Starting phenix.real_space_refine on Wed Mar 4 21:12:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stw_25437/03_2026/7stw_25437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stw_25437/03_2026/7stw_25437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7stw_25437/03_2026/7stw_25437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stw_25437/03_2026/7stw_25437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7stw_25437/03_2026/7stw_25437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stw_25437/03_2026/7stw_25437.map" } resolution = 2.37 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.484 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: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 Zn 12 6.06 5 S 36 5.16 5 C 10632 2.51 5 N 2724 2.21 5 O 3413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16829 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "B" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "C" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "D" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "E" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "F" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "G" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "H" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "I" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "J" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "K" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "L" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "I" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "J" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "K" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 3.70, per 1000 atoms: 0.22 Number of scatterers: 16829 At special positions: 0 Unit cell: (108.288, 114.048, 108.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 Fe 12 26.01 S 36 16.00 O 3413 8.00 N 2724 7.00 C 10632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 521.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 66 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 66 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 66 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" ND1 HIS D 66 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 66 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 66 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 66 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 66 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 66 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 66 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 66 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 66 " 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 77 removed outlier: 4.339A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.561A 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 90 Processing helix chain 'A' and resid 104 through 131 Processing helix chain 'A' and resid 134 through 160 removed outlier: 3.787A 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 'B' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR B 38 " --> pdb=" O TYR B 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.560A 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 90 Processing helix chain 'B' and resid 104 through 131 Processing helix chain 'B' and resid 134 through 160 removed outlier: 3.787A 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 'C' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 38 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.560A 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 90 Processing helix chain 'C' and resid 104 through 131 Processing helix chain 'C' and resid 134 through 160 removed outlier: 3.786A 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 'D' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.560A 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 90 Processing helix chain 'D' and resid 104 through 131 Processing helix chain 'D' and resid 134 through 160 removed outlier: 3.787A 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 'E' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 77 removed outlier: 4.337A pdb=" N ALA E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.560A 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 160 removed outlier: 3.787A 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: 3.770A pdb=" N TYR F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR F 38 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE F 39 " --> pdb=" O TYR F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 77 removed outlier: 4.337A pdb=" N ALA F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.561A 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 90 Processing helix chain 'F' and resid 104 through 131 Processing helix chain 'F' and resid 134 through 160 removed outlier: 3.787A 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 'G' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR G 38 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 4.560A 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 90 Processing helix chain 'G' and resid 104 through 131 Processing helix chain 'G' and resid 134 through 160 removed outlier: 3.787A 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 'H' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE H 39 " --> pdb=" O TYR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.561A 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 90 Processing helix chain 'H' and resid 104 through 131 Processing helix chain 'H' and resid 134 through 160 removed outlier: 3.787A 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: 3.770A pdb=" N TYR I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR I 38 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE I 39 " --> pdb=" O TYR I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 4.337A pdb=" N ALA I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.560A 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 90 Processing helix chain 'I' and resid 104 through 131 Processing helix chain 'I' and resid 134 through 160 removed outlier: 3.787A 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 'J' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR J 35 " --> pdb=" O PHE J 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR J 38 " --> pdb=" O TYR J 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE J 39 " --> pdb=" O TYR J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.560A 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 90 Processing helix chain 'J' and resid 104 through 131 Processing helix chain 'J' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU J 147 " --> pdb=" O ALA J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'K' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR K 35 " --> pdb=" O PHE K 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR K 38 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE K 39 " --> pdb=" O TYR K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 4.560A 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 90 Processing helix chain 'K' and resid 104 through 131 Processing helix chain 'K' and resid 134 through 160 removed outlier: 3.787A 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: 3.770A pdb=" N TYR L 35 " --> pdb=" O PHE L 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR L 38 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE L 39 " --> pdb=" O TYR L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 77 removed outlier: 4.337A pdb=" N ALA L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 4.559A 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 90 Processing helix chain 'L' and resid 104 through 131 Processing helix chain 'L' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 182 1140 hydrogen bonds defined for protein. 3336 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: 2.08 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5472 1.34 - 1.46: 3763 1.46 - 1.58: 7649 1.58 - 1.70: 0 1.70 - 1.81: 36 Bond restraints: 16920 Sorted by residual: bond pdb=" C GLY B 161 " pdb=" O GLY B 161 " ideal model delta sigma weight residual 1.239 1.233 0.005 7.10e-03 1.98e+04 5.84e-01 bond pdb=" C GLY A 161 " pdb=" O GLY A 161 " ideal model delta sigma weight residual 1.239 1.233 0.005 7.10e-03 1.98e+04 5.42e-01 bond pdb=" C GLY I 161 " pdb=" O GLY I 161 " ideal model delta sigma weight residual 1.239 1.233 0.005 7.10e-03 1.98e+04 5.22e-01 bond pdb=" N PRO A 103 " pdb=" CA PRO A 103 " ideal model delta sigma weight residual 1.479 1.468 0.011 1.56e-02 4.11e+03 4.94e-01 bond pdb=" N PRO J 103 " pdb=" CA PRO J 103 " ideal model delta sigma weight residual 1.479 1.468 0.011 1.56e-02 4.11e+03 4.94e-01 ... (remaining 16915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 21192 0.87 - 1.74: 1457 1.74 - 2.62: 191 2.62 - 3.49: 56 3.49 - 4.36: 24 Bond angle restraints: 22920 Sorted by residual: angle pdb=" C VAL F 178 " pdb=" CA VAL F 178 " pdb=" CB VAL F 178 " ideal model delta sigma weight residual 111.85 109.71 2.14 1.27e+00 6.20e-01 2.84e+00 angle pdb=" C VAL D 178 " pdb=" CA VAL D 178 " pdb=" CB VAL D 178 " ideal model delta sigma weight residual 111.85 109.71 2.14 1.27e+00 6.20e-01 2.83e+00 angle pdb=" C VAL G 178 " pdb=" CA VAL G 178 " pdb=" CB VAL G 178 " ideal model delta sigma weight residual 111.85 109.72 2.13 1.27e+00 6.20e-01 2.81e+00 angle pdb=" C VAL J 178 " pdb=" CA VAL J 178 " pdb=" CB VAL J 178 " ideal model delta sigma weight residual 111.85 109.72 2.13 1.27e+00 6.20e-01 2.80e+00 angle pdb=" C VAL B 178 " pdb=" CA VAL B 178 " pdb=" CB VAL B 178 " ideal model delta sigma weight residual 111.85 109.73 2.12 1.27e+00 6.20e-01 2.80e+00 ... (remaining 22915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.83: 8849 13.83 - 27.66: 955 27.66 - 41.48: 324 41.48 - 55.31: 24 55.31 - 69.14: 36 Dihedral angle restraints: 10188 sinusoidal: 4200 harmonic: 5988 Sorted by residual: dihedral pdb=" CG ARG A 73 " pdb=" CD ARG A 73 " pdb=" NE ARG A 73 " pdb=" CZ ARG A 73 " ideal model delta sinusoidal sigma weight residual 90.00 128.35 -38.35 2 1.50e+01 4.44e-03 8.21e+00 dihedral pdb=" CG ARG K 73 " pdb=" CD ARG K 73 " pdb=" NE ARG K 73 " pdb=" CZ ARG K 73 " ideal model delta sinusoidal sigma weight residual 90.00 128.33 -38.33 2 1.50e+01 4.44e-03 8.21e+00 dihedral pdb=" CG ARG H 73 " pdb=" CD ARG H 73 " pdb=" NE ARG H 73 " pdb=" CZ ARG H 73 " ideal model delta sinusoidal sigma weight residual 90.00 128.33 -38.33 2 1.50e+01 4.44e-03 8.21e+00 ... (remaining 10185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1356 0.026 - 0.051: 800 0.051 - 0.076: 292 0.076 - 0.102: 24 0.102 - 0.127: 36 Chirality restraints: 2508 Sorted by residual: chirality pdb=" CA PRO D 135 " pdb=" N PRO D 135 " pdb=" C PRO D 135 " pdb=" CB PRO D 135 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA PRO H 135 " pdb=" N PRO H 135 " pdb=" C PRO H 135 " pdb=" CB PRO H 135 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA PRO G 135 " pdb=" N PRO G 135 " pdb=" C PRO G 135 " pdb=" CB PRO G 135 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 2505 not shown) Planarity restraints: 2976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 175 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO H 176 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO H 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 176 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 175 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO D 176 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 176 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 175 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO B 176 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " 0.014 5.00e-02 4.00e+02 ... (remaining 2973 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 205 2.54 - 3.13: 11886 3.13 - 3.72: 26237 3.72 - 4.31: 36833 4.31 - 4.90: 59545 Nonbonded interactions: 134706 Sorted by model distance: nonbonded pdb=" OE2 GLU K 148 " pdb="ZN ZN K 201 " model vdw 1.947 2.230 nonbonded pdb=" OE2 GLU C 148 " pdb="ZN ZN C 201 " model vdw 2.011 2.230 nonbonded pdb=" NH1 ARG K 60 " pdb=" O HOH K 301 " model vdw 2.023 3.120 nonbonded pdb=" OE2 GLU F 68 " pdb=" O HOH K 301 " model vdw 2.027 3.040 nonbonded pdb=" OE2 GLU G 148 " pdb="ZN ZN G 201 " model vdw 2.031 2.230 ... (remaining 134701 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.50 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: 0.010 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 16932 Z= 0.162 Angle : 0.500 4.361 22920 Z= 0.305 Chirality : 0.035 0.127 2508 Planarity : 0.004 0.026 2976 Dihedral : 12.966 69.139 6348 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.17 (0.17), residues: 2016 helix: 0.33 (0.12), residues: 1428 sheet: None (None), residues: 0 loop : -0.08 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 117 TYR 0.012 0.002 TYR L 123 PHE 0.009 0.002 PHE J 167 TRP 0.004 0.002 TRP L 154 HIS 0.007 0.002 HIS L 151 Details of bonding type rmsd covalent geometry : bond 0.00246 (16920) covalent geometry : angle 0.50013 (22920) hydrogen bonds : bond 0.32111 ( 1140) hydrogen bonds : angle 6.26329 ( 3336) metal coordination : bond 0.12337 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 625 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASP cc_start: 0.7958 (t70) cc_final: 0.7547 (t0) REVERT: D 150 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6213 (mm-30) REVERT: D 152 GLU cc_start: 0.7904 (tt0) cc_final: 0.7683 (tt0) REVERT: E 116 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8263 (mm-30) REVERT: H 133 LYS cc_start: 0.7832 (mttt) cc_final: 0.7631 (mtpp) REVERT: I 30 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8139 (mm-30) REVERT: J 76 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7977 (mt-10) REVERT: J 134 ASP cc_start: 0.7562 (t0) cc_final: 0.7351 (t0) REVERT: L 25 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8450 (mtpp) REVERT: L 156 GLU cc_start: 0.7270 (tt0) cc_final: 0.7065 (tt0) REVERT: L 158 LEU cc_start: 0.8660 (mt) cc_final: 0.8410 (mt) outliers start: 0 outliers final: 0 residues processed: 625 average time/residue: 0.8839 time to fit residues: 592.6399 Evaluate side-chains 480 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 30.0000 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN D 128 ASN H 128 ASN L 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.151536 restraints weight = 10869.281| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 0.61 r_work: 0.3415 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16932 Z= 0.215 Angle : 0.599 4.629 22920 Z= 0.339 Chirality : 0.040 0.149 2508 Planarity : 0.005 0.040 2976 Dihedral : 3.950 17.333 2280 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.91 % Allowed : 13.43 % Favored : 84.66 % 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: 2.30 (0.19), residues: 2016 helix: 2.00 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : 0.41 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.018 0.002 TYR I 123 PHE 0.012 0.002 PHE L 88 TRP 0.009 0.002 TRP K 154 HIS 0.008 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00332 (16920) covalent geometry : angle 0.59919 (22920) hydrogen bonds : bond 0.10865 ( 1140) hydrogen bonds : angle 4.61605 ( 3336) metal coordination : bond 0.00507 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 471 time to evaluate : 0.521 Fit side-chains REVERT: A 54 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 68 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7934 (tp30) REVERT: B 84 ASP cc_start: 0.8006 (t70) cc_final: 0.7794 (t0) REVERT: D 18 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6955 (tmtp) REVERT: E 166 HIS cc_start: 0.7766 (m-70) cc_final: 0.7533 (m-70) REVERT: F 101 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6854 (tm-30) REVERT: F 106 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6934 (mp0) REVERT: I 54 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7530 (pp20) REVERT: J 17 GLU cc_start: 0.7253 (mp0) cc_final: 0.7021 (mp0) REVERT: J 150 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (tp30) REVERT: L 25 LYS cc_start: 0.9002 (mtpp) cc_final: 0.8799 (mtpp) REVERT: L 116 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8710 (mm-30) REVERT: L 154 TRP cc_start: 0.7258 (OUTLIER) cc_final: 0.6644 (m100) outliers start: 33 outliers final: 9 residues processed: 477 average time/residue: 0.8829 time to fit residues: 451.6148 Evaluate side-chains 434 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 422 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 0.1980 chunk 199 optimal weight: 30.0000 chunk 178 optimal weight: 0.1980 chunk 195 optimal weight: 30.0000 chunk 161 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 4 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN C 42 ASN E 128 ASN F 42 ASN F 128 ASN G 42 ASN J 42 ASN K 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.178380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.167084 restraints weight = 11842.992| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 0.50 r_work: 0.3601 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16932 Z= 0.140 Angle : 0.455 4.388 22920 Z= 0.251 Chirality : 0.035 0.118 2508 Planarity : 0.003 0.033 2976 Dihedral : 3.477 17.733 2280 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.56 % Allowed : 16.15 % Favored : 82.29 % 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: 3.17 (0.19), residues: 2016 helix: 2.66 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : 0.75 (0.29), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 168 TYR 0.012 0.001 TYR C 123 PHE 0.006 0.001 PHE E 155 TRP 0.009 0.002 TRP G 154 HIS 0.006 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00228 (16920) covalent geometry : angle 0.45482 (22920) hydrogen bonds : bond 0.07091 ( 1140) hydrogen bonds : angle 4.17819 ( 3336) metal coordination : bond 0.00091 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 392 time to evaluate : 0.584 Fit side-chains REVERT: A 33 THR cc_start: 0.8379 (m) cc_final: 0.8064 (t) REVERT: A 167 PHE cc_start: 0.7420 (p90) cc_final: 0.7175 (p90) REVERT: B 150 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: D 152 GLU cc_start: 0.7851 (tt0) cc_final: 0.7511 (tt0) REVERT: E 95 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.7359 (ttp80) REVERT: E 162 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7258 (pptt) REVERT: G 80 GLU cc_start: 0.7717 (pm20) cc_final: 0.7445 (pm20) REVERT: H 125 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7817 (tm-30) REVERT: J 179 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8683 (t) outliers start: 27 outliers final: 11 residues processed: 398 average time/residue: 0.9134 time to fit residues: 389.5903 Evaluate side-chains 367 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 354 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 150 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 32 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 201 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN B 42 ASN B 107 ASN B 128 ASN C 42 ASN F 42 ASN G 166 HIS H 107 ASN J 128 ASN L 42 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.162381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.148918 restraints weight = 11080.026| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 0.55 r_work: 0.3360 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16932 Z= 0.209 Angle : 0.555 5.799 22920 Z= 0.315 Chirality : 0.039 0.133 2508 Planarity : 0.004 0.034 2976 Dihedral : 3.811 15.047 2280 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.31 % Allowed : 16.20 % Favored : 81.48 % 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: 2.76 (0.19), residues: 2016 helix: 2.31 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.69 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 83 TYR 0.019 0.002 TYR I 123 PHE 0.012 0.002 PHE J 167 TRP 0.009 0.002 TRP K 154 HIS 0.006 0.002 HIS H 146 Details of bonding type rmsd covalent geometry : bond 0.00349 (16920) covalent geometry : angle 0.55478 (22920) hydrogen bonds : bond 0.11128 ( 1140) hydrogen bonds : angle 4.54679 ( 3336) metal coordination : bond 0.00358 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 444 time to evaluate : 0.683 Fit side-chains REVERT: A 47 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7148 (mt) REVERT: A 150 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: B 150 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: C 18 LYS cc_start: 0.7441 (mtpt) cc_final: 0.7183 (tttm) REVERT: D 152 GLU cc_start: 0.8139 (tt0) cc_final: 0.7812 (tt0) REVERT: E 152 GLU cc_start: 0.8400 (tt0) cc_final: 0.8027 (tt0) REVERT: G 18 LYS cc_start: 0.7528 (mttt) cc_final: 0.7201 (ttpt) REVERT: G 80 GLU cc_start: 0.8093 (pm20) cc_final: 0.7821 (pm20) REVERT: H 125 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7997 (tm-30) REVERT: I 21 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7625 (mt-10) REVERT: I 110 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8257 (mttp) REVERT: J 180 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8595 (pttp) REVERT: K 102 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: L 154 TRP cc_start: 0.7302 (OUTLIER) cc_final: 0.6694 (m100) outliers start: 40 outliers final: 18 residues processed: 453 average time/residue: 0.9093 time to fit residues: 440.7311 Evaluate side-chains 453 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 429 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 168 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 135 optimal weight: 0.0470 chunk 96 optimal weight: 7.9990 chunk 161 optimal weight: 30.0000 chunk 73 optimal weight: 0.9980 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 166 HIS C 42 ASN F 107 ASN G 107 ASN G 166 HIS L 42 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.163704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.151485 restraints weight = 10904.211| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.51 r_work: 0.3406 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16932 Z= 0.174 Angle : 0.498 6.063 22920 Z= 0.280 Chirality : 0.037 0.122 2508 Planarity : 0.004 0.026 2976 Dihedral : 3.662 13.740 2280 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.31 % Allowed : 17.42 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.19), residues: 2016 helix: 2.48 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.80 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 95 TYR 0.016 0.002 TYR I 123 PHE 0.009 0.001 PHE J 167 TRP 0.011 0.002 TRP K 154 HIS 0.004 0.001 HIS J 43 Details of bonding type rmsd covalent geometry : bond 0.00275 (16920) covalent geometry : angle 0.49771 (22920) hydrogen bonds : bond 0.09488 ( 1140) hydrogen bonds : angle 4.37279 ( 3336) metal coordination : bond 0.00257 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 403 time to evaluate : 0.704 Fit side-chains REVERT: A 150 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: B 150 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: B 162 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7464 (tppp) REVERT: D 152 GLU cc_start: 0.8081 (tt0) cc_final: 0.7786 (tt0) REVERT: E 106 GLU cc_start: 0.7172 (tt0) cc_final: 0.6933 (mm-30) REVERT: E 130 THR cc_start: 0.7781 (t) cc_final: 0.7580 (m) REVERT: E 152 GLU cc_start: 0.8320 (tt0) cc_final: 0.7961 (tt0) REVERT: F 62 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: G 18 LYS cc_start: 0.7309 (mttt) cc_final: 0.6972 (ttpt) REVERT: G 80 GLU cc_start: 0.7918 (pm20) cc_final: 0.7675 (pm20) REVERT: H 101 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: H 125 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7983 (tm-30) REVERT: I 21 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7531 (mt-10) REVERT: I 110 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8125 (mttp) REVERT: I 114 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: I 116 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8586 (mm-30) REVERT: J 179 SER cc_start: 0.8990 (m) cc_final: 0.8790 (p) REVERT: J 180 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8589 (pttp) REVERT: K 102 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: L 154 TRP cc_start: 0.7177 (OUTLIER) cc_final: 0.6650 (m100) outliers start: 40 outliers final: 20 residues processed: 414 average time/residue: 0.8960 time to fit residues: 397.9308 Evaluate side-chains 430 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 402 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 173 optimal weight: 40.0000 chunk 108 optimal weight: 0.1980 chunk 125 optimal weight: 40.0000 chunk 134 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 166 HIS G 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.162109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.149834 restraints weight = 10815.819| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 0.50 r_work: 0.3383 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16932 Z= 0.181 Angle : 0.507 6.016 22920 Z= 0.286 Chirality : 0.037 0.122 2508 Planarity : 0.004 0.028 2976 Dihedral : 3.683 13.617 2280 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.49 % Allowed : 17.42 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.19), residues: 2016 helix: 2.45 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.77 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 95 TYR 0.017 0.002 TYR I 123 PHE 0.010 0.001 PHE J 167 TRP 0.008 0.002 TRP A 154 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00291 (16920) covalent geometry : angle 0.50734 (22920) hydrogen bonds : bond 0.09854 ( 1140) hydrogen bonds : angle 4.38130 ( 3336) metal coordination : bond 0.00241 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 412 time to evaluate : 0.643 Fit side-chains REVERT: A 150 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: B 150 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: D 152 GLU cc_start: 0.8106 (tt0) cc_final: 0.7809 (tt0) REVERT: E 106 GLU cc_start: 0.7242 (tt0) cc_final: 0.7000 (mm-30) REVERT: E 130 THR cc_start: 0.7947 (t) cc_final: 0.7711 (m) REVERT: E 152 GLU cc_start: 0.8373 (tt0) cc_final: 0.8042 (tt0) REVERT: F 62 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: G 18 LYS cc_start: 0.7356 (mttt) cc_final: 0.7018 (ttpt) REVERT: G 80 GLU cc_start: 0.7951 (pm20) cc_final: 0.7708 (pm20) REVERT: G 150 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: H 101 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: H 125 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7987 (tm-30) REVERT: I 21 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7481 (mt-10) REVERT: I 110 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8184 (mttp) REVERT: I 114 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: I 116 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8643 (mm-30) REVERT: J 180 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8596 (pttp) REVERT: K 102 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: L 154 TRP cc_start: 0.7233 (OUTLIER) cc_final: 0.6676 (m100) outliers start: 43 outliers final: 25 residues processed: 425 average time/residue: 0.9833 time to fit residues: 447.4040 Evaluate side-chains 439 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 405 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 154 TRP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 43 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 166 HIS G 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.157862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.145517 restraints weight = 10626.480| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 0.50 r_work: 0.3330 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16932 Z= 0.209 Angle : 0.551 6.220 22920 Z= 0.313 Chirality : 0.039 0.136 2508 Planarity : 0.004 0.034 2976 Dihedral : 3.851 15.131 2280 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.95 % Allowed : 17.36 % Favored : 79.69 % 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: 2.73 (0.19), residues: 2016 helix: 2.29 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.69 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 95 TYR 0.020 0.002 TYR I 123 PHE 0.011 0.002 PHE J 167 TRP 0.009 0.002 TRP L 154 HIS 0.005 0.001 HIS H 146 Details of bonding type rmsd covalent geometry : bond 0.00347 (16920) covalent geometry : angle 0.55139 (22920) hydrogen bonds : bond 0.11250 ( 1140) hydrogen bonds : angle 4.52719 ( 3336) metal coordination : bond 0.00339 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 435 time to evaluate : 0.639 Fit side-chains REVERT: A 150 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: B 150 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: C 114 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: D 152 GLU cc_start: 0.8139 (tt0) cc_final: 0.7848 (tt0) REVERT: E 154 TRP cc_start: 0.7494 (OUTLIER) cc_final: 0.6370 (m100) REVERT: F 62 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: G 18 LYS cc_start: 0.7542 (mttt) cc_final: 0.7284 (ttpt) REVERT: G 150 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: H 101 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: H 125 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7980 (tm-30) REVERT: H 183 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7653 (mmtp) REVERT: I 21 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7514 (mt-10) REVERT: I 114 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: I 116 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8664 (mm-30) REVERT: J 180 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8595 (pttp) REVERT: K 102 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: L 154 TRP cc_start: 0.7337 (OUTLIER) cc_final: 0.6699 (m100) outliers start: 51 outliers final: 24 residues processed: 449 average time/residue: 0.9856 time to fit residues: 473.3403 Evaluate side-chains 463 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 427 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 154 TRP Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 154 TRP Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 146 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 161 optimal weight: 30.0000 chunk 156 optimal weight: 0.0370 chunk 107 optimal weight: 0.4980 chunk 198 optimal weight: 20.0000 chunk 134 optimal weight: 40.0000 chunk 100 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 overall best weight: 5.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 166 HIS F 107 ASN G 107 ASN G 166 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.158524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.146137 restraints weight = 10711.527| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.50 r_work: 0.3337 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16932 Z= 0.204 Angle : 0.548 6.653 22920 Z= 0.311 Chirality : 0.039 0.129 2508 Planarity : 0.004 0.034 2976 Dihedral : 3.883 19.740 2280 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.66 % Allowed : 18.00 % Favored : 79.34 % 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: 2.74 (0.19), residues: 2016 helix: 2.29 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.69 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.019 0.002 TYR I 123 PHE 0.010 0.002 PHE J 167 TRP 0.011 0.002 TRP C 154 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00337 (16920) covalent geometry : angle 0.54801 (22920) hydrogen bonds : bond 0.10977 ( 1140) hydrogen bonds : angle 4.50098 ( 3336) metal coordination : bond 0.00304 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 422 time to evaluate : 0.696 Fit side-chains REVERT: A 47 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7077 (mt) REVERT: A 150 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: A 167 PHE cc_start: 0.7691 (p90) cc_final: 0.7455 (p90) REVERT: B 150 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: C 114 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: D 152 GLU cc_start: 0.8146 (tt0) cc_final: 0.7860 (tt0) REVERT: E 154 TRP cc_start: 0.7483 (OUTLIER) cc_final: 0.6313 (m100) REVERT: F 62 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: F 101 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6519 (pp20) REVERT: G 18 LYS cc_start: 0.7510 (mttt) cc_final: 0.7253 (ttpt) REVERT: G 150 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: H 101 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6953 (tp30) REVERT: H 114 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: H 125 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7997 (tm-30) REVERT: I 21 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7534 (mt-10) REVERT: I 114 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: I 116 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8670 (mm-30) REVERT: J 180 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8586 (pttp) REVERT: K 102 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: L 154 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.6652 (m100) outliers start: 46 outliers final: 27 residues processed: 438 average time/residue: 1.0187 time to fit residues: 477.5346 Evaluate side-chains 458 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 418 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 154 TRP Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 154 TRP Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 82 optimal weight: 30.0000 chunk 157 optimal weight: 40.0000 chunk 189 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 166 HIS G 107 ASN G 166 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.157114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.144711 restraints weight = 10539.268| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 0.50 r_work: 0.3315 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16932 Z= 0.218 Angle : 0.575 6.515 22920 Z= 0.326 Chirality : 0.040 0.133 2508 Planarity : 0.004 0.035 2976 Dihedral : 3.959 17.554 2280 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.60 % Allowed : 18.29 % Favored : 79.11 % 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: 2016 helix: 2.20 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.63 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 95 TYR 0.021 0.002 TYR I 123 PHE 0.011 0.002 PHE J 167 TRP 0.009 0.002 TRP L 154 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00371 (16920) covalent geometry : angle 0.57483 (22920) hydrogen bonds : bond 0.11614 ( 1140) hydrogen bonds : angle 4.56524 ( 3336) metal coordination : bond 0.00349 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 432 time to evaluate : 0.687 Fit side-chains REVERT: A 47 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7234 (mt) REVERT: A 150 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: A 167 PHE cc_start: 0.7706 (p90) cc_final: 0.7495 (p90) REVERT: B 150 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: C 114 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: D 152 GLU cc_start: 0.8154 (tt0) cc_final: 0.7866 (tt0) REVERT: E 154 TRP cc_start: 0.7551 (OUTLIER) cc_final: 0.6396 (m100) REVERT: F 62 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: G 18 LYS cc_start: 0.7592 (mttt) cc_final: 0.7345 (ttpt) REVERT: G 150 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: H 101 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6982 (tp30) REVERT: H 114 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: H 125 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7976 (tm-30) REVERT: H 183 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7679 (mmtp) REVERT: I 21 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7521 (mt-10) REVERT: I 114 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: I 116 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8597 (mm-30) REVERT: J 180 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8581 (pttp) REVERT: K 102 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: L 154 TRP cc_start: 0.7318 (OUTLIER) cc_final: 0.6646 (m100) outliers start: 45 outliers final: 25 residues processed: 448 average time/residue: 1.0175 time to fit residues: 487.5326 Evaluate side-chains 469 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 430 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 154 TRP Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 154 TRP Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 182 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 166 HIS F 107 ASN G 107 ASN G 166 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.160411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.148137 restraints weight = 10671.321| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 0.50 r_work: 0.3357 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16932 Z= 0.192 Angle : 0.534 6.610 22920 Z= 0.302 Chirality : 0.038 0.127 2508 Planarity : 0.004 0.035 2976 Dihedral : 3.832 14.504 2280 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.37 % Allowed : 18.58 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.81 (0.19), residues: 2016 helix: 2.36 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.69 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 95 TYR 0.018 0.002 TYR I 123 PHE 0.010 0.002 PHE J 167 TRP 0.010 0.002 TRP C 154 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00313 (16920) covalent geometry : angle 0.53422 (22920) hydrogen bonds : bond 0.10422 ( 1140) hydrogen bonds : angle 4.42928 ( 3336) metal coordination : bond 0.00280 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 418 time to evaluate : 0.664 Fit side-chains REVERT: A 47 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7005 (mt) REVERT: A 150 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: A 167 PHE cc_start: 0.7724 (p90) cc_final: 0.7515 (p90) REVERT: B 102 GLU cc_start: 0.7540 (mp0) cc_final: 0.7239 (mp0) REVERT: B 150 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: C 114 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: D 150 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: D 152 GLU cc_start: 0.8125 (tt0) cc_final: 0.7849 (tt0) REVERT: E 154 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.6261 (m100) REVERT: F 62 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: G 18 LYS cc_start: 0.7439 (mttt) cc_final: 0.7144 (ttpt) REVERT: G 150 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: H 101 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6993 (tp30) REVERT: H 114 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: H 125 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8034 (tm-30) REVERT: I 21 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7572 (mt-10) REVERT: I 116 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8664 (mm-30) REVERT: J 180 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8589 (pttp) outliers start: 41 outliers final: 23 residues processed: 432 average time/residue: 1.0097 time to fit residues: 466.9977 Evaluate side-chains 445 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 411 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 154 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 196 optimal weight: 8.9990 chunk 121 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 190 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 166 HIS G 107 ASN G 166 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.166514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.153470 restraints weight = 11185.522| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 0.54 r_work: 0.3421 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16932 Z= 0.182 Angle : 0.518 6.620 22920 Z= 0.292 Chirality : 0.038 0.124 2508 Planarity : 0.004 0.032 2976 Dihedral : 3.773 14.740 2280 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.08 % Allowed : 19.16 % Favored : 78.76 % 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: 2.90 (0.19), residues: 2016 helix: 2.41 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.73 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 95 TYR 0.017 0.002 TYR I 123 PHE 0.009 0.001 PHE J 167 TRP 0.014 0.002 TRP L 154 HIS 0.005 0.001 HIS J 43 Details of bonding type rmsd covalent geometry : bond 0.00294 (16920) covalent geometry : angle 0.51806 (22920) hydrogen bonds : bond 0.09824 ( 1140) hydrogen bonds : angle 4.35286 ( 3336) metal coordination : bond 0.00225 ( 12) =============================================================================== Job complete usr+sys time: 8740.27 seconds wall clock time: 148 minutes 39.85 seconds (8919.85 seconds total)