Starting phenix.real_space_refine on Sun Aug 9 09:07:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tcm_55792/08_2026/9tcm_55792.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tcm_55792/08_2026/9tcm_55792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tcm_55792/08_2026/9tcm_55792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tcm_55792/08_2026/9tcm_55792.map" model { file = "/net/cci-nas-00/data/ceres_data/9tcm_55792/08_2026/9tcm_55792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tcm_55792/08_2026/9tcm_55792.cif" } resolution = 1.79 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 7953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 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: 34281 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: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "O" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "Q" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "R" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "V" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} 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: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Y" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N AHIS A 175 " occ=0.57 ... (18 atoms not shown) pdb=" NE2BHIS A 175 " occ=0.43 residue: pdb=" N AHIS B 175 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS B 175 " occ=0.42 residue: pdb=" N AHIS C 175 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS C 175 " occ=0.42 residue: pdb=" N AHIS D 175 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS D 175 " occ=0.42 residue: pdb=" N AHIS E 175 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS E 175 " occ=0.42 residue: pdb=" N AHIS F 175 " occ=0.59 ... (18 atoms not shown) pdb=" NE2BHIS F 175 " occ=0.41 residue: pdb=" N AHIS G 175 " occ=0.59 ... (18 atoms not shown) pdb=" NE2BHIS G 175 " occ=0.41 residue: pdb=" N AHIS H 175 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS H 175 " occ=0.42 residue: pdb=" N AHIS I 175 " occ=0.59 ... (18 atoms not shown) pdb=" NE2BHIS I 175 " occ=0.41 residue: pdb=" N AHIS J 175 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS J 175 " occ=0.42 residue: pdb=" N AHIS K 175 " occ=0.59 ... (18 atoms not shown) pdb=" NE2BHIS K 175 " occ=0.41 residue: pdb=" N AHIS L 175 " occ=0.57 ... (18 atoms not shown) pdb=" NE2BHIS L 175 " occ=0.43 ... (remaining 12 not shown) Time building chain proxies: 11.80, per 1000 atoms: 0.34 Number of scatterers: 34281 At special positions: 0 Unit cell: (128.763, 128.763, 128.763, 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 7953 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: 3.00 Conformation dependent library (CDL) restraints added in 2.6 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: 0.79 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: 3.557A pdb=" N ALA A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 150 removed outlier: 4.364A pdb=" N TRP A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.823A 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: 3.556A pdb=" N ALA B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 4.366A pdb=" N TRP B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 4.411A 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: 3.826A 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: 3.558A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 150 removed outlier: 4.366A pdb=" N TRP C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.823A 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: 3.551A pdb=" N ALA D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 150 removed outlier: 4.377A pdb=" N TRP D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.824A 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: 3.554A pdb=" N ALA E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 150 removed outlier: 4.367A pdb=" N TRP E 127 " --> pdb=" O GLN E 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE E 128 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.823A 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: 3.556A pdb=" N ALA F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 150 removed outlier: 4.366A pdb=" N TRP F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE F 128 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU F 134 " --> pdb=" O GLN F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 164 removed outlier: 3.826A 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: 3.558A pdb=" N ALA G 91 " --> pdb=" O ARG G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 150 removed outlier: 4.365A pdb=" N TRP G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE G 128 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 164 removed outlier: 3.825A 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: 3.557A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 150 removed outlier: 4.364A pdb=" N TRP H 127 " --> pdb=" O GLN H 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE H 128 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU H 134 " --> pdb=" O GLN H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 164 removed outlier: 3.824A 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: 3.550A pdb=" N ALA I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 150 removed outlier: 4.366A pdb=" N TRP I 127 " --> pdb=" O GLN I 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE I 128 " --> pdb=" O PHE I 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU I 134 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 164 removed outlier: 3.826A 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: 3.556A pdb=" N ALA J 91 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 150 removed outlier: 4.364A pdb=" N TRP J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE J 128 " --> pdb=" O PHE J 124 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU J 134 " --> pdb=" O GLN J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 164 removed outlier: 3.826A 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: 3.553A pdb=" N ALA K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 150 removed outlier: 4.366A pdb=" N TRP K 127 " --> pdb=" O GLN K 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE K 128 " --> pdb=" O PHE K 124 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU K 134 " --> pdb=" O GLN K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 164 removed outlier: 3.825A 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: 3.550A pdb=" N ALA L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 150 removed outlier: 4.367A pdb=" N TRP L 127 " --> pdb=" O GLN L 123 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.825A 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: 3.558A pdb=" N ALA M 91 " --> pdb=" O ARG M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 150 removed outlier: 4.365A pdb=" N TRP M 127 " --> pdb=" O GLN M 123 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE M 128 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 164 removed outlier: 3.826A 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: 3.556A pdb=" N ALA N 91 " --> pdb=" O ARG N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 150 removed outlier: 4.368A pdb=" N TRP N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE N 128 " --> pdb=" O PHE N 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU N 134 " --> pdb=" O GLN N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 164 removed outlier: 3.824A 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: 3.556A pdb=" N ALA O 91 " --> pdb=" O ARG O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 150 removed outlier: 4.367A pdb=" N TRP O 127 " --> pdb=" O GLN O 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE O 128 " --> pdb=" O PHE O 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU O 134 " --> pdb=" O GLN O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 164 removed outlier: 3.826A 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: 3.558A pdb=" N ALA P 91 " --> pdb=" O ARG P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 150 removed outlier: 4.366A pdb=" N TRP P 127 " --> pdb=" O GLN P 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE P 128 " --> pdb=" O PHE P 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU P 134 " --> pdb=" O GLN P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 164 removed outlier: 3.825A 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: 3.556A pdb=" N ALA Q 91 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 150 removed outlier: 4.368A pdb=" N TRP Q 127 " --> pdb=" O GLN Q 123 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE Q 128 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU Q 134 " --> pdb=" O GLN Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 164 removed outlier: 3.826A 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: 3.554A pdb=" N ALA R 91 " --> pdb=" O ARG R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 150 removed outlier: 4.371A pdb=" N TRP R 127 " --> pdb=" O GLN R 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE R 128 " --> pdb=" O PHE R 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU R 134 " --> pdb=" O GLN R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 164 removed outlier: 3.823A 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: 3.554A pdb=" N ALA S 91 " --> pdb=" O ARG S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 150 removed outlier: 4.368A pdb=" N TRP S 127 " --> pdb=" O GLN S 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE S 128 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU S 134 " --> pdb=" O GLN S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 164 removed outlier: 3.824A 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: 3.556A pdb=" N ALA T 91 " --> pdb=" O ARG T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 150 removed outlier: 4.369A pdb=" N TRP T 127 " --> pdb=" O GLN T 123 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE T 128 " --> pdb=" O PHE T 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU T 134 " --> pdb=" O GLN T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 164 removed outlier: 3.823A 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: 3.553A pdb=" N ALA V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 118 through 150 removed outlier: 4.370A pdb=" N TRP V 127 " --> pdb=" O GLN V 123 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE V 128 " --> pdb=" O PHE V 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU V 134 " --> pdb=" O GLN V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 164 removed outlier: 3.823A 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: 3.556A pdb=" N ALA W 91 " --> pdb=" O ARG W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 150 removed outlier: 4.367A pdb=" N TRP W 127 " --> pdb=" O GLN W 123 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE W 128 " --> pdb=" O PHE W 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU W 134 " --> pdb=" O GLN W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 164 removed outlier: 3.826A 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: 3.557A pdb=" N ALA X 91 " --> pdb=" O ARG X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 150 removed outlier: 4.366A pdb=" N TRP X 127 " --> pdb=" O GLN X 123 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE X 128 " --> pdb=" O PHE X 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU X 134 " --> pdb=" O GLN X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 164 removed outlier: 3.825A 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: 3.554A pdb=" N ALA Y 91 " --> pdb=" O ARG Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 150 removed outlier: 4.368A pdb=" N TRP Y 127 " --> pdb=" O GLN Y 123 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE Y 128 " --> pdb=" O PHE Y 124 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU Y 134 " --> pdb=" O GLN Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 164 removed outlier: 3.824A 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: 7.65 Time building geometry restraints manager: 4.01 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: 4862 1.46 - 1.57: 16378 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 33000 Sorted by residual: bond pdb=" C LEU Y 129 " pdb=" O LEU Y 129 " ideal model delta sigma weight residual 1.236 1.250 -0.013 1.15e-02 7.56e+03 1.36e+00 bond pdb=" C LEU K 129 " pdb=" O LEU K 129 " ideal model delta sigma weight residual 1.236 1.250 -0.013 1.15e-02 7.56e+03 1.36e+00 bond pdb=" C LEU L 129 " pdb=" O LEU L 129 " ideal model delta sigma weight residual 1.236 1.250 -0.013 1.15e-02 7.56e+03 1.36e+00 bond pdb=" C LEU J 129 " pdb=" O LEU J 129 " ideal model delta sigma weight residual 1.236 1.250 -0.013 1.15e-02 7.56e+03 1.36e+00 bond pdb=" C LEU Q 129 " pdb=" O LEU Q 129 " ideal model delta sigma weight residual 1.236 1.250 -0.013 1.15e-02 7.56e+03 1.33e+00 ... (remaining 32995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 43158 0.91 - 1.82: 1092 1.82 - 2.73: 222 2.73 - 3.64: 144 3.64 - 4.55: 24 Bond angle restraints: 44640 Sorted by residual: angle pdb=" CB ARG Q 72 " pdb=" CG ARG Q 72 " pdb=" CD ARG Q 72 " ideal model delta sigma weight residual 111.30 115.85 -4.55 2.30e+00 1.89e-01 3.91e+00 angle pdb=" CB ARG I 72 " pdb=" CG ARG I 72 " pdb=" CD ARG I 72 " ideal model delta sigma weight residual 111.30 115.84 -4.54 2.30e+00 1.89e-01 3.90e+00 angle pdb=" CB ARG C 72 " pdb=" CG ARG C 72 " pdb=" CD ARG C 72 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.87e+00 angle pdb=" CB ARG X 72 " pdb=" CG ARG X 72 " pdb=" CD ARG X 72 " ideal model delta sigma weight residual 111.30 115.82 -4.52 2.30e+00 1.89e-01 3.87e+00 angle pdb=" CB ARG L 72 " pdb=" CG ARG L 72 " pdb=" CD ARG L 72 " ideal model delta sigma weight residual 111.30 115.82 -4.52 2.30e+00 1.89e-01 3.86e+00 ... (remaining 44635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 17737 17.85 - 35.70: 1289 35.70 - 53.55: 395 53.55 - 71.40: 211 71.40 - 89.24: 192 Dihedral angle restraints: 19824 sinusoidal: 8064 harmonic: 11760 Sorted by residual: dihedral pdb=" CB GLU X 55 " pdb=" CG GLU X 55 " pdb=" CD GLU X 55 " pdb=" OE1 GLU X 55 " ideal model delta sinusoidal sigma weight residual 0.00 -89.24 89.24 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 55 " pdb=" CG GLU E 55 " pdb=" CD GLU E 55 " pdb=" OE1 GLU E 55 " ideal model delta sinusoidal sigma weight residual 0.00 -89.23 89.23 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU O 55 " pdb=" CG GLU O 55 " pdb=" CD GLU O 55 " pdb=" OE1 GLU O 55 " ideal model delta sinusoidal sigma weight residual 0.00 -89.22 89.22 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 19821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 3397 0.025 - 0.051: 855 0.051 - 0.076: 405 0.076 - 0.101: 134 0.101 - 0.126: 105 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA PRO C 42 " pdb=" N PRO C 42 " pdb=" C PRO C 42 " pdb=" CB PRO C 42 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA PRO E 42 " pdb=" N PRO E 42 " pdb=" C PRO E 42 " pdb=" CB PRO E 42 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PRO Y 42 " pdb=" N PRO Y 42 " pdb=" C PRO Y 42 " pdb=" CB PRO Y 42 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 4893 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 49 " -0.010 2.00e-02 2.50e+03 9.43e-03 1.78e+00 pdb=" CG TYR F 49 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR F 49 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR F 49 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR F 49 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 49 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR F 49 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 49 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 49 " 0.010 2.00e-02 2.50e+03 9.37e-03 1.76e+00 pdb=" CG TYR C 49 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR C 49 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 49 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR C 49 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 49 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR C 49 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 49 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 49 " -0.010 2.00e-02 2.50e+03 9.36e-03 1.75e+00 pdb=" CG TYR M 49 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR M 49 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR M 49 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR M 49 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR M 49 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR M 49 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 49 " 0.003 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 22151 3.01 - 3.48: 40280 3.48 - 3.95: 66292 3.95 - 4.43: 76707 4.43 - 4.90: 112592 Nonbonded interactions: 318022 Sorted by model distance: nonbonded pdb=" O ALA G 33 " pdb=" O HOH G 201 " model vdw 2.534 3.040 nonbonded pdb=" O ALA N 33 " pdb=" O HOH N 201 " model vdw 2.534 3.040 nonbonded pdb=" O ALA C 33 " pdb=" O HOH C 201 " model vdw 2.534 3.040 nonbonded pdb=" O ALA V 33 " pdb=" O HOH V 201 " model vdw 2.534 3.040 nonbonded pdb=" O ALA S 33 " pdb=" O HOH S 201 " model vdw 2.535 3.040 ... (remaining 318017 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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=0.41 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.890 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 40.230 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.002 0.026 33000 Z= 0.142 Angle : 0.421 4.546 44640 Z= 0.245 Chirality : 0.034 0.126 4896 Planarity : 0.003 0.029 6024 Dihedral : 18.410 89.244 12144 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 4.58 (0.12), residues: 3984 helix: 3.43 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.24 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.017 0.003 TYR S 49 PHE 0.019 0.002 PHE Q 48 TRP 0.003 0.001 TRP H 127 HIS 0.003 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (33000) covalent geometry : angle 0.42073 / 0.24 (44640) hydrogen bonds : bond 0.09036 / 6.24 ( 2688) hydrogen bonds : angle 4.32726 / 3.19 ( 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 636 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7967 (mtt180) REVERT: B 114 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7963 (mtt180) REVERT: C 114 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7968 (mtt180) REVERT: D 114 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7941 (mtt90) REVERT: F 114 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7957 (mtt90) REVERT: G 114 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7960 (mtt180) REVERT: H 114 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7952 (mtt180) REVERT: I 114 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7958 (mtt90) REVERT: J 114 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7942 (mtt90) REVERT: L 114 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7968 (mtt180) REVERT: M 114 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7954 (mtt180) REVERT: N 114 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7957 (mtt90) REVERT: O 114 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7938 (mtt90) REVERT: P 114 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7955 (mtt180) REVERT: Q 114 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7939 (mtt90) REVERT: R 114 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7875 (mtt180) REVERT: S 114 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7876 (mtt180) REVERT: T 114 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7969 (mtt90) REVERT: V 114 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7877 (mtt180) REVERT: W 114 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7933 (mtt90) REVERT: X 114 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7953 (mtt180) outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 0.9216 time to fit residues: 674.7844 Evaluate side-chains 623 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 HIS ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 HIS ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 HIS ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 HIS ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 HIS ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.151861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.129172 restraints weight = 72326.503| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.45 r_work: 0.3083 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33000 Z= 0.173 Angle : 0.464 3.771 44640 Z= 0.276 Chirality : 0.035 0.131 4896 Planarity : 0.004 0.038 6024 Dihedral : 3.413 14.829 4392 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 7.70 % 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: 4.39 (0.12), residues: 3984 helix: 3.29 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.22 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 72 TYR 0.015 0.002 TYR G 49 PHE 0.022 0.002 PHE S 48 TRP 0.003 0.001 TRP B 127 HIS 0.005 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 (33000) covalent geometry : angle 0.46420 / 0.28 (44640) hydrogen bonds : bond 0.08316 / 5.70 ( 2688) hydrogen bonds : angle 4.26003 / 3.14 ( 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 647 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 1.393 Fit side-chains REVERT: A 114 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7991 (mtt90) REVERT: B 114 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7997 (mtt90) REVERT: C 114 ARG cc_start: 0.8256 (ttm170) cc_final: 0.8005 (mtt90) REVERT: D 114 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7984 (mtt90) REVERT: F 114 ARG cc_start: 0.8227 (ttm170) cc_final: 0.8000 (mtt180) REVERT: G 114 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7994 (mtt90) REVERT: H 114 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7989 (mtt90) REVERT: I 114 ARG cc_start: 0.8245 (ttm170) cc_final: 0.8012 (mtt90) REVERT: J 114 ARG cc_start: 0.8229 (ttm170) cc_final: 0.7999 (mtt180) REVERT: L 114 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7985 (mtt90) REVERT: M 114 ARG cc_start: 0.8238 (ttm170) cc_final: 0.8005 (mtt90) REVERT: N 114 ARG cc_start: 0.8253 (ttm170) cc_final: 0.8031 (mtt90) REVERT: O 114 ARG cc_start: 0.8241 (ttm170) cc_final: 0.8015 (mtt90) REVERT: P 114 ARG cc_start: 0.8244 (ttm170) cc_final: 0.8011 (mtt90) REVERT: Q 114 ARG cc_start: 0.8242 (ttm170) cc_final: 0.8019 (mtt90) REVERT: R 114 ARG cc_start: 0.8231 (ttm170) cc_final: 0.8025 (mtt90) REVERT: S 114 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7971 (mtt90) REVERT: T 114 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7930 (mtt180) REVERT: V 114 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7976 (mtt90) REVERT: W 114 ARG cc_start: 0.8239 (ttm170) cc_final: 0.8014 (mtt90) REVERT: X 114 ARG cc_start: 0.8248 (ttm170) cc_final: 0.8014 (mtt90) outliers start: 0 outliers final: 0 residues processed: 647 average time/residue: 0.8673 time to fit residues: 646.0604 Evaluate side-chains 645 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 187 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 372 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 chunk 218 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 345 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 HIS ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 HIS ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 HIS ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 HIS ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 HIS ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 HIS ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 HIS ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 HIS ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 HIS ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 HIS ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.151041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.129865 restraints weight = 66064.651| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.28 r_work: 0.3107 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33000 Z= 0.181 Angle : 0.475 3.875 44640 Z= 0.283 Chirality : 0.036 0.137 4896 Planarity : 0.005 0.044 6024 Dihedral : 3.462 15.001 4392 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.21 (0.12), residues: 3984 helix: 3.16 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.15 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 114 TYR 0.015 0.002 TYR G 49 PHE 0.023 0.002 PHE R 48 TRP 0.004 0.001 TRP B 127 HIS 0.005 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.18 (33000) covalent geometry : angle 0.47550 / 0.28 (44640) hydrogen bonds : bond 0.08494 / 5.82 ( 2688) hydrogen bonds : angle 4.30430 / 3.17 ( 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 646 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 1.418 Fit side-chains REVERT: A 114 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7987 (mtt90) REVERT: B 114 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7998 (mtt90) REVERT: C 114 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7996 (mtt90) REVERT: G 114 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7993 (mtt90) REVERT: H 114 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7992 (mtt90) REVERT: I 114 ARG cc_start: 0.8235 (ttm170) cc_final: 0.8002 (mtt90) REVERT: L 114 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7983 (mtt90) REVERT: M 114 ARG cc_start: 0.8244 (ttm170) cc_final: 0.8009 (mtt90) REVERT: N 114 ARG cc_start: 0.8228 (ttm170) cc_final: 0.8009 (mtt90) REVERT: O 114 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7993 (mtt90) REVERT: P 114 ARG cc_start: 0.8244 (ttm170) cc_final: 0.8009 (mtt90) REVERT: Q 114 ARG cc_start: 0.8223 (ttm170) cc_final: 0.8004 (mtt90) REVERT: R 114 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7997 (mtt90) REVERT: S 114 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7985 (mtt90) REVERT: V 114 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7992 (mtt90) REVERT: W 114 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7995 (mtt90) REVERT: X 114 ARG cc_start: 0.8253 (ttm170) cc_final: 0.8016 (mtt90) outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.8948 time to fit residues: 665.6880 Evaluate side-chains 643 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 196 optimal weight: 0.6980 chunk 293 optimal weight: 5.9990 chunk 291 optimal weight: 0.8980 chunk 128 optimal weight: 30.0000 chunk 203 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 320 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 192 optimal weight: 30.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.154663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.133897 restraints weight = 66787.533| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.34 r_work: 0.3148 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33000 Z= 0.152 Angle : 0.428 4.077 44640 Z= 0.252 Chirality : 0.035 0.126 4896 Planarity : 0.004 0.038 6024 Dihedral : 3.358 13.641 4392 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % 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: 4.44 (0.12), residues: 3984 helix: 3.34 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.15 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 114 TYR 0.014 0.002 TYR M 49 PHE 0.020 0.002 PHE W 48 TRP 0.003 0.001 TRP P 127 HIS 0.003 0.001 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (33000) covalent geometry : angle 0.42755 / 0.25 (44640) hydrogen bonds : bond 0.07554 / 5.17 ( 2688) hydrogen bonds : angle 4.08265 / 3.01 ( 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 642 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 time to evaluate : 1.320 Fit side-chains REVERT: A 114 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7970 (mtt90) REVERT: B 114 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7968 (mtt90) REVERT: C 114 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7964 (mtt90) REVERT: G 114 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7986 (mtt90) REVERT: H 114 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7965 (mtt90) REVERT: I 114 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7918 (mtt90) REVERT: L 114 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7934 (mtt180) REVERT: M 114 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7964 (mtt90) REVERT: N 114 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7968 (mtt90) REVERT: O 114 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7945 (mtt90) REVERT: P 114 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7966 (mtt90) REVERT: Q 114 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7952 (mtt90) REVERT: R 114 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7853 (mtt180) REVERT: S 114 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7943 (mtt90) REVERT: V 114 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7948 (mtt90) REVERT: W 114 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7942 (mtt90) REVERT: X 114 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7967 (mtt90) outliers start: 0 outliers final: 0 residues processed: 642 average time/residue: 0.8868 time to fit residues: 655.9701 Evaluate side-chains 642 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 189 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 chunk 200 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 224 optimal weight: 30.0000 chunk 220 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.151378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129676 restraints weight = 62682.107| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.33 r_work: 0.3123 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33000 Z= 0.176 Angle : 0.469 4.059 44640 Z= 0.279 Chirality : 0.036 0.134 4896 Planarity : 0.005 0.044 6024 Dihedral : 3.433 14.892 4392 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.22 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.14 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 114 TYR 0.015 0.002 TYR V 49 PHE 0.021 0.002 PHE Q 48 TRP 0.003 0.001 TRP B 127 HIS 0.004 0.001 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.18 (33000) covalent geometry : angle 0.46876 / 0.28 (44640) hydrogen bonds : bond 0.08366 / 5.73 ( 2688) hydrogen bonds : angle 4.26967 / 3.15 ( 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 643 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.443 Fit side-chains REVERT: A 114 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7943 (mtt90) REVERT: B 114 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7967 (mtt90) REVERT: C 114 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7969 (mtt90) REVERT: F 114 ARG cc_start: 0.8155 (ttt180) cc_final: 0.7931 (mtt180) REVERT: G 114 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7973 (mtt90) REVERT: H 114 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7967 (mtt90) REVERT: I 114 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7921 (mtt90) REVERT: J 114 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7934 (mtt180) REVERT: L 114 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7946 (mtt180) REVERT: M 114 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7954 (mtt90) REVERT: N 114 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7956 (mtt90) REVERT: O 114 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7940 (mtt90) REVERT: P 114 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7962 (mtt90) REVERT: Q 114 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7947 (mtt90) REVERT: R 114 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7838 (mtt180) REVERT: S 114 ARG cc_start: 0.8137 (ttm170) cc_final: 0.7823 (mtt180) REVERT: V 114 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7832 (mtt180) REVERT: W 114 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7941 (mtt90) REVERT: X 114 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7960 (mtt90) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.8952 time to fit residues: 663.8256 Evaluate side-chains 643 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 195 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 291 optimal weight: 0.4980 chunk 99 optimal weight: 8.9990 chunk 364 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.152568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130041 restraints weight = 77070.614| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.52 r_work: 0.3081 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33000 Z= 0.165 Angle : 0.451 4.206 44640 Z= 0.267 Chirality : 0.035 0.129 4896 Planarity : 0.004 0.041 6024 Dihedral : 3.409 14.399 4392 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.31 (0.12), residues: 3984 helix: 3.24 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.12 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 114 TYR 0.014 0.002 TYR N 49 PHE 0.019 0.002 PHE Q 48 TRP 0.003 0.001 TRP A 127 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.17 (33000) covalent geometry : angle 0.45065 / 0.27 (44640) hydrogen bonds : bond 0.08037 / 5.50 ( 2688) hydrogen bonds : angle 4.18879 / 3.09 ( 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 643 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.473 Fit side-chains REVERT: A 114 ARG cc_start: 0.8279 (ttm170) cc_final: 0.8031 (mtt90) REVERT: B 114 ARG cc_start: 0.8278 (ttm170) cc_final: 0.8036 (mtt90) REVERT: C 114 ARG cc_start: 0.8275 (ttm170) cc_final: 0.8034 (mtt90) REVERT: G 114 ARG cc_start: 0.8283 (ttm170) cc_final: 0.8035 (mtt90) REVERT: H 114 ARG cc_start: 0.8271 (ttm170) cc_final: 0.8028 (mtt90) REVERT: I 114 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7993 (mtt90) REVERT: L 114 ARG cc_start: 0.8236 (ttm170) cc_final: 0.8005 (mtt180) REVERT: M 114 ARG cc_start: 0.8266 (ttm170) cc_final: 0.8018 (mtt90) REVERT: N 114 ARG cc_start: 0.8254 (ttm170) cc_final: 0.8029 (mtt90) REVERT: O 114 ARG cc_start: 0.8236 (ttm170) cc_final: 0.8005 (mtt90) REVERT: P 114 ARG cc_start: 0.8272 (ttm170) cc_final: 0.8025 (mtt90) REVERT: Q 114 ARG cc_start: 0.8242 (ttm170) cc_final: 0.8015 (mtt90) REVERT: R 114 ARG cc_start: 0.8206 (ttm170) cc_final: 0.8001 (mtt90) REVERT: S 114 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7882 (mtt180) REVERT: V 114 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7883 (mtt180) REVERT: W 114 ARG cc_start: 0.8238 (ttm170) cc_final: 0.8006 (mtt90) REVERT: X 114 ARG cc_start: 0.8279 (ttm170) cc_final: 0.8028 (mtt90) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.9231 time to fit residues: 683.9856 Evaluate side-chains 641 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 316 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 376 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 208 optimal weight: 30.0000 chunk 95 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.149673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128432 restraints weight = 65346.768| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.24 r_work: 0.3090 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33000 Z= 0.202 Angle : 0.515 4.216 44640 Z= 0.305 Chirality : 0.037 0.148 4896 Planarity : 0.005 0.055 6024 Dihedral : 3.523 15.489 4392 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % 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: 4.03 (0.12), residues: 3984 helix: 3.04 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.05 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 114 TYR 0.015 0.002 TYR N 49 PHE 0.024 0.002 PHE R 48 TRP 0.004 0.002 TRP J 127 HIS 0.005 0.001 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.20 (33000) covalent geometry : angle 0.51472 / 0.31 (44640) hydrogen bonds : bond 0.08906 / 6.11 ( 2688) hydrogen bonds : angle 4.42055 / 3.26 ( 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 654 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 654 time to evaluate : 1.385 Fit side-chains REVERT: A 114 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7985 (mtt90) REVERT: B 114 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7990 (mtt90) REVERT: C 114 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7991 (mtt90) REVERT: G 114 ARG cc_start: 0.8261 (ttm170) cc_final: 0.8001 (mtt90) REVERT: H 114 ARG cc_start: 0.8254 (ttm170) cc_final: 0.7994 (mtt90) REVERT: I 114 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7944 (mtt180) REVERT: M 114 ARG cc_start: 0.8242 (ttm170) cc_final: 0.8000 (mtt90) REVERT: N 114 ARG cc_start: 0.8224 (ttm170) cc_final: 0.8010 (mtt90) REVERT: O 114 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7992 (mtt90) REVERT: P 114 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7986 (mtt90) REVERT: Q 114 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7997 (mtt90) REVERT: R 114 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7945 (mtt90) REVERT: S 114 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7883 (mtt180) REVERT: V 114 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7886 (mtt180) REVERT: W 114 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7991 (mtt90) REVERT: X 114 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7985 (mtt90) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.9367 time to fit residues: 703.2579 Evaluate side-chains 653 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 653 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 287 optimal weight: 8.9990 chunk 345 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 306 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.155050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.134457 restraints weight = 66146.966| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.39 r_work: 0.3154 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33000 Z= 0.152 Angle : 0.432 4.401 44640 Z= 0.254 Chirality : 0.035 0.127 4896 Planarity : 0.004 0.043 6024 Dihedral : 3.391 13.846 4392 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % 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: 4.43 (0.12), residues: 3984 helix: 3.34 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.12 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 114 TYR 0.014 0.002 TYR W 49 PHE 0.019 0.002 PHE Q 48 TRP 0.003 0.001 TRP T 127 HIS 0.003 0.001 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (33000) covalent geometry : angle 0.43154 / 0.25 (44640) hydrogen bonds : bond 0.07473 / 5.12 ( 2688) hydrogen bonds : angle 4.07755 / 3.00 ( 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 641 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.325 Fit side-chains REVERT: A 114 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7965 (mtt90) REVERT: B 114 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7966 (mtt90) REVERT: C 114 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7966 (mtt90) REVERT: G 114 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7976 (mtt90) REVERT: H 114 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7961 (mtt90) REVERT: M 114 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7952 (mtt90) REVERT: N 114 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7958 (mtt90) REVERT: O 114 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7938 (mtt90) REVERT: P 114 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7954 (mtt90) REVERT: Q 114 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7950 (mtt90) REVERT: R 114 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7846 (mtt180) REVERT: S 114 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7889 (mtt90) REVERT: V 114 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7894 (mtt90) REVERT: W 114 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7927 (mtt90) REVERT: X 114 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7965 (mtt90) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.8726 time to fit residues: 644.6492 Evaluate side-chains 641 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 288 optimal weight: 30.0000 chunk 245 optimal weight: 0.8980 chunk 295 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.153327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.131616 restraints weight = 70454.557| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.48 r_work: 0.3105 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33000 Z= 0.161 Angle : 0.446 4.344 44640 Z= 0.264 Chirality : 0.035 0.129 4896 Planarity : 0.004 0.043 6024 Dihedral : 3.402 14.199 4392 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.36 (0.12), residues: 3984 helix: 3.29 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.10 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 114 TYR 0.014 0.002 TYR W 49 PHE 0.019 0.002 PHE E 48 TRP 0.003 0.001 TRP O 127 HIS 0.004 0.001 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (33000) covalent geometry : angle 0.44644 / 0.26 (44640) hydrogen bonds : bond 0.07872 / 5.39 ( 2688) hydrogen bonds : angle 4.14767 / 3.06 ( 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 641 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.439 Fit side-chains REVERT: A 114 ARG cc_start: 0.8252 (ttm170) cc_final: 0.8004 (mtt90) REVERT: B 114 ARG cc_start: 0.8250 (ttm170) cc_final: 0.8007 (mtt90) REVERT: C 114 ARG cc_start: 0.8244 (ttm170) cc_final: 0.8002 (mtt90) REVERT: G 114 ARG cc_start: 0.8256 (ttm170) cc_final: 0.8008 (mtt90) REVERT: H 114 ARG cc_start: 0.8250 (ttm170) cc_final: 0.8005 (mtt90) REVERT: M 114 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7989 (mtt90) REVERT: N 114 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7988 (mtt90) REVERT: O 114 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7978 (mtt90) REVERT: P 114 ARG cc_start: 0.8242 (ttm170) cc_final: 0.7995 (mtt90) REVERT: Q 114 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7982 (mtt90) REVERT: R 114 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7948 (mtt90) REVERT: S 114 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7890 (mtt90) REVERT: V 114 ARG cc_start: 0.8138 (ttm170) cc_final: 0.7892 (mtt90) REVERT: W 114 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7968 (mtt90) REVERT: X 114 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7994 (mtt90) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.9641 time to fit residues: 711.5590 Evaluate side-chains 641 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 341 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 234 optimal weight: 30.0000 chunk 284 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.151798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.130729 restraints weight = 69391.593| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.46 r_work: 0.3097 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33000 Z= 0.173 Angle : 0.468 4.298 44640 Z= 0.277 Chirality : 0.036 0.132 4896 Planarity : 0.005 0.049 6024 Dihedral : 3.445 14.740 4392 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.27 (0.12), residues: 3984 helix: 3.22 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.08 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 114 TYR 0.015 0.002 TYR W 49 PHE 0.021 0.002 PHE X 48 TRP 0.003 0.001 TRP Q 127 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 (33000) covalent geometry : angle 0.46820 / 0.28 (44640) hydrogen bonds : bond 0.08276 / 5.67 ( 2688) hydrogen bonds : angle 4.24381 / 3.13 ( 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 641 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.464 Fit side-chains REVERT: A 114 ARG cc_start: 0.8251 (ttm170) cc_final: 0.8004 (mtt90) REVERT: B 114 ARG cc_start: 0.8251 (ttm170) cc_final: 0.8007 (mtt90) REVERT: C 114 ARG cc_start: 0.8251 (ttm170) cc_final: 0.8010 (mtt90) REVERT: G 114 ARG cc_start: 0.8264 (ttm170) cc_final: 0.8018 (mtt90) REVERT: H 114 ARG cc_start: 0.8247 (ttm170) cc_final: 0.8000 (mtt90) REVERT: I 114 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7897 (mtt180) REVERT: M 114 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7991 (mtt90) REVERT: N 114 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7994 (mtt90) REVERT: O 114 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7984 (mtt90) REVERT: P 114 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7998 (mtt90) REVERT: Q 114 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7981 (mtt90) REVERT: R 114 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7969 (mtt90) REVERT: S 114 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7894 (mtt180) REVERT: V 114 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7900 (mtt180) REVERT: W 114 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7977 (mtt90) REVERT: X 114 ARG cc_start: 0.8251 (ttm170) cc_final: 0.8001 (mtt90) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.9560 time to fit residues: 705.1827 Evaluate side-chains 639 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 104 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 347 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.149738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.128391 restraints weight = 67626.332| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.35 r_work: 0.3077 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 33000 Z= 0.203 Angle : 0.519 4.297 44640 Z= 0.307 Chirality : 0.037 0.149 4896 Planarity : 0.006 0.055 6024 Dihedral : 3.541 15.565 4392 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.01 (0.12), residues: 3984 helix: 3.04 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.00 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 114 TYR 0.015 0.002 TYR W 49 PHE 0.024 0.002 PHE J 48 TRP 0.005 0.002 TRP H 127 HIS 0.004 0.001 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 (33000) covalent geometry : angle 0.51873 / 0.31 (44640) hydrogen bonds : bond 0.08926 / 6.12 ( 2688) hydrogen bonds : angle 4.42370 / 3.26 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21132.17 seconds wall clock time: 357 minutes 36.10 seconds (21456.10 seconds total)