Starting phenix.real_space_refine on Thu Feb 5 20:12:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qnt_53250/02_2026/9qnt_53250.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qnt_53250/02_2026/9qnt_53250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qnt_53250/02_2026/9qnt_53250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qnt_53250/02_2026/9qnt_53250.map" model { file = "/net/cci-nas-00/data/ceres_data/9qnt_53250/02_2026/9qnt_53250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qnt_53250/02_2026/9qnt_53250.cif" } resolution = 3.29 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: 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: "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: 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: "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: 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: "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: 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} Time building chain proxies: 4.87, per 1000 atoms: 0.25 Number of scatterers: 19788 At special positions: 0 Unit cell: (102.148, 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=24, 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 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 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 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 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 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 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 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 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 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 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 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 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: 1.79 Conformation dependent library (CDL) restraints added in 857.8 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: 96 helices and 12 sheets defined 76.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.863A pdb=" N VAL A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 4.264A pdb=" N ASP A 46 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 47 " --> pdb=" O TRP A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 47' Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.538A pdb=" N VAL A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 104 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 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 41 removed outlier: 3.804A pdb=" N VAL B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 removed outlier: 4.260A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 47 " --> pdb=" O TRP B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 47' Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.535A pdb=" N VAL B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 104 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 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 41 removed outlier: 3.803A pdb=" N VAL C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 4.265A pdb=" N ASP C 46 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 47 " --> pdb=" O TRP C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 47' Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.542A pdb=" N VAL C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 104 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 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 24 through 41 removed outlier: 4.615A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 47 removed outlier: 4.261A pdb=" N ASP D 46 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 47 " --> pdb=" O TRP D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 47' Processing helix chain 'D' and resid 59 through 69 removed outlier: 3.537A pdb=" N VAL D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 104 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 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 24 through 41 removed outlier: 4.637A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 4.313A pdb=" N ASP E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 47 " --> pdb=" O TRP E 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 47' Processing helix chain 'E' and resid 59 through 69 removed outlier: 3.530A pdb=" N VAL E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 104 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 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 24 through 41 removed outlier: 4.631A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 47 removed outlier: 4.308A pdb=" N ASP F 46 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU F 47 " --> pdb=" O TRP F 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 47' Processing helix chain 'F' and resid 59 through 69 removed outlier: 3.542A pdb=" N VAL F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 104 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 Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 24 through 41 removed outlier: 4.623A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 47 removed outlier: 4.309A pdb=" N ASP G 46 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU G 47 " --> pdb=" O TRP G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 43 through 47' Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.533A pdb=" N VAL G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 104 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 Processing helix chain 'H' and resid 18 through 23 Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.868A pdb=" N VAL H 27 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 47 removed outlier: 4.304A pdb=" N ASP H 46 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU H 47 " --> pdb=" O TRP H 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 43 through 47' Processing helix chain 'H' and resid 59 through 69 removed outlier: 3.537A pdb=" N VAL H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 104 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 Processing helix chain 'I' and resid 18 through 23 Processing helix chain 'I' and resid 23 through 41 removed outlier: 3.840A pdb=" N VAL I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 47 removed outlier: 4.268A pdb=" N ASP I 46 " --> pdb=" O VAL I 43 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU I 47 " --> pdb=" O TRP I 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 43 through 47' Processing helix chain 'I' and resid 59 through 69 removed outlier: 3.546A pdb=" N VAL I 63 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 104 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 Processing helix chain 'J' and resid 18 through 23 Processing helix chain 'J' and resid 24 through 41 removed outlier: 4.609A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 47 removed outlier: 4.242A pdb=" N ASP J 46 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU J 47 " --> pdb=" O TRP J 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 43 through 47' Processing helix chain 'J' and resid 59 through 69 removed outlier: 3.521A pdb=" N VAL J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 104 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 Processing helix chain 'K' and resid 18 through 23 Processing helix chain 'K' and resid 23 through 41 removed outlier: 3.808A pdb=" N VAL K 27 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 47 removed outlier: 4.235A pdb=" N ASP K 46 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU K 47 " --> pdb=" O TRP K 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 43 through 47' Processing helix chain 'K' and resid 59 through 69 removed outlier: 3.537A pdb=" N VAL K 63 " --> pdb=" O GLY K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 104 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 Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 24 through 41 removed outlier: 4.615A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 47 removed outlier: 4.277A pdb=" N ASP L 46 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU L 47 " --> pdb=" O TRP L 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 43 through 47' Processing helix chain 'L' and resid 59 through 69 removed outlier: 3.542A pdb=" N VAL L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 104 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: 3.749A 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: 3.759A 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: 3.753A 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: 3.754A 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: 3.742A 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: 3.752A 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: 3.747A 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: 3.726A 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: 3.762A 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: 3.756A 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: 3.757A 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: 3.756A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1392 hydrogen bonds defined for protein. 4140 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: 3.27 Time building geometry restraints manager: 2.29 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: 3148 1.33 - 1.45: 5432 1.45 - 1.57: 11460 1.57 - 1.69: 24 1.69 - 1.81: 264 Bond restraints: 20328 Sorted by residual: bond pdb=" C ARG L 183 " pdb=" O ARG L 183 " ideal model delta sigma weight residual 1.235 1.226 0.009 4.70e-03 4.53e+04 3.37e+00 bond pdb=" CA VAL I 13 " pdb=" CB VAL I 13 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.36e-02 5.41e+03 5.38e-01 bond pdb=" CA VAL D 13 " pdb=" CB VAL D 13 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.36e-02 5.41e+03 5.20e-01 bond pdb=" C ARG C 183 " pdb=" O ARG C 183 " ideal model delta sigma weight residual 1.235 1.232 0.003 4.70e-03 4.53e+04 5.20e-01 bond pdb=" CA VAL F 13 " pdb=" CB VAL F 13 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.36e-02 5.41e+03 5.09e-01 ... (remaining 20323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 26560 1.01 - 2.02: 883 2.02 - 3.02: 162 3.02 - 4.03: 43 4.03 - 5.04: 36 Bond angle restraints: 27684 Sorted by residual: angle pdb=" C GLY I 12 " pdb=" N VAL I 13 " pdb=" CA VAL I 13 " ideal model delta sigma weight residual 121.97 126.36 -4.39 1.80e+00 3.09e-01 5.95e+00 angle pdb=" C GLY G 12 " pdb=" N VAL G 13 " pdb=" CA VAL G 13 " ideal model delta sigma weight residual 121.97 126.34 -4.37 1.80e+00 3.09e-01 5.91e+00 angle pdb=" C GLY B 12 " pdb=" N VAL B 13 " pdb=" CA VAL B 13 " ideal model delta sigma weight residual 121.97 126.33 -4.36 1.80e+00 3.09e-01 5.87e+00 angle pdb=" C GLY H 12 " pdb=" N VAL H 13 " pdb=" CA VAL H 13 " ideal model delta sigma weight residual 121.97 126.33 -4.36 1.80e+00 3.09e-01 5.86e+00 angle pdb=" C GLY D 12 " pdb=" N VAL D 13 " pdb=" CA VAL D 13 " ideal model delta sigma weight residual 121.97 126.31 -4.34 1.80e+00 3.09e-01 5.81e+00 ... (remaining 27679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 11387 15.70 - 31.40: 890 31.40 - 47.10: 165 47.10 - 62.79: 56 62.79 - 78.49: 30 Dihedral angle restraints: 12528 sinusoidal: 5580 harmonic: 6948 Sorted by residual: dihedral pdb=" CB CYS A 53 " pdb=" SG CYS A 53 " pdb=" SG CYS A 179 " pdb=" CB CYS A 179 " ideal model delta sinusoidal sigma weight residual -86.00 -117.63 31.63 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CB CYS L 53 " pdb=" SG CYS L 53 " pdb=" SG CYS L 179 " pdb=" CB CYS L 179 " ideal model delta sinusoidal sigma weight residual -86.00 -117.06 31.06 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CB CYS H 53 " pdb=" SG CYS H 53 " pdb=" SG CYS H 179 " pdb=" CB CYS H 179 " ideal model delta sinusoidal sigma weight residual -86.00 -117.06 31.06 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 12525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2039 0.031 - 0.062: 902 0.062 - 0.093: 214 0.093 - 0.124: 85 0.124 - 0.155: 12 Chirality restraints: 3252 Sorted by residual: chirality pdb=" CB VAL J 13 " pdb=" CA VAL J 13 " pdb=" CG1 VAL J 13 " pdb=" CG2 VAL J 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB VAL G 13 " pdb=" CA VAL G 13 " pdb=" CG1 VAL G 13 " pdb=" CG2 VAL G 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CB VAL A 13 " pdb=" CA VAL A 13 " pdb=" CG1 VAL A 13 " pdb=" CG2 VAL A 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 3249 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 57 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.23e-01 pdb=" N PRO J 58 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO J 58 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 58 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 51 " -0.008 2.00e-02 2.50e+03 6.22e-03 6.78e-01 pdb=" CG PHE A 51 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 51 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 51 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 51 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 51 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 51 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 51 " 0.008 2.00e-02 2.50e+03 6.19e-03 6.70e-01 pdb=" CG PHE F 51 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE F 51 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 51 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 51 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 51 " 0.004 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 13150 3.06 - 3.52: 21633 3.52 - 3.98: 30318 3.98 - 4.44: 37190 4.44 - 4.90: 58912 Nonbonded interactions: 161203 Sorted by model distance: nonbonded pdb=" O21 POV K 602 " pdb=" O31 POV K 602 " model vdw 2.596 2.432 nonbonded pdb=" O21 POV J 602 " pdb=" O31 POV J 602 " model vdw 2.598 2.432 nonbonded pdb=" O21 POV F 602 " pdb=" O31 POV F 602 " model vdw 2.606 2.432 nonbonded pdb=" O21 POV H 601 " pdb=" O31 POV H 601 " model vdw 2.606 2.432 nonbonded pdb=" O21 POV E 602 " pdb=" O31 POV E 602 " model vdw 2.606 2.432 ... (remaining 161198 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: 0.01 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: 3.910 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.110 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 20352 Z= 0.147 Angle : 0.481 5.040 27732 Z= 0.256 Chirality : 0.038 0.155 3252 Planarity : 0.003 0.021 3180 Dihedral : 12.150 78.493 7944 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.27 % Allowed : 4.69 % Favored : 93.04 % 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: 2.89 (0.18), residues: 2304 helix: 3.29 (0.12), residues: 1596 sheet: 0.95 (0.53), residues: 132 loop : -2.19 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 75 TYR 0.005 0.001 TYR L 65 PHE 0.014 0.001 PHE F 51 TRP 0.005 0.001 TRP B 77 HIS 0.002 0.001 HIS K 94 Details of bonding type rmsd covalent geometry : bond 0.00345 (20328) covalent geometry : angle 0.47789 (27684) SS BOND : bond 0.00302 ( 24) SS BOND : angle 1.38567 ( 48) hydrogen bonds : bond 0.08901 ( 1392) hydrogen bonds : angle 3.62919 ( 4140) *********************** 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 309 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.9098 (mm) cc_final: 0.8797 (mt) REVERT: B 203 ILE cc_start: 0.9099 (mm) cc_final: 0.8872 (mt) REVERT: C 203 ILE cc_start: 0.9092 (mm) cc_final: 0.8809 (mt) REVERT: D 203 ILE cc_start: 0.9105 (mm) cc_final: 0.8811 (mt) REVERT: E 203 ILE cc_start: 0.9105 (mm) cc_final: 0.8881 (mt) REVERT: F 203 ILE cc_start: 0.9084 (mm) cc_final: 0.8798 (mt) REVERT: G 203 ILE cc_start: 0.9097 (mm) cc_final: 0.8858 (mt) REVERT: H 203 ILE cc_start: 0.9107 (mm) cc_final: 0.8816 (mt) REVERT: I 203 ILE cc_start: 0.9082 (mm) cc_final: 0.8788 (mt) REVERT: K 203 ILE cc_start: 0.9091 (mm) cc_final: 0.8853 (mt) REVERT: L 203 ILE cc_start: 0.9080 (mm) cc_final: 0.8790 (mt) outliers start: 48 outliers final: 40 residues processed: 309 average time/residue: 0.1804 time to fit residues: 81.1217 Evaluate side-chains 257 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG 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: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 175 ASN J 175 ASN L 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.076758 restraints weight = 23143.051| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.26 r_work: 0.2565 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20352 Z= 0.173 Angle : 0.490 5.133 27732 Z= 0.252 Chirality : 0.040 0.251 3252 Planarity : 0.003 0.019 3180 Dihedral : 11.307 77.803 3904 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.17 % Allowed : 8.62 % Favored : 88.21 % 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: 3.08 (0.18), residues: 2304 helix: 3.36 (0.12), residues: 1620 sheet: 1.31 (0.55), residues: 132 loop : -2.21 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 22 TYR 0.006 0.001 TYR D 65 PHE 0.014 0.001 PHE J 51 TRP 0.005 0.001 TRP I 44 HIS 0.002 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00424 (20328) covalent geometry : angle 0.48751 (27684) SS BOND : bond 0.00305 ( 24) SS BOND : angle 1.32952 ( 48) hydrogen bonds : bond 0.03787 ( 1392) hydrogen bonds : angle 3.25889 ( 4140) *********************** 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 284 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9127 (mm) cc_final: 0.8892 (mt) REVERT: C 203 ILE cc_start: 0.9085 (mm) cc_final: 0.8789 (mt) REVERT: D 203 ILE cc_start: 0.9114 (mm) cc_final: 0.8806 (mt) REVERT: E 203 ILE cc_start: 0.9137 (mm) cc_final: 0.8902 (mt) REVERT: F 203 ILE cc_start: 0.9088 (mm) cc_final: 0.8802 (mt) REVERT: G 203 ILE cc_start: 0.9120 (mm) cc_final: 0.8873 (mt) REVERT: I 203 ILE cc_start: 0.9081 (mm) cc_final: 0.8785 (mt) REVERT: K 203 ILE cc_start: 0.9115 (mm) cc_final: 0.8866 (mt) REVERT: L 22 ARG cc_start: 0.9078 (ttm-80) cc_final: 0.8875 (ttm-80) REVERT: L 203 ILE cc_start: 0.9075 (mm) cc_final: 0.8774 (mt) outliers start: 67 outliers final: 55 residues processed: 281 average time/residue: 0.1867 time to fit residues: 75.4267 Evaluate side-chains 253 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 144 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 121 optimal weight: 0.4980 chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 0.0570 chunk 77 optimal weight: 10.0000 chunk 197 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN D 175 ASN H 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.077905 restraints weight = 23250.090| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 1.27 r_work: 0.2583 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20352 Z= 0.125 Angle : 0.454 5.156 27732 Z= 0.232 Chirality : 0.040 0.254 3252 Planarity : 0.002 0.018 3180 Dihedral : 11.228 76.533 3902 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.84 % Allowed : 10.23 % Favored : 86.93 % 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 (0.18), residues: 2304 helix: 3.52 (0.12), residues: 1620 sheet: 1.39 (0.56), residues: 132 loop : -2.23 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 15 TYR 0.006 0.001 TYR I 65 PHE 0.013 0.001 PHE J 51 TRP 0.004 0.001 TRP C 44 HIS 0.002 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00298 (20328) covalent geometry : angle 0.45197 (27684) SS BOND : bond 0.00206 ( 24) SS BOND : angle 1.09192 ( 48) hydrogen bonds : bond 0.03346 ( 1392) hydrogen bonds : angle 3.05158 ( 4140) *********************** 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 279 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9128 (mm) cc_final: 0.8896 (mt) REVERT: C 203 ILE cc_start: 0.9085 (mm) cc_final: 0.8785 (mt) REVERT: D 203 ILE cc_start: 0.9102 (mm) cc_final: 0.8800 (mt) REVERT: E 203 ILE cc_start: 0.9134 (mm) cc_final: 0.8901 (mt) REVERT: F 203 ILE cc_start: 0.9084 (mm) cc_final: 0.8790 (mt) REVERT: G 203 ILE cc_start: 0.9119 (mm) cc_final: 0.8876 (mt) REVERT: I 203 ILE cc_start: 0.9079 (mm) cc_final: 0.8778 (mt) REVERT: K 203 ILE cc_start: 0.9119 (mm) cc_final: 0.8875 (mt) REVERT: L 203 ILE cc_start: 0.9069 (mm) cc_final: 0.8766 (mt) outliers start: 60 outliers final: 41 residues processed: 274 average time/residue: 0.1676 time to fit residues: 65.8039 Evaluate side-chains 242 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 111 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 140 optimal weight: 0.2980 chunk 216 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.104142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.080474 restraints weight = 23110.987| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.27 r_work: 0.2630 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20352 Z= 0.093 Angle : 0.427 4.976 27732 Z= 0.219 Chirality : 0.039 0.266 3252 Planarity : 0.002 0.019 3180 Dihedral : 11.081 75.358 3901 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.89 % Allowed : 10.98 % Favored : 86.13 % 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: 3.50 (0.18), residues: 2304 helix: 3.70 (0.12), residues: 1620 sheet: 1.40 (0.53), residues: 132 loop : -2.14 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 15 TYR 0.005 0.001 TYR I 7 PHE 0.012 0.001 PHE L 51 TRP 0.004 0.001 TRP B 3 HIS 0.001 0.000 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00208 (20328) covalent geometry : angle 0.42537 (27684) SS BOND : bond 0.00121 ( 24) SS BOND : angle 0.89987 ( 48) hydrogen bonds : bond 0.02942 ( 1392) hydrogen bonds : angle 2.86062 ( 4140) *********************** 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 308 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 247 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9125 (mm) cc_final: 0.8891 (mt) REVERT: C 203 ILE cc_start: 0.9077 (mm) cc_final: 0.8783 (mt) REVERT: D 203 ILE cc_start: 0.9092 (mm) cc_final: 0.8794 (mt) REVERT: E 203 ILE cc_start: 0.9129 (mm) cc_final: 0.8897 (mt) REVERT: F 203 ILE cc_start: 0.9079 (mm) cc_final: 0.8786 (mt) REVERT: G 203 ILE cc_start: 0.9119 (mm) cc_final: 0.8877 (mt) REVERT: I 22 ARG cc_start: 0.9031 (ttm-80) cc_final: 0.8794 (ttt180) REVERT: I 203 ILE cc_start: 0.9080 (mm) cc_final: 0.8778 (mt) REVERT: K 203 ILE cc_start: 0.9118 (mm) cc_final: 0.8875 (mt) REVERT: L 203 ILE cc_start: 0.9074 (mm) cc_final: 0.8773 (mt) outliers start: 61 outliers final: 48 residues processed: 305 average time/residue: 0.1533 time to fit residues: 68.5813 Evaluate side-chains 261 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN D 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.077880 restraints weight = 23200.441| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 1.27 r_work: 0.2586 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20352 Z= 0.137 Angle : 0.454 5.072 27732 Z= 0.232 Chirality : 0.040 0.261 3252 Planarity : 0.002 0.019 3180 Dihedral : 11.040 75.419 3899 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.94 % Allowed : 11.22 % Favored : 85.84 % 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: 3.50 (0.18), residues: 2304 helix: 3.71 (0.12), residues: 1620 sheet: 1.52 (0.54), residues: 132 loop : -2.20 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 15 TYR 0.007 0.001 TYR D 65 PHE 0.011 0.001 PHE G 51 TRP 0.005 0.001 TRP F 44 HIS 0.004 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00335 (20328) covalent geometry : angle 0.45214 (27684) SS BOND : bond 0.00252 ( 24) SS BOND : angle 1.10736 ( 48) hydrogen bonds : bond 0.03124 ( 1392) hydrogen bonds : angle 2.84992 ( 4140) *********************** 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 270 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 208 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9127 (mm) cc_final: 0.8890 (mt) REVERT: C 203 ILE cc_start: 0.9087 (mm) cc_final: 0.8782 (mt) REVERT: D 203 ILE cc_start: 0.9112 (mm) cc_final: 0.8810 (mt) REVERT: E 203 ILE cc_start: 0.9132 (mm) cc_final: 0.8897 (mt) REVERT: F 203 ILE cc_start: 0.9079 (mm) cc_final: 0.8777 (mt) REVERT: G 203 ILE cc_start: 0.9123 (mm) cc_final: 0.8879 (mt) REVERT: I 203 ILE cc_start: 0.9082 (mm) cc_final: 0.8774 (mt) REVERT: K 203 ILE cc_start: 0.9117 (mm) cc_final: 0.8878 (mt) REVERT: L 22 ARG cc_start: 0.9009 (ttm-80) cc_final: 0.8735 (ttt180) REVERT: L 203 ILE cc_start: 0.9075 (mm) cc_final: 0.8764 (mt) outliers start: 62 outliers final: 51 residues processed: 269 average time/residue: 0.1692 time to fit residues: 65.7274 Evaluate side-chains 251 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 61 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.080961 restraints weight = 22979.792| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 1.23 r_work: 0.2608 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20352 Z= 0.112 Angle : 0.440 5.011 27732 Z= 0.225 Chirality : 0.040 0.265 3252 Planarity : 0.002 0.019 3180 Dihedral : 10.983 74.334 3899 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.12 % Allowed : 12.36 % Favored : 84.52 % 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: 3.58 (0.18), residues: 2304 helix: 3.71 (0.12), residues: 1632 sheet: 1.49 (0.53), residues: 132 loop : -2.08 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 22 TYR 0.005 0.001 TYR L 65 PHE 0.011 0.001 PHE L 51 TRP 0.005 0.001 TRP H 44 HIS 0.005 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00268 (20328) covalent geometry : angle 0.43815 (27684) SS BOND : bond 0.00189 ( 24) SS BOND : angle 1.01866 ( 48) hydrogen bonds : bond 0.03010 ( 1392) hydrogen bonds : angle 2.78335 ( 4140) *********************** 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 272 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9139 (mm) cc_final: 0.8900 (mt) REVERT: C 203 ILE cc_start: 0.9096 (mm) cc_final: 0.8792 (mt) REVERT: D 203 ILE cc_start: 0.9132 (mm) cc_final: 0.8828 (mt) REVERT: E 203 ILE cc_start: 0.9143 (mm) cc_final: 0.8904 (mt) REVERT: F 203 ILE cc_start: 0.9094 (mm) cc_final: 0.8790 (mt) REVERT: G 203 ILE cc_start: 0.9131 (mm) cc_final: 0.8885 (mt) REVERT: I 203 ILE cc_start: 0.9095 (mm) cc_final: 0.8786 (mt) REVERT: K 203 ILE cc_start: 0.9127 (mm) cc_final: 0.8879 (mt) REVERT: L 22 ARG cc_start: 0.8981 (ttm-80) cc_final: 0.8742 (ttt180) REVERT: L 203 ILE cc_start: 0.9089 (mm) cc_final: 0.8777 (mt) outliers start: 66 outliers final: 53 residues processed: 272 average time/residue: 0.1513 time to fit residues: 60.0444 Evaluate side-chains 258 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 130 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 88 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.103060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.079211 restraints weight = 23294.394| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 1.28 r_work: 0.2612 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20352 Z= 0.107 Angle : 0.434 5.003 27732 Z= 0.222 Chirality : 0.040 0.274 3252 Planarity : 0.002 0.019 3180 Dihedral : 10.921 74.173 3899 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.60 % Allowed : 12.97 % Favored : 84.42 % 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 (0.18), residues: 2304 helix: 3.79 (0.11), residues: 1632 sheet: 1.39 (0.52), residues: 132 loop : -2.00 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 15 TYR 0.006 0.001 TYR J 65 PHE 0.010 0.001 PHE A 51 TRP 0.005 0.001 TRP A 44 HIS 0.006 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00253 (20328) covalent geometry : angle 0.43277 (27684) SS BOND : bond 0.00177 ( 24) SS BOND : angle 1.00978 ( 48) hydrogen bonds : bond 0.02934 ( 1392) hydrogen bonds : angle 2.72587 ( 4140) *********************** 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 261 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9118 (mm) cc_final: 0.8877 (mt) REVERT: C 203 ILE cc_start: 0.9074 (mm) cc_final: 0.8766 (mt) REVERT: D 203 ILE cc_start: 0.9103 (mm) cc_final: 0.8798 (mt) REVERT: E 203 ILE cc_start: 0.9120 (mm) cc_final: 0.8879 (mt) REVERT: F 203 ILE cc_start: 0.9073 (mm) cc_final: 0.8767 (mt) REVERT: G 203 ILE cc_start: 0.9112 (mm) cc_final: 0.8862 (mt) REVERT: I 22 ARG cc_start: 0.8823 (ttt180) cc_final: 0.8598 (ttm-80) REVERT: I 203 ILE cc_start: 0.9076 (mm) cc_final: 0.8763 (mt) REVERT: K 203 ILE cc_start: 0.9106 (mm) cc_final: 0.8854 (mt) REVERT: L 203 ILE cc_start: 0.9070 (mm) cc_final: 0.8753 (mt) outliers start: 55 outliers final: 51 residues processed: 261 average time/residue: 0.1613 time to fit residues: 60.7503 Evaluate side-chains 255 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 64 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 86 optimal weight: 0.0000 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 134 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 overall best weight: 0.3582 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.106172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.082997 restraints weight = 23054.125| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.23 r_work: 0.2660 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20352 Z= 0.088 Angle : 0.419 4.936 27732 Z= 0.214 Chirality : 0.039 0.265 3252 Planarity : 0.002 0.019 3180 Dihedral : 10.827 74.424 3899 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.18 % Allowed : 13.64 % Favored : 84.19 % 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: 3.80 (0.18), residues: 2304 helix: 3.87 (0.11), residues: 1632 sheet: 1.37 (0.50), residues: 132 loop : -1.91 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 22 TYR 0.005 0.001 TYR H 7 PHE 0.010 0.001 PHE G 51 TRP 0.005 0.001 TRP A 44 HIS 0.004 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00192 (20328) covalent geometry : angle 0.41842 (27684) SS BOND : bond 0.00094 ( 24) SS BOND : angle 0.82283 ( 48) hydrogen bonds : bond 0.02726 ( 1392) hydrogen bonds : angle 2.65095 ( 4140) *********************** 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 281 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9139 (mm) cc_final: 0.8898 (mt) REVERT: C 203 ILE cc_start: 0.9097 (mm) cc_final: 0.8795 (mt) REVERT: D 203 ILE cc_start: 0.9125 (mm) cc_final: 0.8841 (mt) REVERT: E 203 ILE cc_start: 0.9143 (mm) cc_final: 0.8904 (mt) REVERT: F 203 ILE cc_start: 0.9089 (mm) cc_final: 0.8788 (mt) REVERT: G 203 ILE cc_start: 0.9140 (mm) cc_final: 0.8893 (mt) REVERT: I 22 ARG cc_start: 0.8815 (ttt180) cc_final: 0.8592 (ttm-80) REVERT: I 203 ILE cc_start: 0.9096 (mm) cc_final: 0.8787 (mt) REVERT: J 36 LEU cc_start: 0.9111 (tp) cc_final: 0.8892 (mt) REVERT: K 203 ILE cc_start: 0.9133 (mm) cc_final: 0.8883 (mt) REVERT: L 203 ILE cc_start: 0.9098 (mm) cc_final: 0.8786 (mt) outliers start: 46 outliers final: 44 residues processed: 281 average time/residue: 0.1784 time to fit residues: 72.2042 Evaluate side-chains 263 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 130 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 146 optimal weight: 3.9990 chunk 92 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 214 optimal weight: 0.0470 chunk 198 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.104084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.080719 restraints weight = 23124.894| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.23 r_work: 0.2668 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20352 Z= 0.115 Angle : 0.440 5.035 27732 Z= 0.224 Chirality : 0.039 0.254 3252 Planarity : 0.002 0.016 3180 Dihedral : 10.818 74.873 3897 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.23 % Allowed : 13.64 % Favored : 84.14 % 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: 3.75 (0.18), residues: 2304 helix: 3.84 (0.11), residues: 1632 sheet: 1.34 (0.50), residues: 132 loop : -1.93 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 15 TYR 0.006 0.001 TYR D 65 PHE 0.009 0.001 PHE F 51 TRP 0.007 0.001 TRP D 44 HIS 0.004 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00277 (20328) covalent geometry : angle 0.43854 (27684) SS BOND : bond 0.00195 ( 24) SS BOND : angle 0.97645 ( 48) hydrogen bonds : bond 0.02876 ( 1392) hydrogen bonds : angle 2.66669 ( 4140) *********************** 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 255 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9132 (mm) cc_final: 0.8885 (mt) REVERT: C 203 ILE cc_start: 0.9090 (mm) cc_final: 0.8775 (mt) REVERT: D 203 ILE cc_start: 0.9101 (mm) cc_final: 0.8790 (mt) REVERT: E 203 ILE cc_start: 0.9139 (mm) cc_final: 0.8892 (mt) REVERT: F 203 ILE cc_start: 0.9076 (mm) cc_final: 0.8762 (mt) REVERT: G 203 ILE cc_start: 0.9131 (mm) cc_final: 0.8878 (mt) REVERT: I 203 ILE cc_start: 0.9084 (mm) cc_final: 0.8763 (mt) REVERT: K 203 ILE cc_start: 0.9132 (mm) cc_final: 0.8877 (mt) REVERT: L 203 ILE cc_start: 0.9077 (mm) cc_final: 0.8763 (mt) outliers start: 47 outliers final: 45 residues processed: 255 average time/residue: 0.1920 time to fit residues: 70.4418 Evaluate side-chains 255 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 198 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 215 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.0010 chunk 103 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3100 r_free = 0.3100 target = 0.103752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.080257 restraints weight = 23186.887| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.28 r_work: 0.2667 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20352 Z= 0.095 Angle : 0.427 5.266 27732 Z= 0.217 Chirality : 0.039 0.263 3252 Planarity : 0.002 0.016 3180 Dihedral : 10.759 75.206 3897 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.39 % Favored : 98.52 % Rotamer: Outliers : 2.27 % Allowed : 13.73 % Favored : 84.00 % 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: 3.80 (0.18), residues: 2304 helix: 3.87 (0.11), residues: 1632 sheet: 1.34 (0.49), residues: 132 loop : -1.91 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 15 TYR 0.005 0.001 TYR D 65 PHE 0.009 0.001 PHE F 51 TRP 0.007 0.001 TRP J 44 HIS 0.004 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00220 (20328) covalent geometry : angle 0.42585 (27684) SS BOND : bond 0.00119 ( 24) SS BOND : angle 0.91850 ( 48) hydrogen bonds : bond 0.02784 ( 1392) hydrogen bonds : angle 2.62910 ( 4140) ********************** 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 262 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.9135 (mm) cc_final: 0.8889 (mt) REVERT: C 203 ILE cc_start: 0.9084 (mm) cc_final: 0.8768 (mt) REVERT: D 203 ILE cc_start: 0.9102 (mm) cc_final: 0.8809 (mt) REVERT: E 203 ILE cc_start: 0.9133 (mm) cc_final: 0.8886 (mt) REVERT: F 203 ILE cc_start: 0.9069 (mm) cc_final: 0.8754 (mt) REVERT: I 203 ILE cc_start: 0.9081 (mm) cc_final: 0.8760 (mt) REVERT: L 203 ILE cc_start: 0.9078 (mm) cc_final: 0.8755 (mt) outliers start: 48 outliers final: 46 residues processed: 262 average time/residue: 0.1757 time to fit residues: 66.0428 Evaluate side-chains 255 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 186 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 120 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.103629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.080091 restraints weight = 23261.030| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 1.28 r_work: 0.2663 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20352 Z= 0.098 Angle : 0.424 4.999 27732 Z= 0.217 Chirality : 0.039 0.245 3252 Planarity : 0.002 0.016 3180 Dihedral : 10.735 75.599 3897 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.52 % Allowed : 1.56 % Favored : 97.92 % Rotamer: Outliers : 2.23 % Allowed : 13.97 % Favored : 83.81 % 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: 3.81 (0.18), residues: 2304 helix: 3.87 (0.11), residues: 1632 sheet: 1.36 (0.50), residues: 132 loop : -1.88 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.005 0.001 TYR J 65 PHE 0.009 0.001 PHE G 51 TRP 0.007 0.001 TRP D 44 HIS 0.004 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00230 (20328) covalent geometry : angle 0.42282 (27684) SS BOND : bond 0.00140 ( 24) SS BOND : angle 0.91688 ( 48) hydrogen bonds : bond 0.02781 ( 1392) hydrogen bonds : angle 2.61877 ( 4140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4051.68 seconds wall clock time: 70 minutes 35.35 seconds (4235.35 seconds total)