Starting phenix.real_space_refine on Thu Feb 5 11:06:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8s_47728/02_2026/9e8s_47728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8s_47728/02_2026/9e8s_47728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e8s_47728/02_2026/9e8s_47728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8s_47728/02_2026/9e8s_47728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e8s_47728/02_2026/9e8s_47728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8s_47728/02_2026/9e8s_47728.map" } resolution = 2.48 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= 0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians Fe 37 7.16 5 S 48 5.16 5 C 10680 2.51 5 N 2724 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16831 Number of models: 1 Model: "" Number of chains: 36 Chain: "B" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "E" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "F" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "D" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "C" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "H" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "I" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "G" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "A" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "K" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "L" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "J" Number of atoms: 1384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} bond proxies already assigned to first conformer: 1402 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 15 Unusual residues: {' O': 6, ' FE': 7, 'OXY': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 13 Unusual residues: {' O': 6, ' FE': 5, 'OXY': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 15 Unusual residues: {' O': 6, ' FE': 7, 'OXY': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 4 Unusual residues: {' FE': 2, 'OXY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 6.63, per 1000 atoms: 0.39 Number of scatterers: 16831 At special positions: 0 Unit cell: (105.57, 113.16, 104.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 37 26.01 S 48 16.00 O 3342 8.00 N 2724 7.00 C 10680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG ACYS E 94 " - pdb=" SG CYS E 118 " distance=3.00 Simple disulfide: pdb=" SG ACYS F 94 " - pdb=" SG CYS F 118 " distance=2.95 Simple disulfide: pdb=" SG ACYS I 94 " - pdb=" SG CYS I 118 " distance=3.00 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: 1.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 15 through 43 removed outlier: 3.843A pdb=" N THR B 38 " --> pdb=" O TYR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 77 removed outlier: 4.146A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 104 through 130 Processing helix chain 'B' and resid 134 through 161 removed outlier: 3.600A pdb=" N GLU B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'E' and resid 15 through 43 removed outlier: 3.521A pdb=" N TYR E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 77 removed outlier: 4.139A pdb=" N ALA E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 104 through 131 Processing helix chain 'E' and resid 134 through 161 removed outlier: 3.632A pdb=" N GLU E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 15 through 43 removed outlier: 3.797A pdb=" N THR F 38 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE F 39 " --> pdb=" O TYR F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 77 removed outlier: 4.130A pdb=" N ALA F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'F' and resid 84 through 91 Processing helix chain 'F' and resid 104 through 131 Processing helix chain 'F' and resid 134 through 161 removed outlier: 3.604A pdb=" N GLU F 147 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'D' and resid 15 through 43 removed outlier: 3.800A pdb=" N THR D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 77 removed outlier: 4.106A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 104 through 130 Processing helix chain 'D' and resid 134 through 161 removed outlier: 3.595A pdb=" N GLU D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'C' and resid 15 through 43 removed outlier: 3.503A pdb=" N TYR C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 38 " --> pdb=" O TYR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 77 removed outlier: 4.140A pdb=" N ALA C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 72 - end of helix Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 104 through 130 Processing helix chain 'C' and resid 134 through 161 removed outlier: 3.597A pdb=" N GLU C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'H' and resid 15 through 43 removed outlier: 3.520A pdb=" N TYR H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE H 39 " --> pdb=" O TYR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 77 removed outlier: 4.165A pdb=" N ALA H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 72 - end of helix Processing helix chain 'H' and resid 84 through 91 Processing helix chain 'H' and resid 104 through 130 Processing helix chain 'H' and resid 134 through 161 removed outlier: 3.631A pdb=" N GLU H 147 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 182 Processing helix chain 'I' and resid 15 through 43 removed outlier: 3.791A pdb=" N THR I 38 " --> pdb=" O TYR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 4.138A pdb=" N ALA I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 72 - end of helix Processing helix chain 'I' and resid 84 through 91 Processing helix chain 'I' and resid 104 through 131 Processing helix chain 'I' and resid 134 through 161 removed outlier: 3.598A pdb=" N GLU I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 182 Processing helix chain 'G' and resid 15 through 43 removed outlier: 3.812A pdb=" N THR G 38 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 77 removed outlier: 4.177A pdb=" N ALA G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 72 - end of helix Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 104 through 130 Processing helix chain 'G' and resid 134 through 160 removed outlier: 3.601A pdb=" N GLU G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'A' and resid 15 through 43 removed outlier: 3.864A pdb=" N THR A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 77 removed outlier: 4.176A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 104 through 130 Processing helix chain 'A' and resid 134 through 161 removed outlier: 3.611A pdb=" N GLU A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'K' and resid 15 through 43 removed outlier: 3.524A pdb=" N TYR K 35 " --> pdb=" O PHE K 31 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR K 38 " --> pdb=" O TYR K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 77 removed outlier: 4.167A pdb=" N ALA K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 72 - end of helix Processing helix chain 'K' and resid 84 through 91 Processing helix chain 'K' and resid 104 through 130 Processing helix chain 'K' and resid 134 through 161 removed outlier: 3.637A pdb=" N GLU K 147 " --> pdb=" O ALA K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 182 Processing helix chain 'L' and resid 15 through 43 removed outlier: 3.789A pdb=" N THR L 38 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE L 39 " --> pdb=" O TYR L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 77 removed outlier: 4.145A pdb=" N ALA L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) Proline residue: L 72 - end of helix Processing helix chain 'L' and resid 84 through 91 Processing helix chain 'L' and resid 104 through 131 Processing helix chain 'L' and resid 134 through 161 removed outlier: 3.602A pdb=" N GLU L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'J' and resid 15 through 43 removed outlier: 3.802A pdb=" N THR J 38 " --> pdb=" O TYR J 34 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE J 39 " --> pdb=" O TYR J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 77 removed outlier: 4.191A pdb=" N ALA J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 72 - end of helix Processing helix chain 'J' and resid 84 through 91 Processing helix chain 'J' and resid 104 through 130 Processing helix chain 'J' and resid 134 through 161 removed outlier: 3.615A pdb=" N GLU J 147 " --> pdb=" O ALA J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 182 1167 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3379 1.33 - 1.45: 3994 1.45 - 1.57: 9595 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 17028 Sorted by residual: bond pdb=" C CYS K 118 " pdb=" O CYS K 118 " ideal model delta sigma weight residual 1.237 1.315 -0.078 1.17e-02 7.31e+03 4.45e+01 bond pdb=" C CYS A 118 " pdb=" O CYS A 118 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.19e-02 7.06e+03 4.45e+01 bond pdb=" C CYS F 118 " pdb=" O CYS F 118 " ideal model delta sigma weight residual 1.237 1.315 -0.079 1.19e-02 7.06e+03 4.39e+01 bond pdb=" C CYS I 118 " pdb=" O CYS I 118 " ideal model delta sigma weight residual 1.237 1.315 -0.079 1.19e-02 7.06e+03 4.38e+01 bond pdb=" C CYS L 118 " pdb=" O CYS L 118 " ideal model delta sigma weight residual 1.237 1.315 -0.079 1.19e-02 7.06e+03 4.38e+01 ... (remaining 17023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 22550 1.66 - 3.32: 418 3.32 - 4.98: 57 4.98 - 6.64: 39 6.64 - 8.30: 24 Bond angle restraints: 23088 Sorted by residual: angle pdb=" O CYS J 118 " pdb=" C CYS J 118 " pdb=" CA ACYS J 118 " ideal model delta sigma weight residual 120.42 128.66 -8.24 1.06e+00 8.90e-01 6.04e+01 angle pdb=" O CYS J 118 " pdb=" C CYS J 118 " pdb=" CA BCYS J 118 " ideal model delta sigma weight residual 120.42 128.66 -8.24 1.06e+00 8.90e-01 6.04e+01 angle pdb=" O CYS G 118 " pdb=" C CYS G 118 " pdb=" CA ACYS G 118 " ideal model delta sigma weight residual 120.42 128.47 -8.05 1.06e+00 8.90e-01 5.77e+01 angle pdb=" O CYS G 118 " pdb=" C CYS G 118 " pdb=" CA BCYS G 118 " ideal model delta sigma weight residual 120.42 128.47 -8.05 1.06e+00 8.90e-01 5.77e+01 angle pdb=" O CYS A 118 " pdb=" C CYS A 118 " pdb=" CA ACYS A 118 " ideal model delta sigma weight residual 120.42 128.12 -7.70 1.06e+00 8.90e-01 5.28e+01 ... (remaining 23083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9434 17.98 - 35.96: 717 35.96 - 53.94: 130 53.94 - 71.92: 12 71.92 - 89.91: 24 Dihedral angle restraints: 10317 sinusoidal: 4233 harmonic: 6084 Sorted by residual: dihedral pdb=" C CYS G 94 " pdb=" N CYS G 94 " pdb=" CA BCYS G 94 " pdb=" CB BCYS G 94 " ideal model delta harmonic sigma weight residual -122.60 -112.17 -10.43 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" C CYS D 94 " pdb=" N CYS D 94 " pdb=" CA BCYS D 94 " pdb=" CB BCYS D 94 " ideal model delta harmonic sigma weight residual -122.60 -112.48 -10.12 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" C CYS F 94 " pdb=" N CYS F 94 " pdb=" CA BCYS F 94 " pdb=" CB BCYS F 94 " ideal model delta harmonic sigma weight residual -122.60 -112.67 -9.93 0 2.50e+00 1.60e-01 1.58e+01 ... (remaining 10314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2282 0.063 - 0.126: 225 0.126 - 0.189: 15 0.189 - 0.251: 0 0.251 - 0.314: 10 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CA BCYS G 94 " pdb=" N CYS G 94 " pdb=" C CYS G 94 " pdb=" CB BCYS G 94 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA BCYS I 94 " pdb=" N CYS I 94 " pdb=" C CYS I 94 " pdb=" CB BCYS I 94 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA BCYS L 94 " pdb=" N CYS L 94 " pdb=" C CYS L 94 " pdb=" CB BCYS L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2529 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS H 118 " 0.046 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" O CYS H 118 " -0.018 2.00e-02 2.50e+03 pdb=" CA ACYS H 118 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA H 119 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS H 118 " 0.040 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" O CYS H 118 " -0.015 2.00e-02 2.50e+03 pdb=" CA BCYS H 118 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA H 119 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 118 " -0.039 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" O CYS B 118 " 0.015 2.00e-02 2.50e+03 pdb=" CA BCYS B 118 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA B 119 " 0.013 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 248 2.49 - 3.09: 11732 3.09 - 3.69: 27917 3.69 - 4.30: 43164 4.30 - 4.90: 68918 Nonbonded interactions: 151979 Sorted by model distance: nonbonded pdb=" O O B 211 " pdb="FE FE A 201 " model vdw 1.883 2.020 nonbonded pdb="FE FE A 201 " pdb=" O O A 211 " model vdw 1.883 2.020 nonbonded pdb=" O O C 209 " pdb="FE FE A 201 " model vdw 1.884 2.020 nonbonded pdb="FE FE B 206 " pdb=" O O B 210 " model vdw 1.918 2.020 nonbonded pdb="FE FE C 205 " pdb=" O O C 208 " model vdw 1.919 2.020 ... (remaining 151974 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'B' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'C' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'D' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'E' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'F' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'G' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'H' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'I' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'J' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'K' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) selection = (chain 'L' and (resid 14 through 93 or resid 95 through 117 or resid 119 through \ 202)) } 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=0.26 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.630 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.013 0.969 17031 Z= 0.701 Angle : 0.700 24.301 23094 Z= 0.449 Chirality : 0.042 0.314 2532 Planarity : 0.005 0.033 3000 Dihedral : 13.445 89.905 6420 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.23 % Allowed : 0.51 % Favored : 99.26 % Cbeta Deviations : 0.36 % 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: 0.45 (0.18), residues: 2040 helix: 0.07 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 1.41 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 86 TYR 0.020 0.002 TYR D 75 PHE 0.010 0.001 PHE C 155 TRP 0.005 0.001 TRP J 154 HIS 0.006 0.001 HIS L 146 Details of bonding type rmsd covalent geometry : bond 0.00440 (17028) covalent geometry : angle 0.64222 (23088) SS BOND : bond 0.95179 ( 3) SS BOND : angle 17.25698 ( 6) hydrogen bonds : bond 0.21583 ( 1167) hydrogen bonds : angle 7.39503 ( 3417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.873 Fit side-chains REVERT: F 18 LYS cc_start: 0.8105 (mttm) cc_final: 0.7379 (tptp) REVERT: F 54 GLU cc_start: 0.7338 (pm20) cc_final: 0.6846 (mp0) REVERT: H 95 ARG cc_start: 0.7071 (mtp-110) cc_final: 0.6646 (ppt90) REVERT: I 54 GLU cc_start: 0.7400 (pm20) cc_final: 0.6916 (mp0) REVERT: A 171 LYS cc_start: 0.4503 (mttt) cc_final: 0.4181 (mttm) REVERT: K 95 ARG cc_start: 0.7266 (mtp-110) cc_final: 0.6895 (ppt170) REVERT: L 54 GLU cc_start: 0.7285 (pm20) cc_final: 0.6755 (mp0) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.8173 time to fit residues: 246.2023 Evaluate side-chains 205 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 HIS ** 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 = 0.4292 r_free = 0.4292 target = 0.192537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.172375 restraints weight = 42054.852| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.01 r_work: 0.3916 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17031 Z= 0.154 Angle : 0.528 4.218 23094 Z= 0.297 Chirality : 0.039 0.129 2532 Planarity : 0.005 0.031 3000 Dihedral : 4.009 13.482 2328 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.66 % Allowed : 6.62 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.96 (0.18), residues: 2040 helix: 1.37 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : 1.44 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 95 TYR 0.021 0.002 TYR J 75 PHE 0.014 0.001 PHE B 31 TRP 0.005 0.001 TRP C 154 HIS 0.005 0.002 HIS L 146 Details of bonding type rmsd covalent geometry : bond 0.00298 (17028) covalent geometry : angle 0.52828 (23088) SS BOND : bond 0.00787 ( 3) SS BOND : angle 0.71337 ( 6) hydrogen bonds : bond 0.07121 ( 1167) hydrogen bonds : angle 5.32878 ( 3417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.793 Fit side-chains REVERT: B 156 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: F 18 LYS cc_start: 0.8005 (mttm) cc_final: 0.7193 (tptp) REVERT: F 54 GLU cc_start: 0.7703 (pm20) cc_final: 0.7491 (mp0) REVERT: D 156 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6808 (tp30) REVERT: C 95 ARG cc_start: 0.7397 (mpt180) cc_final: 0.7187 (mtm180) REVERT: C 156 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: H 95 ARG cc_start: 0.7536 (mtp-110) cc_final: 0.7081 (ppt90) REVERT: I 54 GLU cc_start: 0.7650 (pm20) cc_final: 0.7314 (mp0) REVERT: I 106 GLU cc_start: 0.7731 (pp20) cc_final: 0.7505 (pp20) REVERT: A 114 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: A 156 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: A 162 LYS cc_start: 0.6958 (ptmt) cc_final: 0.6313 (pttp) REVERT: K 21 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7926 (mt-10) REVERT: K 95 ARG cc_start: 0.7692 (mtp-110) cc_final: 0.7252 (ppt170) REVERT: K 147 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: L 18 LYS cc_start: 0.7948 (mttp) cc_final: 0.6955 (tptp) REVERT: L 54 GLU cc_start: 0.7689 (pm20) cc_final: 0.7306 (mp0) REVERT: L 95 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7326 (mtp85) REVERT: L 162 LYS cc_start: 0.6737 (ptmt) cc_final: 0.6335 (pptt) outliers start: 29 outliers final: 11 residues processed: 215 average time/residue: 0.8278 time to fit residues: 193.5456 Evaluate side-chains 209 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain J residue 114 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 142 optimal weight: 0.6980 chunk 199 optimal weight: 0.0980 chunk 178 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.190737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170415 restraints weight = 49646.883| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.09 r_work: 0.3903 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17031 Z= 0.156 Angle : 0.525 4.406 23094 Z= 0.290 Chirality : 0.039 0.137 2532 Planarity : 0.005 0.030 3000 Dihedral : 4.060 22.534 2328 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 2.45 % Allowed : 7.36 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.19), residues: 2040 helix: 1.84 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.77 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.019 0.002 TYR J 75 PHE 0.010 0.001 PHE A 31 TRP 0.008 0.002 TRP C 154 HIS 0.004 0.002 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00327 (17028) covalent geometry : angle 0.52458 (23088) SS BOND : bond 0.00911 ( 3) SS BOND : angle 0.43516 ( 6) hydrogen bonds : bond 0.06621 ( 1167) hydrogen bonds : angle 5.17757 ( 3417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.688 Fit side-chains REVERT: B 156 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: B 157 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: F 18 LYS cc_start: 0.8027 (mttm) cc_final: 0.7165 (tptp) REVERT: F 95 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7348 (mtp85) REVERT: D 147 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: D 156 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6788 (tp30) REVERT: C 156 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: H 95 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7142 (ppt90) REVERT: I 54 GLU cc_start: 0.7644 (pm20) cc_final: 0.7352 (mp0) REVERT: I 106 GLU cc_start: 0.7755 (pp20) cc_final: 0.7553 (pp20) REVERT: G 147 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: A 114 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: A 156 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: A 162 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6470 (pttp) REVERT: K 139 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (t70) REVERT: L 54 GLU cc_start: 0.7729 (pm20) cc_final: 0.7396 (mp0) REVERT: L 95 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7402 (mtp85) REVERT: L 162 LYS cc_start: 0.6873 (ptmt) cc_final: 0.6442 (pptt) REVERT: J 147 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8062 (mt-10) outliers start: 43 outliers final: 13 residues processed: 203 average time/residue: 0.8473 time to fit residues: 186.5995 Evaluate side-chains 197 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 147 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.192318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.172248 restraints weight = 48928.096| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.06 r_work: 0.3927 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17031 Z= 0.134 Angle : 0.486 4.466 23094 Z= 0.269 Chirality : 0.037 0.135 2532 Planarity : 0.004 0.030 3000 Dihedral : 3.929 18.657 2328 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.80 % Allowed : 7.76 % Favored : 89.44 % 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: 2.85 (0.19), residues: 2040 helix: 2.02 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.87 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 95 TYR 0.020 0.002 TYR K 75 PHE 0.013 0.001 PHE B 31 TRP 0.012 0.002 TRP C 154 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00269 (17028) covalent geometry : angle 0.48602 (23088) SS BOND : bond 0.00737 ( 3) SS BOND : angle 0.72633 ( 6) hydrogen bonds : bond 0.05908 ( 1167) hydrogen bonds : angle 5.03567 ( 3417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.683 Fit side-chains REVERT: B 41 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8179 (ttp-170) REVERT: B 157 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: F 18 LYS cc_start: 0.7991 (mttm) cc_final: 0.7146 (tptp) REVERT: F 95 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7310 (mtp85) REVERT: D 147 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: D 156 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6730 (tp30) REVERT: C 41 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8114 (ttp-170) REVERT: C 156 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: H 21 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7847 (mt-10) REVERT: H 95 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.7146 (ppt90) REVERT: H 125 GLU cc_start: 0.8006 (tt0) cc_final: 0.7699 (tt0) REVERT: I 54 GLU cc_start: 0.7565 (pm20) cc_final: 0.7305 (mp0) REVERT: G 147 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: G 174 GLU cc_start: 0.7806 (tt0) cc_final: 0.7399 (tm-30) REVERT: A 41 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7985 (ttp-170) REVERT: A 54 GLU cc_start: 0.7901 (pm20) cc_final: 0.7543 (pm20) REVERT: A 114 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: A 156 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: L 54 GLU cc_start: 0.7704 (pm20) cc_final: 0.7373 (mp0) REVERT: L 95 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7380 (mtp85) REVERT: L 162 LYS cc_start: 0.6879 (ptmt) cc_final: 0.6471 (pptt) REVERT: J 147 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7976 (mt-10) outliers start: 49 outliers final: 17 residues processed: 204 average time/residue: 0.8396 time to fit residues: 186.1935 Evaluate side-chains 203 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 147 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 161 optimal weight: 0.0370 chunk 73 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.192764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172885 restraints weight = 46715.892| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.01 r_work: 0.3935 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17031 Z= 0.128 Angle : 0.474 4.519 23094 Z= 0.261 Chirality : 0.036 0.125 2532 Planarity : 0.004 0.030 3000 Dihedral : 3.869 18.882 2328 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 2.40 % Allowed : 8.90 % Favored : 88.70 % 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: 2.99 (0.18), residues: 2040 helix: 2.11 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.94 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.019 0.002 TYR I 75 PHE 0.012 0.001 PHE B 31 TRP 0.014 0.002 TRP C 154 HIS 0.003 0.001 HIS L 146 Details of bonding type rmsd covalent geometry : bond 0.00249 (17028) covalent geometry : angle 0.47431 (23088) SS BOND : bond 0.00720 ( 3) SS BOND : angle 0.90110 ( 6) hydrogen bonds : bond 0.05665 ( 1167) hydrogen bonds : angle 4.97457 ( 3417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.667 Fit side-chains REVERT: B 41 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8211 (ttp-170) REVERT: B 156 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: B 157 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: F 18 LYS cc_start: 0.8010 (mttm) cc_final: 0.7153 (tptp) REVERT: F 95 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7300 (mtp85) REVERT: D 147 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: C 156 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: C 162 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6553 (pttp) REVERT: H 21 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7811 (mt-10) REVERT: H 95 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.7100 (ppt90) REVERT: H 125 GLU cc_start: 0.8004 (tt0) cc_final: 0.7719 (tt0) REVERT: I 54 GLU cc_start: 0.7547 (pm20) cc_final: 0.7265 (mp0) REVERT: G 147 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: G 174 GLU cc_start: 0.7783 (tt0) cc_final: 0.7358 (tm-30) REVERT: A 41 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8026 (ttp-170) REVERT: A 54 GLU cc_start: 0.7909 (pm20) cc_final: 0.7601 (pm20) REVERT: A 114 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: A 156 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: A 162 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6458 (pttp) REVERT: K 125 GLU cc_start: 0.7952 (tt0) cc_final: 0.7672 (tt0) REVERT: K 139 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7962 (t70) REVERT: L 54 GLU cc_start: 0.7649 (pm20) cc_final: 0.7336 (mp0) REVERT: L 162 LYS cc_start: 0.6957 (ptmt) cc_final: 0.6480 (pptt) REVERT: J 147 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7959 (mt-10) outliers start: 42 outliers final: 13 residues processed: 193 average time/residue: 0.8809 time to fit residues: 184.3352 Evaluate side-chains 198 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 147 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 138 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 161 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.193271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.173442 restraints weight = 46111.542| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.00 r_work: 0.3949 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17031 Z= 0.125 Angle : 0.470 4.557 23094 Z= 0.258 Chirality : 0.036 0.124 2532 Planarity : 0.004 0.030 3000 Dihedral : 3.826 19.144 2328 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.00 % Allowed : 9.47 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.18), residues: 2040 helix: 2.16 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.95 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.017 0.002 TYR I 75 PHE 0.012 0.001 PHE B 31 TRP 0.016 0.002 TRP C 154 HIS 0.003 0.001 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00245 (17028) covalent geometry : angle 0.47005 (23088) SS BOND : bond 0.00709 ( 3) SS BOND : angle 0.99561 ( 6) hydrogen bonds : bond 0.05517 ( 1167) hydrogen bonds : angle 4.92861 ( 3417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.643 Fit side-chains REVERT: B 41 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8191 (ttp-170) REVERT: B 157 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: F 18 LYS cc_start: 0.7984 (mttm) cc_final: 0.7155 (tptp) REVERT: F 95 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7281 (mtp85) REVERT: D 147 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: C 156 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: C 162 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6593 (pttp) REVERT: H 21 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7831 (mt-10) REVERT: H 125 GLU cc_start: 0.7998 (tt0) cc_final: 0.7706 (tt0) REVERT: I 54 GLU cc_start: 0.7559 (pm20) cc_final: 0.7286 (mp0) REVERT: G 41 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7839 (ttp-170) REVERT: G 147 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: G 174 GLU cc_start: 0.7812 (tt0) cc_final: 0.7373 (tm-30) REVERT: A 41 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8028 (ttp-170) REVERT: A 54 GLU cc_start: 0.7888 (pm20) cc_final: 0.7496 (pm20) REVERT: A 114 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: A 156 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: A 162 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6481 (pttp) REVERT: K 125 GLU cc_start: 0.7964 (tt0) cc_final: 0.7699 (tt0) REVERT: K 139 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7945 (t70) REVERT: L 54 GLU cc_start: 0.7653 (pm20) cc_final: 0.7321 (mp0) REVERT: L 162 LYS cc_start: 0.6974 (ptmt) cc_final: 0.6516 (pptt) REVERT: J 147 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7954 (mt-10) outliers start: 35 outliers final: 14 residues processed: 189 average time/residue: 0.7681 time to fit residues: 157.6088 Evaluate side-chains 197 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 147 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 145 optimal weight: 0.0010 chunk 47 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 200 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.190245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169824 restraints weight = 49450.880| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.12 r_work: 0.3902 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17031 Z= 0.160 Angle : 0.528 5.487 23094 Z= 0.290 Chirality : 0.039 0.151 2532 Planarity : 0.004 0.030 3000 Dihedral : 4.012 22.074 2328 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 2.57 % Allowed : 9.25 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.18), residues: 2040 helix: 1.98 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.88 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 95 TYR 0.019 0.002 TYR D 123 PHE 0.008 0.001 PHE C 155 TRP 0.020 0.002 TRP C 154 HIS 0.005 0.002 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00342 (17028) covalent geometry : angle 0.52733 (23088) SS BOND : bond 0.00771 ( 3) SS BOND : angle 1.04620 ( 6) hydrogen bonds : bond 0.06267 ( 1167) hydrogen bonds : angle 5.03548 ( 3417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.683 Fit side-chains REVERT: B 41 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8241 (ttp-170) REVERT: B 156 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: B 157 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: F 95 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7275 (mtp85) REVERT: D 147 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: D 179 SER cc_start: 0.8438 (m) cc_final: 0.8209 (m) REVERT: C 156 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: C 162 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6631 (pttp) REVERT: H 21 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7823 (mt-10) REVERT: H 125 GLU cc_start: 0.8084 (tt0) cc_final: 0.7741 (tt0) REVERT: I 41 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8122 (ttp-170) REVERT: I 54 GLU cc_start: 0.7573 (pm20) cc_final: 0.7282 (mp0) REVERT: G 41 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7904 (ttp-170) REVERT: G 147 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: G 174 GLU cc_start: 0.7791 (tt0) cc_final: 0.7361 (tm-30) REVERT: A 41 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8037 (ttp-170) REVERT: A 54 GLU cc_start: 0.7920 (pm20) cc_final: 0.7516 (pm20) REVERT: A 114 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: A 156 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: A 162 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6503 (pttp) REVERT: K 125 GLU cc_start: 0.7985 (tt0) cc_final: 0.7703 (tt0) REVERT: K 139 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7998 (t70) REVERT: L 54 GLU cc_start: 0.7698 (pm20) cc_final: 0.7384 (mp0) REVERT: L 162 LYS cc_start: 0.6987 (ptmt) cc_final: 0.6514 (pptt) REVERT: J 147 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8044 (mt-10) outliers start: 45 outliers final: 15 residues processed: 192 average time/residue: 0.8676 time to fit residues: 180.4384 Evaluate side-chains 200 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 147 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 49 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171109 restraints weight = 52683.894| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.15 r_work: 0.3908 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17031 Z= 0.138 Angle : 0.498 5.152 23094 Z= 0.274 Chirality : 0.037 0.139 2532 Planarity : 0.004 0.032 3000 Dihedral : 3.920 18.751 2328 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.28 % Allowed : 9.76 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.93 (0.18), residues: 2040 helix: 2.07 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.91 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 95 TYR 0.017 0.002 TYR I 75 PHE 0.010 0.001 PHE B 31 TRP 0.022 0.003 TRP C 154 HIS 0.003 0.001 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00281 (17028) covalent geometry : angle 0.49825 (23088) SS BOND : bond 0.00738 ( 3) SS BOND : angle 1.08085 ( 6) hydrogen bonds : bond 0.05850 ( 1167) hydrogen bonds : angle 4.97075 ( 3417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.711 Fit side-chains REVERT: B 41 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8238 (ttp-170) REVERT: B 156 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: B 157 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: F 95 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7286 (mtp85) REVERT: D 147 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: D 174 GLU cc_start: 0.7659 (tt0) cc_final: 0.7307 (tm-30) REVERT: D 179 SER cc_start: 0.8424 (m) cc_final: 0.8194 (m) REVERT: C 156 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: C 162 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6612 (pttp) REVERT: H 21 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7854 (mt-10) REVERT: H 125 GLU cc_start: 0.8053 (tt0) cc_final: 0.7731 (tt0) REVERT: I 41 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8125 (ttp-170) REVERT: I 54 GLU cc_start: 0.7554 (pm20) cc_final: 0.7328 (pm20) REVERT: G 41 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7909 (ttp-170) REVERT: G 147 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: G 174 GLU cc_start: 0.7804 (tt0) cc_final: 0.7360 (tm-30) REVERT: A 41 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8072 (ttp-170) REVERT: A 54 GLU cc_start: 0.7937 (pm20) cc_final: 0.7537 (pm20) REVERT: A 114 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: A 156 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: A 162 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6503 (pttp) REVERT: K 125 GLU cc_start: 0.8008 (tt0) cc_final: 0.7733 (tt0) REVERT: K 139 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7999 (t70) REVERT: L 54 GLU cc_start: 0.7695 (pm20) cc_final: 0.7375 (mp0) REVERT: L 162 LYS cc_start: 0.6975 (ptmt) cc_final: 0.6471 (pptt) REVERT: J 147 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8016 (mt-10) outliers start: 40 outliers final: 17 residues processed: 191 average time/residue: 0.8084 time to fit residues: 167.5904 Evaluate side-chains 206 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 147 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 134 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.191020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.170742 restraints weight = 51310.970| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.10 r_work: 0.3926 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17031 Z= 0.143 Angle : 0.508 4.854 23094 Z= 0.280 Chirality : 0.037 0.137 2532 Planarity : 0.004 0.038 3000 Dihedral : 3.939 18.811 2328 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 2.11 % Allowed : 9.99 % Favored : 87.90 % 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: 2.89 (0.18), residues: 2040 helix: 2.04 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.91 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 95 TYR 0.017 0.002 TYR I 75 PHE 0.009 0.001 PHE B 31 TRP 0.027 0.003 TRP C 154 HIS 0.004 0.001 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00295 (17028) covalent geometry : angle 0.50812 (23088) SS BOND : bond 0.00741 ( 3) SS BOND : angle 1.09119 ( 6) hydrogen bonds : bond 0.05946 ( 1167) hydrogen bonds : angle 4.98084 ( 3417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.609 Fit side-chains REVERT: B 41 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8178 (ttp-170) REVERT: B 156 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: B 157 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: F 95 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7248 (mtp85) REVERT: D 147 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: D 179 SER cc_start: 0.8426 (m) cc_final: 0.8189 (m) REVERT: C 156 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: C 162 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6591 (pttp) REVERT: H 21 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7787 (mt-10) REVERT: H 125 GLU cc_start: 0.8001 (tt0) cc_final: 0.7675 (tt0) REVERT: I 41 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8072 (ttp-170) REVERT: I 54 GLU cc_start: 0.7499 (pm20) cc_final: 0.7272 (pm20) REVERT: G 41 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7870 (ttp-170) REVERT: G 147 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: G 174 GLU cc_start: 0.7720 (tt0) cc_final: 0.7294 (tm-30) REVERT: A 41 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8019 (ttp-170) REVERT: A 54 GLU cc_start: 0.7898 (pm20) cc_final: 0.7478 (pm20) REVERT: A 114 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: A 156 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: A 162 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6505 (pttp) REVERT: K 125 GLU cc_start: 0.8012 (tt0) cc_final: 0.7718 (tt0) REVERT: K 139 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7947 (t70) REVERT: L 54 GLU cc_start: 0.7609 (pm20) cc_final: 0.7306 (mp0) REVERT: L 162 LYS cc_start: 0.6930 (ptmt) cc_final: 0.6437 (pptt) REVERT: J 147 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8009 (mt-10) outliers start: 37 outliers final: 17 residues processed: 184 average time/residue: 0.8213 time to fit residues: 164.0884 Evaluate side-chains 204 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 146 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 0.0000 chunk 167 optimal weight: 0.3980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.193734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173597 restraints weight = 51753.207| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.10 r_work: 0.3961 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17031 Z= 0.120 Angle : 0.469 4.788 23094 Z= 0.258 Chirality : 0.035 0.131 2532 Planarity : 0.004 0.039 3000 Dihedral : 3.784 19.042 2328 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 1.94 % Allowed : 10.16 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.18), residues: 2040 helix: 2.22 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.99 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.017 0.002 TYR I 75 PHE 0.014 0.001 PHE B 31 TRP 0.028 0.003 TRP C 154 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00231 (17028) covalent geometry : angle 0.46852 (23088) SS BOND : bond 0.00681 ( 3) SS BOND : angle 1.11018 ( 6) hydrogen bonds : bond 0.05274 ( 1167) hydrogen bonds : angle 4.85917 ( 3417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.597 Fit side-chains REVERT: B 41 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8161 (ttp-170) REVERT: B 156 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: B 157 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: E 125 GLU cc_start: 0.8004 (tt0) cc_final: 0.7767 (tt0) REVERT: F 95 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7220 (mtp85) REVERT: D 147 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: C 156 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: C 162 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6531 (pttp) REVERT: H 125 GLU cc_start: 0.7938 (tt0) cc_final: 0.7692 (tt0) REVERT: I 41 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8045 (ttp-170) REVERT: I 54 GLU cc_start: 0.7485 (pm20) cc_final: 0.7266 (pm20) REVERT: G 41 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7826 (ttp-170) REVERT: G 147 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: G 174 GLU cc_start: 0.7651 (tt0) cc_final: 0.7240 (tm-30) REVERT: A 41 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7973 (ttp-170) REVERT: A 54 GLU cc_start: 0.7862 (pm20) cc_final: 0.7449 (pm20) REVERT: A 114 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: A 156 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: A 162 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6499 (pttp) REVERT: K 125 GLU cc_start: 0.8016 (tt0) cc_final: 0.7712 (tt0) REVERT: L 54 GLU cc_start: 0.7582 (pm20) cc_final: 0.7248 (mp0) REVERT: L 162 LYS cc_start: 0.6906 (ptmt) cc_final: 0.6393 (pptt) REVERT: J 147 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7945 (mt-10) outliers start: 34 outliers final: 13 residues processed: 192 average time/residue: 0.8017 time to fit residues: 166.8853 Evaluate side-chains 195 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS G 166 HIS J 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.192288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.172970 restraints weight = 43446.808| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.89 r_work: 0.3960 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17031 Z= 0.132 Angle : 0.492 4.813 23094 Z= 0.271 Chirality : 0.036 0.140 2532 Planarity : 0.004 0.039 3000 Dihedral : 3.832 18.368 2328 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 1.77 % Allowed : 10.39 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.18), residues: 2040 helix: 2.18 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.98 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 95 TYR 0.017 0.002 TYR I 75 PHE 0.010 0.001 PHE B 31 TRP 0.031 0.003 TRP C 154 HIS 0.003 0.001 HIS L 146 Details of bonding type rmsd covalent geometry : bond 0.00265 (17028) covalent geometry : angle 0.49173 (23088) SS BOND : bond 0.00704 ( 3) SS BOND : angle 1.07522 ( 6) hydrogen bonds : bond 0.05570 ( 1167) hydrogen bonds : angle 4.88967 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5701.09 seconds wall clock time: 97 minutes 58.64 seconds (5878.64 seconds total)