Starting phenix.real_space_refine on Thu Feb 5 20:09:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qnf_53245/02_2026/9qnf_53245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qnf_53245/02_2026/9qnf_53245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qnf_53245/02_2026/9qnf_53245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qnf_53245/02_2026/9qnf_53245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qnf_53245/02_2026/9qnf_53245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qnf_53245/02_2026/9qnf_53245.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 180 5.16 5 C 13320 2.51 5 N 3036 2.21 5 O 3240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19788 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "E" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "G" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "H" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "J" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "K" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "L" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.51, per 1000 atoms: 0.23 Number of scatterers: 19788 At special positions: 0 Unit cell: (104.751, 93.0395, 159.403, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 12 15.00 O 3240 8.00 N 3036 7.00 C 13320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 824.4 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 74.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.710A pdb=" N THR A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.505A pdb=" N TRP A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 105 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 128 through 157 Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.678A pdb=" N THR B 8 " --> pdb=" O THR B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 41 removed outlier: 3.510A pdb=" N TRP B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 105 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 128 through 157 Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.673A pdb=" N THR C 8 " --> pdb=" O THR C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 41 removed outlier: 3.505A pdb=" N TRP C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 105 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 128 through 157 Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.681A pdb=" N THR D 8 " --> pdb=" O THR D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 41 removed outlier: 3.501A pdb=" N TRP D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 105 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 128 through 157 Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 2 through 12 removed outlier: 3.673A pdb=" N THR E 8 " --> pdb=" O THR E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.506A pdb=" N TRP E 24 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 105 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 128 through 157 Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 2 through 12 removed outlier: 3.682A pdb=" N THR F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 41 removed outlier: 3.507A pdb=" N TRP F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL F 27 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 105 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 128 through 157 Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 2 through 12 removed outlier: 3.744A pdb=" N THR G 8 " --> pdb=" O THR G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 41 removed outlier: 3.512A pdb=" N TRP G 24 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL G 27 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 105 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 128 through 157 Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 2 through 12 removed outlier: 3.677A pdb=" N THR H 8 " --> pdb=" O THR H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 41 removed outlier: 3.512A pdb=" N TRP H 24 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL H 27 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 105 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 128 through 157 Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 2 through 12 removed outlier: 3.669A pdb=" N THR I 8 " --> pdb=" O THR I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 41 removed outlier: 3.506A pdb=" N TRP I 24 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 105 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 128 through 157 Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 2 through 12 removed outlier: 3.685A pdb=" N THR J 8 " --> pdb=" O THR J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 24 through 41 removed outlier: 4.365A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 105 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 128 through 157 Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 2 through 12 removed outlier: 3.676A pdb=" N THR K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 24 Processing helix chain 'K' and resid 24 through 41 removed outlier: 4.364A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 105 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 128 through 157 Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 2 through 12 removed outlier: 3.700A pdb=" N THR L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 41 removed outlier: 3.503A pdb=" N TRP L 24 " --> pdb=" O ILE L 20 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL L 27 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 105 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 128 through 157 Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.851A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.862A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.862A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.853A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.857A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.858A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.855A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.862A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.862A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.853A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.861A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.866A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1406 hydrogen bonds defined for protein. 4182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3002 1.33 - 1.45: 5578 1.45 - 1.57: 11460 1.57 - 1.69: 24 1.69 - 1.81: 264 Bond restraints: 20328 Sorted by residual: bond pdb=" CA THR J 86 " pdb=" C THR J 86 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 4.02e-01 bond pdb=" CA THR C 86 " pdb=" C THR C 86 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.92e-01 bond pdb=" CA THR F 86 " pdb=" C THR F 86 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.71e-01 bond pdb=" CA THR I 86 " pdb=" C THR I 86 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.57e-01 bond pdb=" CA THR H 86 " pdb=" C THR H 86 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.56e-01 ... (remaining 20323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 26827 1.00 - 2.00: 697 2.00 - 3.00: 112 3.00 - 4.00: 24 4.00 - 5.00: 24 Bond angle restraints: 27684 Sorted by residual: angle pdb=" C THR H 86 " pdb=" N PRO H 87 " pdb=" CD PRO H 87 " ideal model delta sigma weight residual 125.00 130.00 -5.00 4.10e+00 5.95e-02 1.49e+00 angle pdb=" N PRO D 172 " pdb=" CA PRO D 172 " pdb=" C PRO D 172 " ideal model delta sigma weight residual 112.10 115.26 -3.16 2.60e+00 1.48e-01 1.48e+00 angle pdb=" C THR C 86 " pdb=" N PRO C 87 " pdb=" CD PRO C 87 " ideal model delta sigma weight residual 125.00 129.99 -4.99 4.10e+00 5.95e-02 1.48e+00 angle pdb=" N PRO I 172 " pdb=" CA PRO I 172 " pdb=" C PRO I 172 " ideal model delta sigma weight residual 112.10 115.25 -3.15 2.60e+00 1.48e-01 1.47e+00 angle pdb=" N PRO G 172 " pdb=" CA PRO G 172 " pdb=" C PRO G 172 " ideal model delta sigma weight residual 112.10 115.25 -3.15 2.60e+00 1.48e-01 1.47e+00 ... (remaining 27679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 11534 15.16 - 30.32: 721 30.32 - 45.48: 237 45.48 - 60.64: 36 60.64 - 75.79: 36 Dihedral angle restraints: 12564 sinusoidal: 5616 harmonic: 6948 Sorted by residual: dihedral pdb=" CA ASP G 66 " pdb=" CB ASP G 66 " pdb=" CG ASP G 66 " pdb=" OD1 ASP G 66 " ideal model delta sinusoidal sigma weight residual -30.00 -85.77 55.77 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP J 66 " pdb=" CB ASP J 66 " pdb=" CG ASP J 66 " pdb=" OD1 ASP J 66 " ideal model delta sinusoidal sigma weight residual -30.00 -85.65 55.65 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP A 66 " pdb=" CB ASP A 66 " pdb=" CG ASP A 66 " pdb=" OD1 ASP A 66 " ideal model delta sinusoidal sigma weight residual -30.00 -85.50 55.50 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 12561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1823 0.024 - 0.048: 807 0.048 - 0.072: 451 0.072 - 0.097: 108 0.097 - 0.121: 63 Chirality restraints: 3252 Sorted by residual: chirality pdb=" CA THR E 86 " pdb=" N THR E 86 " pdb=" C THR E 86 " pdb=" CB THR E 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA THR I 86 " pdb=" N THR I 86 " pdb=" C THR I 86 " pdb=" CB THR I 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 3249 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 183 " 0.014 5.00e-02 4.00e+02 2.08e-02 6.94e-01 pdb=" N PRO G 184 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO G 184 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO G 184 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 183 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.85e-01 pdb=" N PRO C 184 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO C 184 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 184 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 183 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.83e-01 pdb=" N PRO L 184 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO L 184 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO L 184 " 0.012 5.00e-02 4.00e+02 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 8787 2.96 - 3.45: 20924 3.45 - 3.93: 33492 3.93 - 4.42: 35722 4.42 - 4.90: 61501 Nonbonded interactions: 160426 Sorted by model distance: nonbonded pdb=" O21 POV H 602 " pdb=" O31 POV H 602 " model vdw 2.479 2.432 nonbonded pdb=" O21 POV A 601 " pdb=" O31 POV A 601 " model vdw 2.479 2.432 nonbonded pdb=" O21 POV C 602 " pdb=" O31 POV C 602 " model vdw 2.480 2.432 nonbonded pdb=" O21 POV D 602 " pdb=" O31 POV D 602 " model vdw 2.481 2.432 nonbonded pdb=" O21 POV J 602 " pdb=" O31 POV J 602 " model vdw 2.482 2.432 ... (remaining 160421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 217) selection = (chain 'B' and resid 1 through 217) selection = (chain 'C' and resid 1 through 217) selection = (chain 'D' and resid 1 through 217) selection = (chain 'E' and resid 1 through 217) selection = (chain 'F' and resid 1 through 217) selection = (chain 'G' and resid 1 through 217) selection = (chain 'H' and resid 1 through 217) selection = (chain 'I' and resid 1 through 217) selection = (chain 'J' and resid 1 through 217) selection = (chain 'K' and resid 1 through 217) selection = (chain 'L' and resid 1 through 217) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.730 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 20364 Z= 0.101 Angle : 0.419 4.997 27756 Z= 0.218 Chirality : 0.037 0.121 3252 Planarity : 0.003 0.021 3180 Dihedral : 11.784 75.794 7944 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.14 % Allowed : 3.41 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.17), residues: 2304 helix: 3.31 (0.12), residues: 1632 sheet: 0.73 (0.46), residues: 132 loop : -2.26 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 164 TYR 0.006 0.001 TYR I 7 PHE 0.006 0.001 PHE C 31 TRP 0.006 0.001 TRP G 77 HIS 0.002 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00231 (20328) covalent geometry : angle 0.41798 (27684) SS BOND : bond 0.00163 ( 36) SS BOND : angle 0.78192 ( 72) hydrogen bonds : bond 0.10182 ( 1406) hydrogen bonds : angle 3.99456 ( 4182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.762 Fit side-chains REVERT: A 144 LEU cc_start: 0.8787 (tt) cc_final: 0.8119 (mt) REVERT: B 144 LEU cc_start: 0.8727 (tt) cc_final: 0.8084 (mt) REVERT: B 194 MET cc_start: 0.9062 (mmm) cc_final: 0.8814 (mmm) REVERT: C 144 LEU cc_start: 0.8786 (tt) cc_final: 0.8133 (mt) REVERT: D 144 LEU cc_start: 0.8793 (tt) cc_final: 0.8123 (mt) REVERT: E 144 LEU cc_start: 0.8738 (tt) cc_final: 0.8099 (mt) REVERT: E 194 MET cc_start: 0.9064 (mmm) cc_final: 0.8809 (mmm) REVERT: F 144 LEU cc_start: 0.8798 (tt) cc_final: 0.8152 (mt) REVERT: G 144 LEU cc_start: 0.8790 (tt) cc_final: 0.8118 (mt) REVERT: H 144 LEU cc_start: 0.8750 (tt) cc_final: 0.8086 (mt) REVERT: H 194 MET cc_start: 0.9065 (mmm) cc_final: 0.8825 (mmm) REVERT: I 144 LEU cc_start: 0.8799 (tt) cc_final: 0.8141 (mt) REVERT: J 144 LEU cc_start: 0.8794 (tt) cc_final: 0.8127 (mt) REVERT: J 217 CYS cc_start: 0.7082 (t) cc_final: 0.6857 (m) REVERT: K 144 LEU cc_start: 0.8750 (tt) cc_final: 0.8101 (mt) REVERT: K 194 MET cc_start: 0.9061 (mmm) cc_final: 0.8809 (mmm) REVERT: L 144 LEU cc_start: 0.8794 (tt) cc_final: 0.8133 (mt) outliers start: 24 outliers final: 7 residues processed: 233 average time/residue: 0.1516 time to fit residues: 53.9342 Evaluate side-chains 189 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain L residue 13 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.0670 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN C 99 GLN D 99 GLN E 99 GLN F 99 GLN G 99 GLN H 99 GLN I 99 GLN J 99 GLN K 99 GLN L 99 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.091096 restraints weight = 21567.889| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 0.92 r_work: 0.2812 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 20364 Z= 0.130 Angle : 0.438 5.051 27756 Z= 0.225 Chirality : 0.038 0.128 3252 Planarity : 0.003 0.023 3180 Dihedral : 11.257 75.516 3838 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.14 % Allowed : 5.59 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.26 (0.17), residues: 2304 helix: 3.50 (0.12), residues: 1632 sheet: 0.83 (0.47), residues: 132 loop : -2.10 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 164 TYR 0.007 0.001 TYR F 65 PHE 0.009 0.001 PHE B 190 TRP 0.004 0.001 TRP D 77 HIS 0.004 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00320 (20328) covalent geometry : angle 0.43753 (27684) SS BOND : bond 0.00241 ( 36) SS BOND : angle 0.57681 ( 72) hydrogen bonds : bond 0.03737 ( 1406) hydrogen bonds : angle 3.07624 ( 4182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.766 Fit side-chains REVERT: A 144 LEU cc_start: 0.8840 (tt) cc_final: 0.8244 (mt) REVERT: B 144 LEU cc_start: 0.8781 (tt) cc_final: 0.8110 (mt) REVERT: B 194 MET cc_start: 0.9082 (mmm) cc_final: 0.8843 (mmm) REVERT: C 101 ILE cc_start: 0.8572 (mt) cc_final: 0.8324 (mm) REVERT: C 144 LEU cc_start: 0.8821 (tt) cc_final: 0.8136 (mt) REVERT: D 144 LEU cc_start: 0.8827 (tt) cc_final: 0.8229 (mt) REVERT: E 144 LEU cc_start: 0.8785 (tt) cc_final: 0.8119 (mt) REVERT: E 194 MET cc_start: 0.9087 (mmm) cc_final: 0.8842 (mmm) REVERT: F 144 LEU cc_start: 0.8802 (tt) cc_final: 0.8142 (mt) REVERT: G 144 LEU cc_start: 0.8844 (tt) cc_final: 0.8151 (mt) REVERT: H 144 LEU cc_start: 0.8794 (tt) cc_final: 0.8118 (mt) REVERT: H 194 MET cc_start: 0.9084 (mmm) cc_final: 0.8847 (mmm) REVERT: I 101 ILE cc_start: 0.8543 (mt) cc_final: 0.8282 (mm) REVERT: I 144 LEU cc_start: 0.8832 (tt) cc_final: 0.8149 (mt) REVERT: J 105 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6611 (ptp) REVERT: J 144 LEU cc_start: 0.8841 (tt) cc_final: 0.8157 (mt) REVERT: K 144 LEU cc_start: 0.8793 (tt) cc_final: 0.8114 (mt) REVERT: K 194 MET cc_start: 0.9080 (mmm) cc_final: 0.8839 (mmm) REVERT: L 144 LEU cc_start: 0.8833 (tt) cc_final: 0.8142 (mt) outliers start: 24 outliers final: 17 residues processed: 216 average time/residue: 0.1445 time to fit residues: 48.6473 Evaluate side-chains 210 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 218 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN D 99 GLN E 99 GLN G 99 GLN H 99 GLN J 99 GLN K 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.091293 restraints weight = 21569.582| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 0.86 r_work: 0.2826 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20364 Z= 0.099 Angle : 0.405 4.972 27756 Z= 0.207 Chirality : 0.037 0.115 3252 Planarity : 0.003 0.020 3180 Dihedral : 11.178 75.785 3838 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.08 % Allowed : 5.73 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.45 (0.17), residues: 2304 helix: 3.64 (0.11), residues: 1632 sheet: 0.89 (0.47), residues: 132 loop : -2.05 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 164 TYR 0.006 0.001 TYR F 65 PHE 0.007 0.001 PHE G 190 TRP 0.004 0.001 TRP I 44 HIS 0.006 0.001 HIS J 97 Details of bonding type rmsd covalent geometry : bond 0.00234 (20328) covalent geometry : angle 0.40497 (27684) SS BOND : bond 0.00177 ( 36) SS BOND : angle 0.54395 ( 72) hydrogen bonds : bond 0.03292 ( 1406) hydrogen bonds : angle 2.91343 ( 4182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.712 Fit side-chains REVERT: A 144 LEU cc_start: 0.8792 (tt) cc_final: 0.8098 (mp) REVERT: A 167 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8903 (mmtm) REVERT: B 144 LEU cc_start: 0.8763 (tt) cc_final: 0.8073 (mt) REVERT: B 194 MET cc_start: 0.9107 (mmm) cc_final: 0.8847 (mmm) REVERT: C 144 LEU cc_start: 0.8775 (tt) cc_final: 0.8103 (mt) REVERT: D 131 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8417 (mm) REVERT: D 144 LEU cc_start: 0.8790 (tt) cc_final: 0.8103 (mp) REVERT: D 167 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8898 (mmtm) REVERT: E 144 LEU cc_start: 0.8765 (tt) cc_final: 0.8082 (mt) REVERT: E 194 MET cc_start: 0.9097 (mmm) cc_final: 0.8832 (mmm) REVERT: F 144 LEU cc_start: 0.8794 (tt) cc_final: 0.8126 (mt) REVERT: G 131 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8425 (mm) REVERT: G 144 LEU cc_start: 0.8789 (tt) cc_final: 0.8088 (mt) REVERT: H 144 LEU cc_start: 0.8774 (tt) cc_final: 0.8085 (mt) REVERT: H 194 MET cc_start: 0.9102 (mmm) cc_final: 0.8843 (mmm) REVERT: I 144 LEU cc_start: 0.8798 (tt) cc_final: 0.8111 (mt) REVERT: J 105 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6530 (ptp) REVERT: J 144 LEU cc_start: 0.8795 (tt) cc_final: 0.8089 (mt) REVERT: K 144 LEU cc_start: 0.8758 (tt) cc_final: 0.8063 (mt) REVERT: K 194 MET cc_start: 0.9104 (mmm) cc_final: 0.8843 (mmm) REVERT: L 144 LEU cc_start: 0.8781 (tt) cc_final: 0.8094 (mt) outliers start: 44 outliers final: 16 residues processed: 229 average time/residue: 0.1346 time to fit residues: 49.1308 Evaluate side-chains 200 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 111 optimal weight: 0.0000 chunk 49 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.093307 restraints weight = 21438.682| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 0.91 r_work: 0.2842 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 20364 Z= 0.085 Angle : 0.389 4.942 27756 Z= 0.200 Chirality : 0.036 0.114 3252 Planarity : 0.002 0.018 3180 Dihedral : 11.072 76.057 3838 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.14 % Allowed : 8.14 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.59 (0.17), residues: 2304 helix: 3.76 (0.11), residues: 1632 sheet: 0.92 (0.47), residues: 132 loop : -2.05 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 15 TYR 0.005 0.001 TYR G 7 PHE 0.006 0.001 PHE G 190 TRP 0.004 0.001 TRP A 44 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00189 (20328) covalent geometry : angle 0.38861 (27684) SS BOND : bond 0.00158 ( 36) SS BOND : angle 0.47283 ( 72) hydrogen bonds : bond 0.03021 ( 1406) hydrogen bonds : angle 2.82053 ( 4182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.656 Fit side-chains REVERT: A 144 LEU cc_start: 0.8826 (tt) cc_final: 0.8166 (mp) REVERT: A 167 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8853 (mmtm) REVERT: B 144 LEU cc_start: 0.8784 (tt) cc_final: 0.8107 (mt) REVERT: B 194 MET cc_start: 0.9062 (mmm) cc_final: 0.8802 (mmm) REVERT: C 144 LEU cc_start: 0.8819 (tt) cc_final: 0.8156 (mt) REVERT: D 144 LEU cc_start: 0.8835 (tt) cc_final: 0.8180 (mp) REVERT: D 167 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8851 (mmtm) REVERT: E 144 LEU cc_start: 0.8789 (tt) cc_final: 0.8120 (mt) REVERT: E 194 MET cc_start: 0.9058 (mmm) cc_final: 0.8792 (mmm) REVERT: F 144 LEU cc_start: 0.8817 (tt) cc_final: 0.8160 (mt) REVERT: G 131 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8403 (mm) REVERT: G 144 LEU cc_start: 0.8829 (tt) cc_final: 0.8171 (mp) REVERT: H 144 LEU cc_start: 0.8797 (tt) cc_final: 0.8125 (mt) REVERT: H 194 MET cc_start: 0.9063 (mmm) cc_final: 0.8803 (mmm) REVERT: I 144 LEU cc_start: 0.8824 (tt) cc_final: 0.8158 (mt) REVERT: J 144 LEU cc_start: 0.8827 (tt) cc_final: 0.8176 (mp) REVERT: K 144 LEU cc_start: 0.8792 (tt) cc_final: 0.8109 (mt) REVERT: K 194 MET cc_start: 0.9058 (mmm) cc_final: 0.8794 (mmm) REVERT: L 144 LEU cc_start: 0.8822 (tt) cc_final: 0.8148 (mt) outliers start: 24 outliers final: 7 residues processed: 206 average time/residue: 0.1377 time to fit residues: 45.7979 Evaluate side-chains 193 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 13 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN D 99 GLN E 99 GLN G 99 GLN H 99 GLN J 99 GLN K 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.090461 restraints weight = 21457.224| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 0.89 r_work: 0.2827 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 20364 Z= 0.103 Angle : 0.403 4.985 27756 Z= 0.204 Chirality : 0.037 0.118 3252 Planarity : 0.002 0.024 3180 Dihedral : 10.999 76.006 3835 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.23 % Allowed : 8.24 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.60 (0.17), residues: 2304 helix: 3.77 (0.11), residues: 1632 sheet: 0.87 (0.47), residues: 132 loop : -2.06 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 15 TYR 0.007 0.001 TYR F 65 PHE 0.008 0.001 PHE C 190 TRP 0.004 0.001 TRP F 44 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00250 (20328) covalent geometry : angle 0.40286 (27684) SS BOND : bond 0.00166 ( 36) SS BOND : angle 0.42801 ( 72) hydrogen bonds : bond 0.03129 ( 1406) hydrogen bonds : angle 2.80834 ( 4182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.749 Fit side-chains REVERT: A 144 LEU cc_start: 0.8806 (tt) cc_final: 0.8123 (mp) REVERT: A 167 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8908 (mmtm) REVERT: B 144 LEU cc_start: 0.8771 (tt) cc_final: 0.8063 (mt) REVERT: B 194 MET cc_start: 0.9103 (mmm) cc_final: 0.8839 (mmm) REVERT: C 144 LEU cc_start: 0.8805 (tt) cc_final: 0.8117 (mt) REVERT: D 144 LEU cc_start: 0.8795 (tt) cc_final: 0.8116 (mp) REVERT: D 167 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8909 (mmtm) REVERT: E 144 LEU cc_start: 0.8773 (tt) cc_final: 0.8075 (mt) REVERT: E 194 MET cc_start: 0.9098 (mmm) cc_final: 0.8826 (mmm) REVERT: F 144 LEU cc_start: 0.8800 (tt) cc_final: 0.8129 (mt) REVERT: G 144 LEU cc_start: 0.8791 (tt) cc_final: 0.8112 (mp) REVERT: H 144 LEU cc_start: 0.8785 (tt) cc_final: 0.8092 (mt) REVERT: H 194 MET cc_start: 0.9100 (mmm) cc_final: 0.8835 (mmm) REVERT: I 144 LEU cc_start: 0.8811 (tt) cc_final: 0.8125 (mt) REVERT: J 144 LEU cc_start: 0.8788 (tt) cc_final: 0.8116 (mp) REVERT: K 144 LEU cc_start: 0.8773 (tt) cc_final: 0.8070 (mt) REVERT: K 194 MET cc_start: 0.9100 (mmm) cc_final: 0.8833 (mmm) REVERT: L 144 LEU cc_start: 0.8808 (tt) cc_final: 0.8109 (mt) outliers start: 26 outliers final: 13 residues processed: 212 average time/residue: 0.1519 time to fit residues: 50.2654 Evaluate side-chains 197 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 61 optimal weight: 0.9990 chunk 156 optimal weight: 0.0270 chunk 141 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.085328 restraints weight = 21814.387| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 0.97 r_work: 0.2694 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20364 Z= 0.087 Angle : 0.386 4.940 27756 Z= 0.197 Chirality : 0.036 0.115 3252 Planarity : 0.002 0.025 3180 Dihedral : 10.930 76.230 3835 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.28 % Allowed : 8.52 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.65 (0.17), residues: 2304 helix: 3.75 (0.11), residues: 1644 sheet: 0.94 (0.47), residues: 132 loop : -1.95 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.005 0.001 TYR F 65 PHE 0.009 0.001 PHE D 29 TRP 0.003 0.001 TRP K 132 HIS 0.002 0.000 HIS L 73 Details of bonding type rmsd covalent geometry : bond 0.00198 (20328) covalent geometry : angle 0.38573 (27684) SS BOND : bond 0.00150 ( 36) SS BOND : angle 0.42218 ( 72) hydrogen bonds : bond 0.02951 ( 1406) hydrogen bonds : angle 2.77530 ( 4182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.762 Fit side-chains REVERT: A 144 LEU cc_start: 0.8843 (tt) cc_final: 0.8176 (mp) REVERT: A 167 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8895 (mmtm) REVERT: B 144 LEU cc_start: 0.8799 (tt) cc_final: 0.8114 (mt) REVERT: B 194 MET cc_start: 0.9078 (mmm) cc_final: 0.8816 (mmm) REVERT: C 144 LEU cc_start: 0.8833 (tt) cc_final: 0.8164 (mt) REVERT: D 144 LEU cc_start: 0.8822 (tt) cc_final: 0.8178 (mp) REVERT: D 167 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8895 (mmtm) REVERT: E 76 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8894 (tt) REVERT: E 144 LEU cc_start: 0.8795 (tt) cc_final: 0.8113 (mt) REVERT: E 194 MET cc_start: 0.9085 (mmm) cc_final: 0.8813 (mmm) REVERT: F 144 LEU cc_start: 0.8831 (tt) cc_final: 0.8164 (mt) REVERT: G 144 LEU cc_start: 0.8844 (tt) cc_final: 0.8177 (mp) REVERT: H 144 LEU cc_start: 0.8810 (tt) cc_final: 0.8126 (mt) REVERT: H 194 MET cc_start: 0.9089 (mmm) cc_final: 0.8823 (mmm) REVERT: I 144 LEU cc_start: 0.8840 (tt) cc_final: 0.8166 (mt) REVERT: J 144 LEU cc_start: 0.8852 (tt) cc_final: 0.8183 (mp) REVERT: K 144 LEU cc_start: 0.8807 (tt) cc_final: 0.8122 (mt) REVERT: K 194 MET cc_start: 0.9092 (mmm) cc_final: 0.8824 (mmm) REVERT: L 144 LEU cc_start: 0.8849 (tt) cc_final: 0.8165 (mt) outliers start: 27 outliers final: 11 residues processed: 210 average time/residue: 0.1344 time to fit residues: 46.0392 Evaluate side-chains 200 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 88 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.085096 restraints weight = 22066.905| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.06 r_work: 0.2677 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20364 Z= 0.098 Angle : 0.400 5.095 27756 Z= 0.205 Chirality : 0.037 0.118 3252 Planarity : 0.002 0.017 3180 Dihedral : 10.880 76.172 3833 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.47 % Allowed : 9.04 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.66 (0.17), residues: 2304 helix: 3.76 (0.11), residues: 1644 sheet: 0.92 (0.47), residues: 132 loop : -1.95 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 164 TYR 0.006 0.001 TYR F 65 PHE 0.018 0.001 PHE D 29 TRP 0.003 0.001 TRP J 132 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00235 (20328) covalent geometry : angle 0.39984 (27684) SS BOND : bond 0.00164 ( 36) SS BOND : angle 0.40749 ( 72) hydrogen bonds : bond 0.03026 ( 1406) hydrogen bonds : angle 2.77003 ( 4182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.769 Fit side-chains REVERT: A 144 LEU cc_start: 0.8821 (tt) cc_final: 0.8133 (mp) REVERT: A 167 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8939 (mmtm) REVERT: B 144 LEU cc_start: 0.8775 (tt) cc_final: 0.8076 (mt) REVERT: B 194 MET cc_start: 0.9103 (mmm) cc_final: 0.8827 (mmm) REVERT: C 144 LEU cc_start: 0.8814 (tt) cc_final: 0.8128 (mt) REVERT: D 144 LEU cc_start: 0.8817 (tt) cc_final: 0.8131 (mp) REVERT: D 167 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8936 (mmtm) REVERT: E 76 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8887 (tt) REVERT: E 144 LEU cc_start: 0.8759 (tt) cc_final: 0.8064 (mt) REVERT: E 194 MET cc_start: 0.9111 (mmm) cc_final: 0.8825 (mmm) REVERT: F 76 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8877 (tt) REVERT: F 144 LEU cc_start: 0.8800 (tt) cc_final: 0.8124 (mt) REVERT: G 144 LEU cc_start: 0.8825 (tt) cc_final: 0.8140 (mp) REVERT: H 131 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8401 (mt) REVERT: H 144 LEU cc_start: 0.8785 (tt) cc_final: 0.8091 (mt) REVERT: H 194 MET cc_start: 0.9112 (mmm) cc_final: 0.8837 (mmm) REVERT: I 144 LEU cc_start: 0.8806 (tt) cc_final: 0.8121 (mt) REVERT: J 76 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8885 (tt) REVERT: J 144 LEU cc_start: 0.8827 (tt) cc_final: 0.8138 (mp) REVERT: K 144 LEU cc_start: 0.8778 (tt) cc_final: 0.8074 (mt) REVERT: K 194 MET cc_start: 0.9106 (mmm) cc_final: 0.8828 (mmm) REVERT: L 144 LEU cc_start: 0.8817 (tt) cc_final: 0.8119 (mt) outliers start: 31 outliers final: 15 residues processed: 216 average time/residue: 0.1362 time to fit residues: 48.0064 Evaluate side-chains 208 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 64 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.088043 restraints weight = 21830.801| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 0.83 r_work: 0.2662 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 20364 Z= 0.169 Angle : 0.468 5.126 27756 Z= 0.238 Chirality : 0.039 0.128 3252 Planarity : 0.003 0.018 3180 Dihedral : 10.988 75.523 3833 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.75 % Allowed : 9.19 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.48 (0.17), residues: 2304 helix: 3.59 (0.11), residues: 1644 sheet: 1.05 (0.48), residues: 132 loop : -1.93 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 164 TYR 0.012 0.001 TYR B 65 PHE 0.013 0.002 PHE F 68 TRP 0.006 0.001 TRP E 44 HIS 0.003 0.001 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00426 (20328) covalent geometry : angle 0.46766 (27684) SS BOND : bond 0.00228 ( 36) SS BOND : angle 0.46731 ( 72) hydrogen bonds : bond 0.03657 ( 1406) hydrogen bonds : angle 2.90493 ( 4182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.779 Fit side-chains REVERT: A 66 ASP cc_start: 0.8943 (t70) cc_final: 0.8678 (t0) REVERT: A 76 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8844 (tt) REVERT: A 83 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8994 (mm) REVERT: A 144 LEU cc_start: 0.8780 (tt) cc_final: 0.8081 (mp) REVERT: B 76 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8846 (tt) REVERT: B 144 LEU cc_start: 0.8741 (tt) cc_final: 0.8130 (mt) REVERT: B 194 MET cc_start: 0.9113 (mmm) cc_final: 0.8836 (mmm) REVERT: C 144 LEU cc_start: 0.8794 (tt) cc_final: 0.8087 (mt) REVERT: D 66 ASP cc_start: 0.8941 (t70) cc_final: 0.8674 (t0) REVERT: D 83 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9005 (mm) REVERT: D 144 LEU cc_start: 0.8783 (tt) cc_final: 0.8087 (mp) REVERT: E 76 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8833 (tt) REVERT: E 144 LEU cc_start: 0.8753 (tt) cc_final: 0.8024 (mt) REVERT: E 194 MET cc_start: 0.9110 (mmm) cc_final: 0.8830 (mmm) REVERT: F 76 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8847 (tt) REVERT: F 144 LEU cc_start: 0.8804 (tt) cc_final: 0.8090 (mt) REVERT: G 22 ARG cc_start: 0.8714 (ttt180) cc_final: 0.8491 (mtt-85) REVERT: G 66 ASP cc_start: 0.8938 (t70) cc_final: 0.8676 (t0) REVERT: G 76 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8845 (tt) REVERT: G 83 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8998 (mm) REVERT: G 144 LEU cc_start: 0.8803 (tt) cc_final: 0.8101 (mp) REVERT: H 66 ASP cc_start: 0.8961 (t70) cc_final: 0.8715 (t0) REVERT: H 144 LEU cc_start: 0.8759 (tt) cc_final: 0.8032 (mt) REVERT: H 194 MET cc_start: 0.9116 (mmm) cc_final: 0.8855 (mmm) REVERT: I 144 LEU cc_start: 0.8792 (tt) cc_final: 0.8091 (mt) REVERT: J 66 ASP cc_start: 0.8938 (t70) cc_final: 0.8671 (t0) REVERT: J 76 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8834 (tt) REVERT: J 83 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9010 (mm) REVERT: J 144 LEU cc_start: 0.8797 (tt) cc_final: 0.8089 (mp) REVERT: K 76 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8840 (tt) REVERT: K 144 LEU cc_start: 0.8774 (tt) cc_final: 0.8037 (mt) REVERT: K 194 MET cc_start: 0.9101 (mmm) cc_final: 0.8826 (mmm) REVERT: L 144 LEU cc_start: 0.8802 (tt) cc_final: 0.8089 (mt) outliers start: 37 outliers final: 18 residues processed: 220 average time/residue: 0.1401 time to fit residues: 49.3187 Evaluate side-chains 208 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 146 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 137 optimal weight: 0.2980 chunk 214 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN J 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.089085 restraints weight = 21475.687| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 1.05 r_work: 0.2648 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 20364 Z= 0.107 Angle : 0.414 5.418 27756 Z= 0.212 Chirality : 0.037 0.119 3252 Planarity : 0.002 0.018 3180 Dihedral : 10.920 75.864 3833 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.66 % Allowed : 9.56 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.62 (0.17), residues: 2304 helix: 3.70 (0.11), residues: 1644 sheet: 1.08 (0.48), residues: 132 loop : -1.90 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.006 0.001 TYR F 65 PHE 0.009 0.001 PHE A 29 TRP 0.004 0.001 TRP B 133 HIS 0.002 0.001 HIS K 73 Details of bonding type rmsd covalent geometry : bond 0.00260 (20328) covalent geometry : angle 0.41358 (27684) SS BOND : bond 0.00178 ( 36) SS BOND : angle 0.43739 ( 72) hydrogen bonds : bond 0.03235 ( 1406) hydrogen bonds : angle 2.83776 ( 4182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.759 Fit side-chains REVERT: A 76 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 83 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8970 (mm) REVERT: A 144 LEU cc_start: 0.8783 (tt) cc_final: 0.8091 (mp) REVERT: B 76 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (tt) REVERT: B 144 LEU cc_start: 0.8752 (tt) cc_final: 0.8040 (mt) REVERT: B 194 MET cc_start: 0.9117 (mmm) cc_final: 0.8841 (mmm) REVERT: C 144 LEU cc_start: 0.8796 (tt) cc_final: 0.8095 (mt) REVERT: D 83 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8972 (mm) REVERT: D 144 LEU cc_start: 0.8786 (tt) cc_final: 0.8088 (mp) REVERT: E 76 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8846 (tt) REVERT: E 144 LEU cc_start: 0.8760 (tt) cc_final: 0.8055 (mt) REVERT: E 194 MET cc_start: 0.9108 (mmm) cc_final: 0.8829 (mmm) REVERT: F 76 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8853 (tt) REVERT: F 144 LEU cc_start: 0.8815 (tt) cc_final: 0.8109 (mt) REVERT: G 22 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8463 (mtt-85) REVERT: G 76 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8869 (tt) REVERT: G 83 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8984 (mm) REVERT: G 144 LEU cc_start: 0.8789 (tt) cc_final: 0.8101 (mp) REVERT: H 144 LEU cc_start: 0.8779 (tt) cc_final: 0.8082 (mt) REVERT: H 194 MET cc_start: 0.9117 (mmm) cc_final: 0.8849 (mmm) REVERT: I 144 LEU cc_start: 0.8812 (tt) cc_final: 0.8113 (mt) REVERT: J 76 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8857 (tt) REVERT: J 83 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8995 (mm) REVERT: J 144 LEU cc_start: 0.8783 (tt) cc_final: 0.8092 (mp) REVERT: J 167 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8907 (mmtm) REVERT: K 76 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8850 (tt) REVERT: K 144 LEU cc_start: 0.8783 (tt) cc_final: 0.8064 (mt) REVERT: K 194 MET cc_start: 0.9106 (mmm) cc_final: 0.8830 (mmm) REVERT: L 144 LEU cc_start: 0.8822 (tt) cc_final: 0.8114 (mt) outliers start: 35 outliers final: 18 residues processed: 209 average time/residue: 0.1329 time to fit residues: 45.4158 Evaluate side-chains 207 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 198 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN K 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.117510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.090102 restraints weight = 21631.557| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.05 r_work: 0.2686 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20364 Z= 0.086 Angle : 0.394 5.905 27756 Z= 0.204 Chirality : 0.036 0.119 3252 Planarity : 0.002 0.017 3180 Dihedral : 10.784 76.220 3833 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.23 % Allowed : 10.23 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.17), residues: 2304 helix: 3.82 (0.11), residues: 1644 sheet: 1.03 (0.48), residues: 132 loop : -1.89 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 15 TYR 0.006 0.001 TYR A 7 PHE 0.012 0.001 PHE A 29 TRP 0.005 0.001 TRP H 132 HIS 0.002 0.001 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00195 (20328) covalent geometry : angle 0.39369 (27684) SS BOND : bond 0.00130 ( 36) SS BOND : angle 0.42751 ( 72) hydrogen bonds : bond 0.02915 ( 1406) hydrogen bonds : angle 2.77301 ( 4182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.732 Fit side-chains REVERT: A 76 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8889 (tt) REVERT: A 83 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8968 (mm) REVERT: A 144 LEU cc_start: 0.8812 (tt) cc_final: 0.8133 (mp) REVERT: B 76 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8896 (tt) REVERT: B 144 LEU cc_start: 0.8765 (tt) cc_final: 0.8065 (mt) REVERT: B 194 MET cc_start: 0.9082 (mmm) cc_final: 0.8794 (mmm) REVERT: C 144 LEU cc_start: 0.8804 (tt) cc_final: 0.8127 (mt) REVERT: D 83 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8965 (mm) REVERT: D 144 LEU cc_start: 0.8799 (tt) cc_final: 0.8131 (mp) REVERT: E 76 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8881 (tt) REVERT: E 144 LEU cc_start: 0.8767 (tt) cc_final: 0.8073 (mt) REVERT: E 194 MET cc_start: 0.9091 (mmm) cc_final: 0.8799 (mmm) REVERT: F 76 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8873 (tt) REVERT: F 144 LEU cc_start: 0.8792 (tt) cc_final: 0.8110 (mt) REVERT: G 76 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8886 (tt) REVERT: G 83 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8965 (mm) REVERT: G 144 LEU cc_start: 0.8821 (tt) cc_final: 0.8150 (mp) REVERT: H 76 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8906 (tt) REVERT: H 144 LEU cc_start: 0.8774 (tt) cc_final: 0.8080 (mt) REVERT: H 194 MET cc_start: 0.9111 (mmm) cc_final: 0.8829 (mmm) REVERT: I 144 LEU cc_start: 0.8801 (tt) cc_final: 0.8121 (mt) REVERT: J 76 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8884 (tt) REVERT: J 83 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8979 (mm) REVERT: J 144 LEU cc_start: 0.8812 (tt) cc_final: 0.8132 (mp) REVERT: J 167 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8914 (mmtm) REVERT: K 76 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8884 (tt) REVERT: K 144 LEU cc_start: 0.8778 (tt) cc_final: 0.8074 (mt) REVERT: K 194 MET cc_start: 0.9089 (mmm) cc_final: 0.8799 (mmm) REVERT: L 144 LEU cc_start: 0.8806 (tt) cc_final: 0.8116 (mt) outliers start: 26 outliers final: 8 residues processed: 205 average time/residue: 0.1279 time to fit residues: 42.7075 Evaluate side-chains 202 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 186 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN G 99 GLN H 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.091293 restraints weight = 21678.456| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 0.86 r_work: 0.2687 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 20364 Z= 0.129 Angle : 0.430 5.601 27756 Z= 0.219 Chirality : 0.038 0.122 3252 Planarity : 0.002 0.017 3180 Dihedral : 10.775 75.878 3831 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.09 % Allowed : 10.27 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.68 (0.17), residues: 2304 helix: 3.75 (0.11), residues: 1644 sheet: 1.04 (0.47), residues: 132 loop : -1.88 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 22 TYR 0.009 0.001 TYR F 65 PHE 0.010 0.001 PHE A 68 TRP 0.005 0.001 TRP F 3 HIS 0.003 0.001 HIS L 73 Details of bonding type rmsd covalent geometry : bond 0.00319 (20328) covalent geometry : angle 0.43041 (27684) SS BOND : bond 0.00194 ( 36) SS BOND : angle 0.41770 ( 72) hydrogen bonds : bond 0.03248 ( 1406) hydrogen bonds : angle 2.82106 ( 4182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4066.33 seconds wall clock time: 70 minutes 55.77 seconds (4255.77 seconds total)