Starting phenix.real_space_refine on Sun Aug 9 08:58:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tcn_55793/08_2026/9tcn_55793.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tcn_55793/08_2026/9tcn_55793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tcn_55793/08_2026/9tcn_55793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tcn_55793/08_2026/9tcn_55793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tcn_55793/08_2026/9tcn_55793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tcn_55793/08_2026/9tcn_55793.map" } resolution = 1.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.020 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 120 5.16 5 C 20352 2.51 5 N 5856 2.21 5 O 7905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34233 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "B" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "C" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "D" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "E" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "F" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "G" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "H" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "I" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "J" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "K" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "L" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "M" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "N" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "O" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "P" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "Q" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "R" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "S" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "T" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "V" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "W" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "X" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "Y" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 167, 1340 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1351 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "K" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "N" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "Q" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "T" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "V" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "W" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "X" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N AHIS A 175 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS A 175 " occ=0.44 residue: pdb=" N AHIS B 175 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS B 175 " occ=0.44 residue: pdb=" N AHIS C 175 " occ=0.55 ... (18 atoms not shown) pdb=" NE2BHIS C 175 " occ=0.45 residue: pdb=" N AHIS D 175 " occ=0.55 ... (18 atoms not shown) pdb=" NE2BHIS D 175 " occ=0.45 residue: pdb=" N AHIS E 175 " occ=0.55 ... (18 atoms not shown) pdb=" NE2BHIS E 175 " occ=0.45 residue: pdb=" N AHIS F 175 " occ=0.55 ... (18 atoms not shown) pdb=" NE2BHIS F 175 " occ=0.45 residue: pdb=" N AHIS G 175 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS G 175 " occ=0.44 residue: pdb=" N AHIS H 175 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS H 175 " occ=0.44 residue: pdb=" N AHIS I 175 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS I 175 " occ=0.44 residue: pdb=" N AHIS J 175 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS J 175 " occ=0.44 residue: pdb=" N AHIS K 175 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS K 175 " occ=0.44 residue: pdb=" N AHIS L 175 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS L 175 " occ=0.44 ... (remaining 12 not shown) Time building chain proxies: 12.24, per 1000 atoms: 0.36 Number of scatterers: 34233 At special positions: 0 Unit cell: (130.815, 130.815, 130.815, 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 120 16.00 O 7905 8.00 N 5856 7.00 C 20352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 82.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 Processing helix chain 'A' and resid 41 through 69 Processing helix chain 'A' and resid 87 through 117 removed outlier: 3.588A pdb=" N ALA A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 150 removed outlier: 4.388A pdb=" N TRP A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 39 Processing helix chain 'B' and resid 41 through 69 Processing helix chain 'B' and resid 87 through 117 removed outlier: 3.589A pdb=" N ALA B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 4.388A pdb=" N TRP B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 39 Processing helix chain 'C' and resid 41 through 69 Processing helix chain 'C' and resid 87 through 117 removed outlier: 3.589A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 4.013A pdb=" N LEU C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 39 Processing helix chain 'D' and resid 41 through 69 Processing helix chain 'D' and resid 87 through 117 removed outlier: 3.587A pdb=" N ALA D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 150 removed outlier: 4.384A pdb=" N TRP D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 39 Processing helix chain 'E' and resid 41 through 69 Processing helix chain 'E' and resid 87 through 117 removed outlier: 3.588A pdb=" N ALA E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP E 127 " --> pdb=" O GLN E 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE E 128 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU E 156 " --> pdb=" O ASN E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 39 Processing helix chain 'F' and resid 41 through 69 Processing helix chain 'F' and resid 87 through 117 removed outlier: 3.586A pdb=" N ALA F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE F 128 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU F 134 " --> pdb=" O GLN F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU F 156 " --> pdb=" O ASN F 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 39 Processing helix chain 'G' and resid 41 through 69 Processing helix chain 'G' and resid 87 through 117 removed outlier: 3.587A pdb=" N ALA G 91 " --> pdb=" O ARG G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 150 removed outlier: 4.388A pdb=" N TRP G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE G 128 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 164 removed outlier: 4.013A pdb=" N LEU G 156 " --> pdb=" O ASN G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 39 Processing helix chain 'H' and resid 41 through 69 Processing helix chain 'H' and resid 87 through 117 removed outlier: 3.587A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 150 removed outlier: 4.388A pdb=" N TRP H 127 " --> pdb=" O GLN H 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE H 128 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU H 134 " --> pdb=" O GLN H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 164 removed outlier: 4.013A pdb=" N LEU H 156 " --> pdb=" O ASN H 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 39 Processing helix chain 'I' and resid 41 through 69 Processing helix chain 'I' and resid 87 through 117 removed outlier: 3.587A pdb=" N ALA I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP I 127 " --> pdb=" O GLN I 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE I 128 " --> pdb=" O PHE I 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU I 134 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU I 156 " --> pdb=" O ASN I 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 39 Processing helix chain 'J' and resid 41 through 69 Processing helix chain 'J' and resid 87 through 117 removed outlier: 3.587A pdb=" N ALA J 91 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE J 128 " --> pdb=" O PHE J 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU J 134 " --> pdb=" O GLN J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 164 removed outlier: 4.005A pdb=" N LEU J 156 " --> pdb=" O ASN J 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 39 Processing helix chain 'K' and resid 41 through 69 Processing helix chain 'K' and resid 87 through 117 removed outlier: 3.588A pdb=" N ALA K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP K 127 " --> pdb=" O GLN K 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE K 128 " --> pdb=" O PHE K 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU K 134 " --> pdb=" O GLN K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU K 156 " --> pdb=" O ASN K 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 39 Processing helix chain 'L' and resid 41 through 69 Processing helix chain 'L' and resid 87 through 117 removed outlier: 3.587A pdb=" N ALA L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP L 127 " --> pdb=" O GLN L 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU L 156 " --> pdb=" O ASN L 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 39 Processing helix chain 'M' and resid 41 through 69 Processing helix chain 'M' and resid 87 through 117 removed outlier: 3.586A pdb=" N ALA M 91 " --> pdb=" O ARG M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 150 removed outlier: 4.388A pdb=" N TRP M 127 " --> pdb=" O GLN M 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE M 128 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 164 removed outlier: 4.004A pdb=" N LEU M 156 " --> pdb=" O ASN M 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 39 Processing helix chain 'N' and resid 41 through 69 Processing helix chain 'N' and resid 87 through 117 removed outlier: 3.586A pdb=" N ALA N 91 " --> pdb=" O ARG N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE N 128 " --> pdb=" O PHE N 124 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU N 134 " --> pdb=" O GLN N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 164 removed outlier: 4.013A pdb=" N LEU N 156 " --> pdb=" O ASN N 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 39 Processing helix chain 'O' and resid 41 through 69 Processing helix chain 'O' and resid 87 through 117 removed outlier: 3.588A pdb=" N ALA O 91 " --> pdb=" O ARG O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP O 127 " --> pdb=" O GLN O 123 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE O 128 " --> pdb=" O PHE O 124 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU O 134 " --> pdb=" O GLN O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 164 removed outlier: 3.993A pdb=" N LEU O 156 " --> pdb=" O ASN O 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 39 Processing helix chain 'P' and resid 41 through 69 Processing helix chain 'P' and resid 87 through 117 removed outlier: 3.586A pdb=" N ALA P 91 " --> pdb=" O ARG P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP P 127 " --> pdb=" O GLN P 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE P 128 " --> pdb=" O PHE P 124 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU P 134 " --> pdb=" O GLN P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU P 156 " --> pdb=" O ASN P 152 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 39 Processing helix chain 'Q' and resid 41 through 69 Processing helix chain 'Q' and resid 87 through 117 removed outlier: 3.586A pdb=" N ALA Q 91 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 150 removed outlier: 4.388A pdb=" N TRP Q 127 " --> pdb=" O GLN Q 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE Q 128 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU Q 134 " --> pdb=" O GLN Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 164 removed outlier: 4.005A pdb=" N LEU Q 156 " --> pdb=" O ASN Q 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 39 Processing helix chain 'R' and resid 41 through 69 Processing helix chain 'R' and resid 87 through 117 removed outlier: 3.586A pdb=" N ALA R 91 " --> pdb=" O ARG R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 150 removed outlier: 4.384A pdb=" N TRP R 127 " --> pdb=" O GLN R 123 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE R 128 " --> pdb=" O PHE R 124 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU R 134 " --> pdb=" O GLN R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU R 156 " --> pdb=" O ASN R 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 39 Processing helix chain 'S' and resid 41 through 69 Processing helix chain 'S' and resid 87 through 117 removed outlier: 3.587A pdb=" N ALA S 91 " --> pdb=" O ARG S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP S 127 " --> pdb=" O GLN S 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE S 128 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU S 134 " --> pdb=" O GLN S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 164 removed outlier: 4.001A pdb=" N LEU S 156 " --> pdb=" O ASN S 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 39 Processing helix chain 'T' and resid 41 through 69 Processing helix chain 'T' and resid 87 through 117 removed outlier: 3.588A pdb=" N ALA T 91 " --> pdb=" O ARG T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP T 127 " --> pdb=" O GLN T 123 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE T 128 " --> pdb=" O PHE T 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU T 134 " --> pdb=" O GLN T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 164 removed outlier: 4.013A pdb=" N LEU T 156 " --> pdb=" O ASN T 152 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 39 Processing helix chain 'V' and resid 41 through 69 Processing helix chain 'V' and resid 87 through 117 removed outlier: 3.584A pdb=" N ALA V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 118 through 150 removed outlier: 4.387A pdb=" N TRP V 127 " --> pdb=" O GLN V 123 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE V 128 " --> pdb=" O PHE V 124 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU V 134 " --> pdb=" O GLN V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 164 removed outlier: 4.005A pdb=" N LEU V 156 " --> pdb=" O ASN V 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 39 Processing helix chain 'W' and resid 41 through 69 Processing helix chain 'W' and resid 87 through 117 removed outlier: 3.587A pdb=" N ALA W 91 " --> pdb=" O ARG W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 150 removed outlier: 4.388A pdb=" N TRP W 127 " --> pdb=" O GLN W 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE W 128 " --> pdb=" O PHE W 124 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU W 134 " --> pdb=" O GLN W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 164 removed outlier: 4.013A pdb=" N LEU W 156 " --> pdb=" O ASN W 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 39 Processing helix chain 'X' and resid 41 through 69 Processing helix chain 'X' and resid 87 through 117 removed outlier: 3.586A pdb=" N ALA X 91 " --> pdb=" O ARG X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP X 127 " --> pdb=" O GLN X 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE X 128 " --> pdb=" O PHE X 124 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU X 134 " --> pdb=" O GLN X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 164 removed outlier: 4.013A pdb=" N LEU X 156 " --> pdb=" O ASN X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 39 Processing helix chain 'Y' and resid 41 through 69 Processing helix chain 'Y' and resid 87 through 117 removed outlier: 3.583A pdb=" N ALA Y 91 " --> pdb=" O ARG Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 150 removed outlier: 4.384A pdb=" N TRP Y 127 " --> pdb=" O GLN Y 123 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE Y 128 " --> pdb=" O PHE Y 124 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU Y 134 " --> pdb=" O GLN Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 164 removed outlier: 4.013A pdb=" N LEU Y 156 " --> pdb=" O ASN Y 152 " (cutoff:3.500A) 2688 hydrogen bonds defined for protein. 8064 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: 6.34 Time building geometry restraints manager: 3.97 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: 11520 1.34 - 1.46: 4524 1.46 - 1.57: 16716 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 33000 Sorted by residual: bond pdb=" C LEU A 129 " pdb=" O LEU A 129 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.41e+00 bond pdb=" C LEU H 129 " pdb=" O LEU H 129 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.41e+00 bond pdb=" C LEU M 129 " pdb=" O LEU M 129 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.41e+00 bond pdb=" C LEU X 129 " pdb=" O LEU X 129 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.41e+00 bond pdb=" C LEU B 129 " pdb=" O LEU B 129 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.41e+00 ... (remaining 32995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 42594 0.90 - 1.80: 1501 1.80 - 2.69: 289 2.69 - 3.59: 197 3.59 - 4.49: 59 Bond angle restraints: 44640 Sorted by residual: angle pdb=" CB ARG S 72 " pdb=" CG ARG S 72 " pdb=" CD ARG S 72 " ideal model delta sigma weight residual 111.30 115.79 -4.49 2.30e+00 1.89e-01 3.81e+00 angle pdb=" CA ARG E 72 " pdb=" CB ARG E 72 " pdb=" CG ARG E 72 " ideal model delta sigma weight residual 114.10 117.97 -3.87 2.00e+00 2.50e-01 3.74e+00 angle pdb=" CB ARG I 72 " pdb=" CG ARG I 72 " pdb=" CD ARG I 72 " ideal model delta sigma weight residual 111.30 115.73 -4.43 2.30e+00 1.89e-01 3.71e+00 angle pdb=" CB ARG C 72 " pdb=" CG ARG C 72 " pdb=" CD ARG C 72 " ideal model delta sigma weight residual 111.30 115.73 -4.43 2.30e+00 1.89e-01 3.71e+00 angle pdb=" CA ARG B 72 " pdb=" CB ARG B 72 " pdb=" CG ARG B 72 " ideal model delta sigma weight residual 114.10 117.95 -3.85 2.00e+00 2.50e-01 3.70e+00 ... (remaining 44635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 17963 17.81 - 35.63: 1252 35.63 - 53.44: 296 53.44 - 71.25: 145 71.25 - 89.07: 168 Dihedral angle restraints: 19824 sinusoidal: 8064 harmonic: 11760 Sorted by residual: dihedral pdb=" CG ARG O 89 " pdb=" CD ARG O 89 " pdb=" NE ARG O 89 " pdb=" CZ ARG O 89 " ideal model delta sinusoidal sigma weight residual 180.00 -135.01 -44.99 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG H 89 " pdb=" CD ARG H 89 " pdb=" NE ARG H 89 " pdb=" CZ ARG H 89 " ideal model delta sinusoidal sigma weight residual 180.00 -135.04 -44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG W 89 " pdb=" CD ARG W 89 " pdb=" NE ARG W 89 " pdb=" CZ ARG W 89 " ideal model delta sinusoidal sigma weight residual -180.00 -135.04 -44.96 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 19821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3471 0.027 - 0.054: 938 0.054 - 0.082: 318 0.082 - 0.109: 97 0.109 - 0.136: 72 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE E 75 " pdb=" N ILE E 75 " pdb=" C ILE E 75 " pdb=" CB ILE E 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE G 75 " pdb=" N ILE G 75 " pdb=" C ILE G 75 " pdb=" CB ILE G 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 4893 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 84 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" CD GLN Q 84 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 84 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN M 84 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" CD GLN M 84 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN M 84 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN M 84 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 84 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" CD GLN O 84 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN O 84 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN O 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 24506 3.04 - 3.51: 40587 3.51 - 3.97: 63940 3.97 - 4.44: 77879 4.44 - 4.90: 110458 Nonbonded interactions: 317370 Sorted by model distance: nonbonded pdb=" NE2 GLN S 84 " pdb=" OE2 GLU Y 74 " model vdw 2.576 3.120 nonbonded pdb=" NE2 GLN J 84 " pdb=" OE2 GLU N 74 " model vdw 2.577 3.120 nonbonded pdb=" NE2 GLN K 84 " pdb=" OE1 GLU T 74 " model vdw 2.605 3.120 nonbonded pdb=" NE2 GLN L 84 " pdb=" OE1 GLU V 74 " model vdw 2.605 3.120 nonbonded pdb=" OE1 GLU A 74 " pdb=" NE2 GLN M 84 " model vdw 2.623 3.120 ... (remaining 317365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'B' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'C' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'D' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'E' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'F' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'G' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'H' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'I' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'J' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'K' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'L' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'M' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'N' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'O' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'P' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'Q' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'R' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'S' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'T' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'V' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'W' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'X' and (resid 8 through 174 or resid 176 through 181)) selection = (chain 'Y' and (resid 8 through 174 or resid 176 through 181)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 36.950 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 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:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 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 : 0.003 0.025 33000 Z= 0.153 Angle : 0.474 4.490 44640 Z= 0.270 Chirality : 0.034 0.136 4896 Planarity : 0.003 0.027 6024 Dihedral : 17.278 89.066 12144 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.89 (0.12), residues: 3984 helix: 3.69 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.14 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.009 0.002 TYR O 49 PHE 0.017 0.002 PHE V 48 TRP 0.003 0.001 TRP O 127 HIS 0.004 0.001 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (33000) covalent geometry : angle 0.47417 / 0.27 (44640) hydrogen bonds : bond 0.09421 / 6.49 ( 2688) hydrogen bonds : angle 4.40367 / 3.25 ( 8064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.9040 time to fit residues: 643.2519 Evaluate side-chains 592 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 84 GLN C 84 GLN D 84 GLN E 84 GLN F 65 HIS F 84 GLN G 65 HIS G 84 GLN H 84 GLN I 84 GLN J 84 GLN M 65 HIS N 65 HIS P 84 GLN R 84 GLN S 84 GLN T 65 HIS V 65 HIS V 84 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.148163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.122114 restraints weight = 76011.496| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.32 r_work: 0.3111 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 33000 Z= 0.205 Angle : 0.545 3.862 44640 Z= 0.318 Chirality : 0.037 0.135 4896 Planarity : 0.006 0.062 6024 Dihedral : 3.633 14.876 4392 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.72 % Allowed : 7.10 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.28 (0.12), residues: 3984 helix: 3.26 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.95 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 72 TYR 0.005 0.002 TYR K 49 PHE 0.026 0.002 PHE V 48 TRP 0.006 0.003 TRP N 127 HIS 0.006 0.002 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.21 (33000) covalent geometry : angle 0.54508 / 0.32 (44640) hydrogen bonds : bond 0.09103 / 6.25 ( 2688) hydrogen bonds : angle 4.48954 / 3.32 ( 8064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 588 time to evaluate : 1.449 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 588 average time/residue: 0.8036 time to fit residues: 546.1425 Evaluate side-chains 575 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 50 optimal weight: 0.9990 chunk 229 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 84 GLN D 84 GLN E 84 GLN F 84 GLN G 84 GLN I 84 GLN J 84 GLN S 84 GLN T 84 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.153618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133810 restraints weight = 67787.750| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.29 r_work: 0.3177 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33000 Z= 0.150 Angle : 0.438 3.780 44640 Z= 0.254 Chirality : 0.034 0.136 4896 Planarity : 0.003 0.029 6024 Dihedral : 3.453 12.974 4392 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.71 (0.12), residues: 3984 helix: 3.56 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.09 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 72 TYR 0.007 0.001 TYR M 49 PHE 0.015 0.001 PHE V 48 TRP 0.003 0.001 TRP H 127 HIS 0.004 0.001 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (33000) covalent geometry : angle 0.43771 / 0.25 (44640) hydrogen bonds : bond 0.07429 / 5.10 ( 2688) hydrogen bonds : angle 4.05848 / 3.00 ( 8064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 1.357 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 573 average time/residue: 0.9376 time to fit residues: 617.6686 Evaluate side-chains 572 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 7 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 275 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 84 GLN C 84 GLN D 84 GLN E 84 GLN F 84 GLN G 84 GLN I 84 GLN J 84 GLN K 84 GLN L 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN Q 84 GLN S 84 GLN V 84 GLN W 84 GLN X 84 GLN Y 84 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.149116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.123636 restraints weight = 76175.438| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.25 r_work: 0.3132 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33000 Z= 0.191 Angle : 0.514 3.945 44640 Z= 0.301 Chirality : 0.036 0.132 4896 Planarity : 0.005 0.061 6024 Dihedral : 3.584 14.649 4392 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.32 (0.12), residues: 3984 helix: 3.28 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.97 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 72 TYR 0.005 0.001 TYR K 49 PHE 0.024 0.002 PHE D 48 TRP 0.006 0.002 TRP G 127 HIS 0.005 0.002 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.19 (33000) covalent geometry : angle 0.51361 / 0.30 (44640) hydrogen bonds : bond 0.08772 / 6.02 ( 2688) hydrogen bonds : angle 4.38349 / 3.24 ( 8064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.438 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.9076 time to fit residues: 601.3981 Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 155 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 334 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 379 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 381 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN C 84 GLN D 84 GLN F 84 GLN G 84 GLN H 84 GLN I 84 GLN J 84 GLN R 84 GLN T 84 GLN Y 84 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.147028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125909 restraints weight = 69192.416| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.43 r_work: 0.3055 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 33000 Z= 0.255 Angle : 0.605 4.197 44640 Z= 0.355 Chirality : 0.039 0.135 4896 Planarity : 0.007 0.073 6024 Dihedral : 3.785 15.401 4392 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.72 % Allowed : 7.13 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.12), residues: 3984 helix: 2.89 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.81 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 72 TYR 0.007 0.002 TYR P 29 PHE 0.028 0.003 PHE V 48 TRP 0.008 0.003 TRP Y 127 HIS 0.007 0.002 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.25 (33000) covalent geometry : angle 0.60545 / 0.35 (44640) hydrogen bonds : bond 0.09633 / 6.62 ( 2688) hydrogen bonds : angle 4.69005 / 3.47 ( 8064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 576 time to evaluate : 1.545 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 576 average time/residue: 0.9321 time to fit residues: 618.4496 Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 251 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 348 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 359 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 84 GLN C 84 GLN D 84 GLN E 84 GLN F 84 GLN G 84 GLN I 84 GLN J 84 GLN S 84 GLN Y 84 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128231 restraints weight = 71909.933| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.46 r_work: 0.3080 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33000 Z= 0.188 Angle : 0.512 3.863 44640 Z= 0.300 Chirality : 0.036 0.132 4896 Planarity : 0.005 0.057 6024 Dihedral : 3.682 14.563 4392 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.42 % Allowed : 8.18 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.12), residues: 3984 helix: 3.14 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.93 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 72 TYR 0.006 0.001 TYR G 49 PHE 0.023 0.002 PHE F 48 TRP 0.005 0.002 TRP Q 127 HIS 0.005 0.002 HIS I 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.19 (33000) covalent geometry : angle 0.51166 / 0.30 (44640) hydrogen bonds : bond 0.08691 / 5.97 ( 2688) hydrogen bonds : angle 4.38126 / 3.24 ( 8064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 576 time to evaluate : 1.386 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 590 average time/residue: 0.9353 time to fit residues: 634.4347 Evaluate side-chains 572 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 359 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 343 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 GLN K 84 GLN L 84 GLN M 84 GLN O 84 GLN P 84 GLN Q 84 GLN R 84 GLN V 84 GLN W 84 GLN X 84 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.147400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126249 restraints weight = 67462.562| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.36 r_work: 0.3057 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 33000 Z= 0.230 Angle : 0.579 4.135 44640 Z= 0.339 Chirality : 0.038 0.136 4896 Planarity : 0.006 0.060 6024 Dihedral : 3.754 15.290 4392 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.30 % Allowed : 7.40 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.83 (0.12), residues: 3984 helix: 2.93 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.87 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 72 TYR 0.006 0.002 TYR O 29 PHE 0.027 0.003 PHE R 48 TRP 0.007 0.003 TRP Y 127 HIS 0.007 0.002 HIS V 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.23 (33000) covalent geometry : angle 0.57877 / 0.34 (44640) hydrogen bonds : bond 0.09378 / 6.44 ( 2688) hydrogen bonds : angle 4.59881 / 3.40 ( 8064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 576 time to evaluate : 1.210 Fit side-chains outliers start: 10 outliers final: 0 residues processed: 586 average time/residue: 0.8501 time to fit residues: 573.5799 Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 280 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 238 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN C 84 GLN D 84 GLN F 84 GLN G 84 GLN H 84 GLN I 84 GLN J 84 GLN L 84 GLN O 84 GLN P 84 GLN R 84 GLN V 84 GLN W 84 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.148490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.122442 restraints weight = 71803.169| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.13 r_work: 0.3127 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 33000 Z= 0.197 Angle : 0.536 4.064 44640 Z= 0.313 Chirality : 0.036 0.134 4896 Planarity : 0.005 0.056 6024 Dihedral : 3.706 14.688 4392 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.12), residues: 3984 helix: 3.06 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.93 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 72 TYR 0.007 0.002 TYR V 29 PHE 0.024 0.002 PHE D 48 TRP 0.006 0.002 TRP H 127 HIS 0.006 0.002 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.20 (33000) covalent geometry : angle 0.53607 / 0.31 (44640) hydrogen bonds : bond 0.08881 / 6.10 ( 2688) hydrogen bonds : angle 4.43660 / 3.28 ( 8064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.740 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.9516 time to fit residues: 630.2781 Evaluate side-chains 574 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 574 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 253 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 259 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 378 optimal weight: 8.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN E 84 GLN K 84 GLN L 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN Q 84 GLN R 84 GLN T 84 GLN V 84 GLN W 84 GLN X 84 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.147621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121457 restraints weight = 69577.766| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.14 r_work: 0.3113 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 33000 Z= 0.223 Angle : 0.576 4.256 44640 Z= 0.337 Chirality : 0.037 0.137 4896 Planarity : 0.006 0.056 6024 Dihedral : 3.757 15.206 4392 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.84 (0.12), residues: 3984 helix: 2.94 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.86 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 72 TYR 0.006 0.002 TYR V 29 PHE 0.027 0.003 PHE D 48 TRP 0.007 0.003 TRP H 127 HIS 0.007 0.002 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.22 (33000) covalent geometry : angle 0.57557 / 0.34 (44640) hydrogen bonds : bond 0.09307 / 6.39 ( 2688) hydrogen bonds : angle 4.57907 / 3.38 ( 8064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.9403 time to fit residues: 623.5233 Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 267 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 382 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 361 optimal weight: 20.0000 chunk 79 optimal weight: 0.0070 chunk 126 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 84 GLN C 84 GLN D 84 GLN E 84 GLN F 84 GLN G 84 GLN I 84 GLN J 84 GLN L 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN R 84 GLN T 84 GLN W 84 GLN X 84 GLN Y 84 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.126314 restraints weight = 74524.882| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.19 r_work: 0.3174 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33000 Z= 0.168 Angle : 0.495 4.332 44640 Z= 0.288 Chirality : 0.035 0.132 4896 Planarity : 0.004 0.039 6024 Dihedral : 3.625 13.773 4392 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.38 (0.12), residues: 3984 helix: 3.32 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.03 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 72 TYR 0.008 0.002 TYR X 49 PHE 0.018 0.002 PHE I 48 TRP 0.004 0.002 TRP Y 127 HIS 0.005 0.001 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.17 (33000) covalent geometry : angle 0.49476 / 0.29 (44640) hydrogen bonds : bond 0.08104 / 5.56 ( 2688) hydrogen bonds : angle 4.22675 / 3.12 ( 8064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.9482 time to fit residues: 628.4301 Evaluate side-chains 570 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 199 optimal weight: 8.9990 chunk 359 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 174 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 291 optimal weight: 0.1980 chunk 194 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 370 optimal weight: 20.0000 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 GLN K 84 GLN P 84 GLN S 84 GLN T 84 GLN V 84 GLN Y 84 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.148497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.123365 restraints weight = 76263.295| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.21 r_work: 0.3130 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 33000 Z= 0.201 Angle : 0.548 4.178 44640 Z= 0.320 Chirality : 0.036 0.135 4896 Planarity : 0.005 0.063 6024 Dihedral : 3.705 14.702 4392 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.07 (0.12), residues: 3984 helix: 3.10 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.96 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 72 TYR 0.006 0.002 TYR I 49 PHE 0.024 0.002 PHE D 48 TRP 0.006 0.002 TRP Y 127 HIS 0.006 0.002 HIS T 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.20 (33000) covalent geometry : angle 0.54757 / 0.32 (44640) hydrogen bonds : bond 0.08978 / 6.17 ( 2688) hydrogen bonds : angle 4.44896 / 3.29 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19720.55 seconds wall clock time: 334 minutes 24.40 seconds (20064.40 seconds total)