676 (mtpt) REVERT: E 170 SER cc_start: 0.9166 (t) cc_final: 0.8830 (t) REVERT: F 68 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: F 95 LEU cc_start: 0.8753 (mt) cc_final: 0.8416 (tt) REVERT: F 140 GLU cc_start: 0.6083 (pm20) cc_final: 0.5852 (pm20) REVERT: F 170 SER cc_start: 0.9136 (t) cc_final: 0.8804 (t) REVERT: F 185 CYS cc_start: 0.8831 (m) cc_final: 0.8168 (m) REVERT: G 68 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: G 95 LEU cc_start: 0.8683 (mt) cc_final: 0.8397 (tp) REVERT: G 102 MET cc_start: 0.8524 (tpp) cc_final: 0.8105 (tpp) REVERT: G 160 LYS cc_start: 0.7629 (tppt) cc_final: 0.7428 (tppt) REVERT: G 167 GLU cc_start: 0.7819 (pp20) cc_final: 0.7523 (pp20) REVERT: G 170 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8813 (t) REVERT: H 68 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: H 95 LEU cc_start: 0.8744 (mt) cc_final: 0.8433 (tp) REVERT: H 170 SER cc_start: 0.9106 (t) cc_final: 0.8776 (t) REVERT: H 185 CYS cc_start: 0.8799 (m) cc_final: 0.8124 (m) outliers start: 42 outliers final: 26 residues processed: 513 average time/residue: 0.2128 time to fit residues: 158.1395 Evaluate side-chains 515 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 480 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 161 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.0270 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.156672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124085 restraints weight = 23408.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.127183 restraints weight = 14096.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129264 restraints weight = 10522.462| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12120 Z= 0.221 Angle : 0.803 15.059 16472 Z= 0.376 Chirality : 0.043 0.171 1936 Planarity : 0.005 0.055 2024 Dihedral : 4.123 26.421 1792 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.30 % Allowed : 29.06 % Favored : 66.64 % 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 (0.23), residues: 1480 helix: 2.35 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.31 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 62 HIS 0.001 0.000 HIS E 166 PHE 0.027 0.001 PHE D 99 TYR 0.013 0.001 TYR H 51 ARG 0.004 0.000 ARG E 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3389.18 seconds wall clock time: 60 minutes 57.85 seconds (3657.85 seconds total)