Starting phenix.real_space_refine on Sun Aug 24 02:26:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv5_37865/08_2025/8wv5_37865.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv5_37865/08_2025/8wv5_37865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wv5_37865/08_2025/8wv5_37865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv5_37865/08_2025/8wv5_37865.map" model { file = "/net/cci-nas-00/data/ceres_data/8wv5_37865/08_2025/8wv5_37865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv5_37865/08_2025/8wv5_37865.cif" } resolution = 3.5 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= 0.005 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 Ca 20 9.91 5 S 40 5.16 5 C 10580 2.51 5 N 2610 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16340 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "F" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "H" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.46, per 1000 atoms: 0.21 Number of scatterers: 16340 At special positions: 0 Unit cell: (118.77, 155.15, 109.14, 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) Ca 20 19.99 S 40 16.00 O 3090 8.00 N 2610 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS F 36 " - pdb=" SG CYS F 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 36 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 36 " - pdb=" SG CYS J 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 97 " distance=2.04 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: 1.08 Conformation dependent library (CDL) restraints added in 569.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 42 sheets defined 7.3% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'E' and resid 43 through 46 removed outlier: 3.538A pdb=" N THR E 46 " --> pdb=" O LEU E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 167 through 177 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.873A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'B' and resid 43 through 46 removed outlier: 3.579A pdb=" N THR B 46 " --> pdb=" O LEU B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'D' and resid 43 through 46 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'F' and resid 43 through 46 removed outlier: 3.535A pdb=" N THR F 46 " --> pdb=" O LEU F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 46' Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'G' and resid 43 through 46 Processing helix chain 'G' and resid 167 through 177 Processing helix chain 'I' and resid 43 through 46 Processing helix chain 'I' and resid 167 through 177 Processing helix chain 'J' and resid 43 through 46 Processing helix chain 'J' and resid 167 through 177 Processing helix chain 'H' and resid 43 through 46 Processing helix chain 'H' and resid 167 through 177 Processing sheet with id=AA1, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.937A pdb=" N THR E 34 " --> pdb=" O TRP E 162 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N HIS E 38 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASN E 158 " --> pdb=" O HIS E 38 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR E 40 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE E 156 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE E 199 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 80 through 85 removed outlier: 3.655A pdb=" N SER E 80 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR E 73 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 66 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR E 76 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 64 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 21 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'E' and resid 139 through 141 removed outlier: 6.251A pdb=" N ASN E 145 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.770A pdb=" N THR A 34 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N HIS A 38 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASN A 158 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR A 40 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE A 156 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 199 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 80 through 85 removed outlier: 3.541A pdb=" N TYR A 73 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 64 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 52 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 21 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 193 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA8, first strand: chain 'A' and resid 139 through 141 removed outlier: 6.267A pdb=" N ASN A 145 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.309A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 199 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.655A pdb=" N TYR B 73 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 76 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 64 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 20 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER B 21 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 193 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.021A pdb=" N VAL B 107 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG B 118 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B 109 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 139 through 141 removed outlier: 6.375A pdb=" N ASN B 145 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 115 removed outlier: 4.375A pdb=" N ILE C 96 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 37 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 98 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 35 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 199 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 80 through 85 removed outlier: 3.595A pdb=" N THR C 76 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 64 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 20 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 195 " --> pdb=" O TYR C 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 21 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB7, first strand: chain 'C' and resid 139 through 141 removed outlier: 6.392A pdb=" N ASN C 145 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.765A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 96 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 37 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 98 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 199 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.689A pdb=" N TYR D 73 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.659A pdb=" N THR D 76 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 64 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE D 52 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 21 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 139 through 141 removed outlier: 6.393A pdb=" N ASN D 145 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 114 through 115 removed outlier: 4.239A pdb=" N ILE F 96 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU F 37 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR F 98 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 35 " --> pdb=" O THR F 98 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS F 38 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASN F 158 " --> pdb=" O HIS F 38 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR F 40 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE F 156 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASN F 158 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N LYS F 7 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE F 199 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 80 through 85 removed outlier: 3.674A pdb=" N TYR F 73 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR F 76 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 64 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE F 52 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP F 67 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER F 50 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL F 20 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER F 21 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU F 193 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AC7, first strand: chain 'F' and resid 139 through 141 removed outlier: 6.321A pdb=" N ASN F 145 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 114 through 115 Processing sheet with id=AC9, first strand: chain 'G' and resid 114 through 115 removed outlier: 3.941A pdb=" N ILE G 106 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR G 34 " --> pdb=" O TRP G 162 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS G 38 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASN G 158 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR G 40 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE G 156 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN G 158 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N LYS G 7 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE G 199 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 80 through 85 removed outlier: 3.614A pdb=" N TYR G 73 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR G 76 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU G 64 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TRP G 67 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER G 50 " --> pdb=" O TRP G 67 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE G 133 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL G 20 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN G 195 " --> pdb=" O TYR G 19 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER G 21 " --> pdb=" O GLU G 193 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 139 through 141 removed outlier: 6.357A pdb=" N ASN G 145 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 100 through 101 removed outlier: 6.833A pdb=" N THR I 34 " --> pdb=" O MET I 161 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET I 161 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS I 36 " --> pdb=" O VAL I 159 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL I 159 " --> pdb=" O CYS I 36 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN I 158 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N LYS I 7 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE I 199 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 80 through 83 removed outlier: 3.626A pdb=" N SER I 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE I 66 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR I 76 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU I 64 " --> pdb=" O THR I 76 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TRP I 67 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER I 50 " --> pdb=" O TRP I 67 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE I 133 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL I 20 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER I 21 " --> pdb=" O GLU I 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 96 through 97 Processing sheet with id=AD6, first strand: chain 'I' and resid 106 through 107 Processing sheet with id=AD7, first strand: chain 'J' and resid 114 through 115 removed outlier: 4.282A pdb=" N ILE J 96 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU J 37 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR J 98 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL J 35 " --> pdb=" O THR J 98 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR J 34 " --> pdb=" O TRP J 162 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS J 38 " --> pdb=" O ASN J 158 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN J 158 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR J 40 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE J 156 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN J 158 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N LYS J 7 " --> pdb=" O ASN J 158 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE J 199 " --> pdb=" O VAL J 10 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 80 through 85 removed outlier: 3.592A pdb=" N TYR J 73 " --> pdb=" O PHE J 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE J 66 " --> pdb=" O SER J 74 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 76 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU J 64 " --> pdb=" O THR J 76 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TRP J 67 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER J 50 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE J 133 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL J 20 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER J 21 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU J 193 " --> pdb=" O SER J 21 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 106 through 107 Processing sheet with id=AE1, first strand: chain 'J' and resid 139 through 141 removed outlier: 6.312A pdb=" N ASN J 145 " --> pdb=" O ASP J 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 114 through 115 removed outlier: 4.264A pdb=" N ILE H 96 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU H 37 " --> pdb=" O ILE H 96 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR H 98 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL H 35 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR H 34 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET H 161 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS H 36 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL H 159 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE H 199 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 80 through 81 removed outlier: 3.597A pdb=" N SER H 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR H 73 " --> pdb=" O PHE H 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 80 through 81 removed outlier: 3.597A pdb=" N SER H 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE H 66 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 76 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU H 64 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP H 67 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER H 50 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL H 20 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 106 through 107 Processing sheet with id=AE6, first strand: chain 'H' and resid 139 through 141 removed outlier: 6.338A pdb=" N ASN H 145 " --> pdb=" O ASP H 140 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5080 1.35 - 1.47: 4492 1.47 - 1.59: 7148 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 16780 Sorted by residual: bond pdb=" N VAL F 86 " pdb=" CA VAL F 86 " ideal model delta sigma weight residual 1.454 1.462 -0.007 7.70e-03 1.69e+04 9.32e-01 bond pdb=" N VAL C 86 " pdb=" CA VAL C 86 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 7.71e-01 bond pdb=" N GLY I 178 " pdb=" CA GLY I 178 " ideal model delta sigma weight residual 1.434 1.444 -0.010 1.22e-02 6.72e+03 6.92e-01 bond pdb=" N SER C 181 " pdb=" CA SER C 181 " ideal model delta sigma weight residual 1.463 1.455 0.007 8.80e-03 1.29e+04 6.87e-01 bond pdb=" C VAL E 153 " pdb=" N GLY E 154 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 6.85e-01 ... (remaining 16775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 22020 1.08 - 2.15: 601 2.15 - 3.23: 167 3.23 - 4.31: 14 4.31 - 5.38: 8 Bond angle restraints: 22810 Sorted by residual: angle pdb=" N THR G 17 " pdb=" CA THR G 17 " pdb=" C THR G 17 " ideal model delta sigma weight residual 114.31 109.95 4.36 1.29e+00 6.01e-01 1.14e+01 angle pdb=" N THR E 17 " pdb=" CA THR E 17 " pdb=" C THR E 17 " ideal model delta sigma weight residual 114.31 110.46 3.85 1.29e+00 6.01e-01 8.91e+00 angle pdb=" N THR D 17 " pdb=" CA THR D 17 " pdb=" C THR D 17 " ideal model delta sigma weight residual 114.31 110.55 3.76 1.29e+00 6.01e-01 8.49e+00 angle pdb=" N THR H 17 " pdb=" CA THR H 17 " pdb=" C THR H 17 " ideal model delta sigma weight residual 114.31 110.65 3.66 1.29e+00 6.01e-01 8.06e+00 angle pdb=" N THR A 17 " pdb=" CA THR A 17 " pdb=" C THR A 17 " ideal model delta sigma weight residual 114.56 110.95 3.61 1.27e+00 6.20e-01 8.06e+00 ... (remaining 22805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9084 17.80 - 35.59: 573 35.59 - 53.39: 90 53.39 - 71.19: 33 71.19 - 88.98: 10 Dihedral angle restraints: 9790 sinusoidal: 3880 harmonic: 5910 Sorted by residual: dihedral pdb=" CB CYS I 36 " pdb=" SG CYS I 36 " pdb=" SG CYS I 97 " pdb=" CB CYS I 97 " ideal model delta sinusoidal sigma weight residual 93.00 14.18 78.82 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS D 36 " pdb=" SG CYS D 36 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual -86.00 -40.91 -45.09 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS E 36 " pdb=" SG CYS E 36 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual -86.00 -44.00 -42.00 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 9787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1400 0.026 - 0.051: 610 0.051 - 0.077: 182 0.077 - 0.103: 160 0.103 - 0.129: 118 Chirality restraints: 2470 Sorted by residual: chirality pdb=" CA ILE A 63 " pdb=" N ILE A 63 " pdb=" C ILE A 63 " pdb=" CB ILE A 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE F 63 " pdb=" N ILE F 63 " pdb=" C ILE F 63 " pdb=" CB ILE F 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE C 63 " pdb=" N ILE C 63 " pdb=" C ILE C 63 " pdb=" CB ILE C 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 2467 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 167 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO D 168 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 168 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 35 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C VAL C 35 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL C 35 " 0.008 2.00e-02 2.50e+03 pdb=" N CYS C 36 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 167 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO E 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.016 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 138 2.43 - 3.05: 9726 3.05 - 3.66: 24069 3.66 - 4.28: 36448 4.28 - 4.90: 62114 Nonbonded interactions: 132495 Sorted by model distance: nonbonded pdb=" CD GLU H 147 " pdb="CA CA H 301 " model vdw 1.812 2.740 nonbonded pdb=" OE1 GLU H 147 " pdb="CA CA H 301 " model vdw 2.018 2.510 nonbonded pdb=" OG1 THR I 98 " pdb=" O GLU I 108 " model vdw 2.207 3.040 nonbonded pdb=" CG GLU I 147 " pdb="CA CA I 301 " model vdw 2.221 2.910 nonbonded pdb=" OG1 THR J 98 " pdb=" O GLU J 108 " model vdw 2.231 3.040 ... (remaining 132490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.190 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16790 Z= 0.104 Angle : 0.473 5.760 22830 Z= 0.291 Chirality : 0.043 0.129 2470 Planarity : 0.003 0.032 2900 Dihedral : 12.215 88.982 5980 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.38 (0.15), residues: 2040 helix: 1.67 (0.44), residues: 110 sheet: -2.26 (0.19), residues: 570 loop : -2.74 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 118 TYR 0.006 0.001 TYR F 54 PHE 0.006 0.001 PHE J 199 TRP 0.004 0.000 TRP J 100 HIS 0.002 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00176 (16780) covalent geometry : angle 0.46831 (22810) SS BOND : bond 0.00643 ( 10) SS BOND : angle 2.18805 ( 20) hydrogen bonds : bond 0.28576 ( 495) hydrogen bonds : angle 10.99372 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 ARG cc_start: 0.8396 (mmm160) cc_final: 0.8121 (mmm160) REVERT: E 54 TYR cc_start: 0.9058 (t80) cc_final: 0.8646 (t80) REVERT: E 108 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8058 (mt-10) REVERT: E 130 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 172 ASN cc_start: 0.9367 (t0) cc_final: 0.8967 (t0) REVERT: A 3 ASP cc_start: 0.8999 (t0) cc_final: 0.8797 (t0) REVERT: A 186 ASN cc_start: 0.9316 (t0) cc_final: 0.8949 (t0) REVERT: B 47 ARG cc_start: 0.7970 (ptt90) cc_final: 0.7708 (ptt-90) REVERT: B 195 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7580 (tp40) REVERT: C 19 TYR cc_start: 0.8563 (p90) cc_final: 0.7329 (p90) REVERT: C 114 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8691 (mmmt) REVERT: C 122 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8645 (mmtt) REVERT: C 186 ASN cc_start: 0.9284 (t0) cc_final: 0.8818 (t0) REVERT: D 3 ASP cc_start: 0.8970 (t0) cc_final: 0.8516 (t70) REVERT: D 70 ASP cc_start: 0.8383 (t0) cc_final: 0.8103 (t0) REVERT: D 98 THR cc_start: 0.8083 (t) cc_final: 0.7599 (t) REVERT: D 195 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8076 (mm-40) REVERT: F 23 LYS cc_start: 0.8843 (mptt) cc_final: 0.8070 (mmtt) REVERT: F 82 ILE cc_start: 0.8944 (pt) cc_final: 0.8594 (pt) REVERT: F 122 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8491 (mmtm) REVERT: F 150 GLN cc_start: 0.7896 (mt0) cc_final: 0.7343 (mm-40) REVERT: F 170 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7258 (mp0) REVERT: I 6 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8491 (mmm-85) REVERT: I 28 LYS cc_start: 0.9288 (mtpt) cc_final: 0.9013 (ttpt) REVERT: I 40 TYR cc_start: 0.9041 (t80) cc_final: 0.8644 (t80) REVERT: I 125 TYR cc_start: 0.8743 (t80) cc_final: 0.8512 (t80) REVERT: I 158 ASN cc_start: 0.8130 (m-40) cc_final: 0.7586 (t0) REVERT: J 172 ASN cc_start: 0.9093 (t0) cc_final: 0.8859 (t0) REVERT: H 122 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8272 (mmtp) REVERT: H 195 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7450 (tp-100) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.1590 time to fit residues: 106.1977 Evaluate side-chains 273 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.0070 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 203 GLN D 1 GLN D 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS H 38 HIS H 137 GLN H 195 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.061176 restraints weight = 47147.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.063383 restraints weight = 20904.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.064895 restraints weight = 12258.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065932 restraints weight = 8401.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.066599 restraints weight = 6371.177| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16790 Z= 0.112 Angle : 0.542 9.133 22830 Z= 0.287 Chirality : 0.047 0.143 2470 Planarity : 0.004 0.063 2900 Dihedral : 3.686 15.795 2200 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.44 % Allowed : 12.00 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.17), residues: 2040 helix: 2.63 (0.45), residues: 110 sheet: -1.88 (0.16), residues: 870 loop : -2.18 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 58 TYR 0.020 0.001 TYR H 54 PHE 0.020 0.001 PHE A 39 TRP 0.010 0.001 TRP D 110 HIS 0.006 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00252 (16780) covalent geometry : angle 0.53398 (22810) SS BOND : bond 0.00678 ( 10) SS BOND : angle 3.11478 ( 20) hydrogen bonds : bond 0.04485 ( 495) hydrogen bonds : angle 6.98201 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 285 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 6 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8069 (mmm160) REVERT: E 54 TYR cc_start: 0.9161 (t80) cc_final: 0.8914 (t80) REVERT: E 172 ASN cc_start: 0.9419 (t0) cc_final: 0.8951 (t0) REVERT: E 176 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8698 (mm) REVERT: E 203 GLN cc_start: 0.8707 (pt0) cc_final: 0.8466 (pt0) REVERT: A 3 ASP cc_start: 0.9109 (t0) cc_final: 0.8891 (t0) REVERT: A 19 TYR cc_start: 0.8279 (p90) cc_final: 0.7944 (p90) REVERT: A 186 ASN cc_start: 0.9263 (t0) cc_final: 0.8903 (t0) REVERT: C 60 ASP cc_start: 0.7468 (p0) cc_final: 0.7253 (p0) REVERT: C 122 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8810 (mmtt) REVERT: C 125 TYR cc_start: 0.8827 (t80) cc_final: 0.8444 (t80) REVERT: C 161 MET cc_start: 0.8309 (ttp) cc_final: 0.8011 (ttp) REVERT: C 186 ASN cc_start: 0.9250 (t0) cc_final: 0.8708 (t0) REVERT: D 3 ASP cc_start: 0.9048 (t0) cc_final: 0.8732 (t70) REVERT: D 49 TYR cc_start: 0.9263 (p90) cc_final: 0.8982 (p90) REVERT: D 70 ASP cc_start: 0.8285 (t0) cc_final: 0.8069 (t0) REVERT: D 172 ASN cc_start: 0.9257 (t0) cc_final: 0.9010 (t0) REVERT: F 16 ASP cc_start: 0.8160 (m-30) cc_final: 0.7833 (m-30) REVERT: F 23 LYS cc_start: 0.8948 (mptt) cc_final: 0.8618 (mmtt) REVERT: G 150 GLN cc_start: 0.8702 (mt0) cc_final: 0.8261 (mt0) REVERT: I 6 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8449 (mmm-85) REVERT: I 125 TYR cc_start: 0.8776 (t80) cc_final: 0.8519 (t80) REVERT: I 150 GLN cc_start: 0.9032 (mt0) cc_final: 0.8806 (mt0) REVERT: I 158 ASN cc_start: 0.8263 (m-40) cc_final: 0.7611 (t0) REVERT: J 161 MET cc_start: 0.8409 (ttt) cc_final: 0.8083 (ttm) REVERT: J 172 ASN cc_start: 0.9169 (t0) cc_final: 0.8961 (t0) REVERT: H 122 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8185 (mmtp) outliers start: 26 outliers final: 10 residues processed: 305 average time/residue: 0.1305 time to fit residues: 58.7496 Evaluate side-chains 249 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 238 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain H residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 172 ASN ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN C 145 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 ASN ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.061707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.049659 restraints weight = 50056.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.051682 restraints weight = 22579.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.053055 restraints weight = 13556.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.054020 restraints weight = 9630.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.054616 restraints weight = 7537.078| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 16790 Z= 0.389 Angle : 0.725 13.143 22830 Z= 0.382 Chirality : 0.050 0.238 2470 Planarity : 0.005 0.058 2900 Dihedral : 4.957 36.074 2200 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.50 % Allowed : 14.33 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.17), residues: 2040 helix: 2.91 (0.42), residues: 110 sheet: -1.75 (0.15), residues: 940 loop : -1.98 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 58 TYR 0.022 0.002 TYR G 175 PHE 0.020 0.002 PHE C 52 TRP 0.016 0.002 TRP C 100 HIS 0.009 0.003 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00897 (16780) covalent geometry : angle 0.71035 (22810) SS BOND : bond 0.01785 ( 10) SS BOND : angle 5.02184 ( 20) hydrogen bonds : bond 0.05115 ( 495) hydrogen bonds : angle 6.42714 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9415 (t0) cc_final: 0.9017 (t0) REVERT: E 176 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8842 (mm) REVERT: E 203 GLN cc_start: 0.8760 (pt0) cc_final: 0.8010 (pt0) REVERT: B 91 VAL cc_start: 0.8899 (m) cc_final: 0.8599 (p) REVERT: C 60 ASP cc_start: 0.7516 (p0) cc_final: 0.7189 (p0) REVERT: C 122 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8856 (mmtt) REVERT: C 186 ASN cc_start: 0.9440 (t0) cc_final: 0.9171 (t0) REVERT: D 49 TYR cc_start: 0.9337 (p90) cc_final: 0.9075 (p90) REVERT: D 203 GLN cc_start: 0.9066 (pt0) cc_final: 0.8592 (pt0) REVERT: F 23 LYS cc_start: 0.8866 (mptt) cc_final: 0.8554 (mmtt) REVERT: I 125 TYR cc_start: 0.8841 (t80) cc_final: 0.8640 (t80) REVERT: J 49 TYR cc_start: 0.9268 (p90) cc_final: 0.8945 (p90) REVERT: J 172 ASN cc_start: 0.9360 (t0) cc_final: 0.9138 (t0) REVERT: J 195 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7818 (mm-40) outliers start: 45 outliers final: 27 residues processed: 248 average time/residue: 0.1349 time to fit residues: 48.8356 Evaluate side-chains 208 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 187 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 137 optimal weight: 0.0870 chunk 174 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS F 158 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.064544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.052639 restraints weight = 48919.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.054709 restraints weight = 21698.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056115 restraints weight = 12861.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.057093 restraints weight = 9002.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.057719 restraints weight = 6970.654| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16790 Z= 0.143 Angle : 0.564 12.447 22830 Z= 0.297 Chirality : 0.047 0.178 2470 Planarity : 0.004 0.046 2900 Dihedral : 4.496 31.749 2200 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.00 % Allowed : 15.67 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.18), residues: 2040 helix: 3.47 (0.41), residues: 110 sheet: -1.37 (0.17), residues: 850 loop : -1.61 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 58 TYR 0.016 0.001 TYR C 19 PHE 0.013 0.001 PHE A 39 TRP 0.010 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00340 (16780) covalent geometry : angle 0.55030 (22810) SS BOND : bond 0.00983 ( 10) SS BOND : angle 4.24713 ( 20) hydrogen bonds : bond 0.03817 ( 495) hydrogen bonds : angle 6.14005 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.9182 (t80) cc_final: 0.8969 (t80) REVERT: E 172 ASN cc_start: 0.9374 (t0) cc_final: 0.8863 (t0) REVERT: E 176 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8848 (mm) REVERT: E 203 GLN cc_start: 0.8808 (pt0) cc_final: 0.8197 (pt0) REVERT: A 112 ASP cc_start: 0.9172 (m-30) cc_final: 0.8971 (m-30) REVERT: A 186 ASN cc_start: 0.9243 (t0) cc_final: 0.8918 (t0) REVERT: B 91 VAL cc_start: 0.8817 (m) cc_final: 0.8547 (p) REVERT: C 60 ASP cc_start: 0.7627 (p0) cc_final: 0.7332 (p0) REVERT: C 122 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8782 (mmtt) REVERT: C 186 ASN cc_start: 0.9428 (t0) cc_final: 0.9103 (t0) REVERT: D 49 TYR cc_start: 0.9330 (p90) cc_final: 0.8980 (p90) REVERT: D 203 GLN cc_start: 0.8970 (pt0) cc_final: 0.8531 (pt0) REVERT: F 23 LYS cc_start: 0.8830 (mptt) cc_final: 0.8433 (mmtt) REVERT: F 192 TYR cc_start: 0.9010 (p90) cc_final: 0.8782 (p90) REVERT: J 49 TYR cc_start: 0.9283 (p90) cc_final: 0.9021 (p90) REVERT: J 172 ASN cc_start: 0.9349 (t0) cc_final: 0.9129 (t0) REVERT: J 175 TYR cc_start: 0.9497 (t80) cc_final: 0.9201 (t80) REVERT: J 195 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7694 (mm-40) REVERT: H 122 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8164 (mmtp) outliers start: 36 outliers final: 27 residues processed: 245 average time/residue: 0.1335 time to fit residues: 47.7786 Evaluate side-chains 222 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 97 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 188 optimal weight: 0.0020 chunk 142 optimal weight: 0.6980 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN A 195 GLN C 160 ASN C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 ASN ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.065062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.053054 restraints weight = 48403.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.055165 restraints weight = 21521.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.056600 restraints weight = 12779.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.057604 restraints weight = 8952.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.058243 restraints weight = 6926.406| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16790 Z= 0.113 Angle : 0.544 13.720 22830 Z= 0.284 Chirality : 0.047 0.158 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.249 27.947 2200 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.28 % Allowed : 16.28 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.18), residues: 2040 helix: 3.76 (0.41), residues: 110 sheet: -1.16 (0.18), residues: 850 loop : -1.38 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 6 TYR 0.021 0.001 TYR G 125 PHE 0.011 0.001 PHE A 39 TRP 0.010 0.001 TRP D 110 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00271 (16780) covalent geometry : angle 0.53097 (22810) SS BOND : bond 0.01163 ( 10) SS BOND : angle 3.95719 ( 20) hydrogen bonds : bond 0.03446 ( 495) hydrogen bonds : angle 5.95599 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.9174 (t80) cc_final: 0.8973 (t80) REVERT: E 172 ASN cc_start: 0.9369 (t0) cc_final: 0.8882 (t0) REVERT: E 176 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8774 (mm) REVERT: E 203 GLN cc_start: 0.8743 (pt0) cc_final: 0.8170 (pt0) REVERT: A 112 ASP cc_start: 0.9179 (m-30) cc_final: 0.8970 (m-30) REVERT: A 186 ASN cc_start: 0.9279 (t0) cc_final: 0.8949 (t0) REVERT: B 91 VAL cc_start: 0.8860 (m) cc_final: 0.8593 (p) REVERT: C 60 ASP cc_start: 0.7691 (p0) cc_final: 0.7398 (p0) REVERT: C 122 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8793 (mmtt) REVERT: C 186 ASN cc_start: 0.9434 (t0) cc_final: 0.9147 (t0) REVERT: D 49 TYR cc_start: 0.9326 (p90) cc_final: 0.8947 (p90) REVERT: D 203 GLN cc_start: 0.8896 (pt0) cc_final: 0.8495 (pt0) REVERT: F 23 LYS cc_start: 0.8890 (mptt) cc_final: 0.8478 (mmtt) REVERT: I 37 LEU cc_start: 0.8766 (pt) cc_final: 0.8505 (pp) REVERT: I 98 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7764 (t) REVERT: I 125 TYR cc_start: 0.8601 (t80) cc_final: 0.7864 (t80) REVERT: J 49 TYR cc_start: 0.9277 (p90) cc_final: 0.9069 (p90) REVERT: J 172 ASN cc_start: 0.9350 (t0) cc_final: 0.9123 (t0) REVERT: J 195 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7864 (mm-40) REVERT: H 161 MET cc_start: 0.8208 (ttt) cc_final: 0.7992 (ttt) outliers start: 41 outliers final: 28 residues processed: 252 average time/residue: 0.1396 time to fit residues: 50.7088 Evaluate side-chains 229 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 194 optimal weight: 0.0170 chunk 51 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 overall best weight: 2.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN B 195 GLN C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.064519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.052674 restraints weight = 48810.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.054768 restraints weight = 21613.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.056183 restraints weight = 12780.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.057168 restraints weight = 8928.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.057795 restraints weight = 6912.546| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16790 Z= 0.155 Angle : 0.560 12.367 22830 Z= 0.294 Chirality : 0.047 0.162 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.309 29.928 2200 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.56 % Allowed : 17.06 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.18), residues: 2040 helix: 3.85 (0.40), residues: 110 sheet: -1.06 (0.18), residues: 850 loop : -1.26 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 58 TYR 0.026 0.001 TYR G 125 PHE 0.017 0.001 PHE D 180 TRP 0.009 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00366 (16780) covalent geometry : angle 0.54636 (22810) SS BOND : bond 0.01120 ( 10) SS BOND : angle 4.24534 ( 20) hydrogen bonds : bond 0.03514 ( 495) hydrogen bonds : angle 5.88441 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9364 (t0) cc_final: 0.8858 (t0) REVERT: E 176 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8733 (mm) REVERT: E 203 GLN cc_start: 0.8743 (pt0) cc_final: 0.8179 (pt0) REVERT: A 112 ASP cc_start: 0.9183 (m-30) cc_final: 0.8975 (m-30) REVERT: A 186 ASN cc_start: 0.9291 (t0) cc_final: 0.8949 (t0) REVERT: A 194 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8969 (t) REVERT: B 91 VAL cc_start: 0.8840 (m) cc_final: 0.8580 (p) REVERT: B 195 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: C 60 ASP cc_start: 0.7707 (p0) cc_final: 0.7411 (p0) REVERT: C 122 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8786 (mmtt) REVERT: C 186 ASN cc_start: 0.9434 (t0) cc_final: 0.9126 (t0) REVERT: D 49 TYR cc_start: 0.9332 (p90) cc_final: 0.8970 (p90) REVERT: F 23 LYS cc_start: 0.8861 (mptt) cc_final: 0.8429 (mmtt) REVERT: F 195 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8239 (mm-40) REVERT: G 195 GLN cc_start: 0.7627 (tp40) cc_final: 0.7279 (tp40) REVERT: I 6 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8416 (mmm-85) REVERT: I 125 TYR cc_start: 0.8681 (t80) cc_final: 0.7997 (t80) REVERT: J 172 ASN cc_start: 0.9365 (t0) cc_final: 0.9135 (t0) REVERT: J 195 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7985 (mm-40) outliers start: 46 outliers final: 35 residues processed: 244 average time/residue: 0.1255 time to fit residues: 45.1110 Evaluate side-chains 229 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 180 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 102 optimal weight: 0.0470 chunk 109 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS H 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.062211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.050221 restraints weight = 48903.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.052261 restraints weight = 22038.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.053657 restraints weight = 13231.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.054566 restraints weight = 9365.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.055231 restraints weight = 7394.741| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16790 Z= 0.269 Angle : 0.637 12.430 22830 Z= 0.333 Chirality : 0.048 0.200 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.735 35.880 2200 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.83 % Allowed : 17.78 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.18), residues: 2040 helix: 3.56 (0.41), residues: 110 sheet: -1.10 (0.17), residues: 940 loop : -1.41 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 58 TYR 0.022 0.001 TYR G 125 PHE 0.018 0.002 PHE D 75 TRP 0.012 0.001 TRP C 100 HIS 0.007 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00629 (16780) covalent geometry : angle 0.61915 (22810) SS BOND : bond 0.01135 ( 10) SS BOND : angle 5.05827 ( 20) hydrogen bonds : bond 0.03998 ( 495) hydrogen bonds : angle 5.95895 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9344 (t0) cc_final: 0.8881 (t0) REVERT: E 176 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8892 (mm) REVERT: E 203 GLN cc_start: 0.8766 (pt0) cc_final: 0.8218 (pt0) REVERT: A 186 ASN cc_start: 0.9270 (t0) cc_final: 0.8918 (t0) REVERT: B 91 VAL cc_start: 0.8876 (m) cc_final: 0.8627 (p) REVERT: C 60 ASP cc_start: 0.7684 (p0) cc_final: 0.7418 (p0) REVERT: C 122 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8814 (mmtt) REVERT: C 186 ASN cc_start: 0.9466 (t0) cc_final: 0.9149 (t0) REVERT: D 49 TYR cc_start: 0.9367 (p90) cc_final: 0.9054 (p90) REVERT: F 23 LYS cc_start: 0.8871 (mptt) cc_final: 0.8474 (mmtt) REVERT: F 73 TYR cc_start: 0.9110 (m-80) cc_final: 0.8825 (m-80) REVERT: F 195 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8460 (mm-40) REVERT: G 195 GLN cc_start: 0.7661 (tp40) cc_final: 0.7371 (tp40) REVERT: I 6 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8654 (mmm-85) REVERT: I 125 TYR cc_start: 0.8727 (t80) cc_final: 0.8110 (t80) REVERT: J 172 ASN cc_start: 0.9398 (t0) cc_final: 0.9177 (t0) REVERT: J 195 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8060 (mm-40) outliers start: 51 outliers final: 39 residues processed: 238 average time/residue: 0.1299 time to fit residues: 45.4199 Evaluate side-chains 225 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 163 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.052433 restraints weight = 48500.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.054527 restraints weight = 21523.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.055951 restraints weight = 12748.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.056930 restraints weight = 8916.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.057547 restraints weight = 6913.390| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16790 Z= 0.132 Angle : 0.584 11.552 22830 Z= 0.305 Chirality : 0.047 0.170 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.508 31.174 2200 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.39 % Allowed : 18.89 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.18), residues: 2040 helix: 3.73 (0.41), residues: 110 sheet: -0.96 (0.17), residues: 940 loop : -1.23 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 58 TYR 0.018 0.001 TYR B 73 PHE 0.016 0.001 PHE J 39 TRP 0.010 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00315 (16780) covalent geometry : angle 0.56578 (22810) SS BOND : bond 0.01261 ( 10) SS BOND : angle 4.87565 ( 20) hydrogen bonds : bond 0.03467 ( 495) hydrogen bonds : angle 5.91898 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 ILE cc_start: 0.9267 (pp) cc_final: 0.9031 (pp) REVERT: E 172 ASN cc_start: 0.9342 (t0) cc_final: 0.8832 (t0) REVERT: E 176 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8744 (mm) REVERT: E 203 GLN cc_start: 0.8717 (pt0) cc_final: 0.8157 (pt0) REVERT: A 186 ASN cc_start: 0.9277 (t0) cc_final: 0.8897 (t0) REVERT: B 91 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8593 (p) REVERT: B 195 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7565 (mp10) REVERT: C 60 ASP cc_start: 0.7608 (p0) cc_final: 0.7298 (p0) REVERT: C 122 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8790 (mmtt) REVERT: C 186 ASN cc_start: 0.9437 (t0) cc_final: 0.9077 (t0) REVERT: C 195 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6290 (pp30) REVERT: D 14 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: D 49 TYR cc_start: 0.9375 (p90) cc_final: 0.9040 (p90) REVERT: D 203 GLN cc_start: 0.8831 (pt0) cc_final: 0.8495 (pt0) REVERT: F 23 LYS cc_start: 0.8840 (mptt) cc_final: 0.8423 (mmtt) REVERT: F 73 TYR cc_start: 0.9052 (m-80) cc_final: 0.8763 (m-80) REVERT: F 195 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8430 (mm-40) REVERT: G 195 GLN cc_start: 0.7594 (tp40) cc_final: 0.7245 (tp40) REVERT: I 6 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8540 (mmm-85) REVERT: I 125 TYR cc_start: 0.8667 (t80) cc_final: 0.8024 (t80) REVERT: J 161 MET cc_start: 0.8687 (ttm) cc_final: 0.8435 (ttm) REVERT: J 172 ASN cc_start: 0.9389 (t0) cc_final: 0.9169 (t0) REVERT: J 195 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7894 (mm-40) outliers start: 43 outliers final: 35 residues processed: 237 average time/residue: 0.1339 time to fit residues: 46.3327 Evaluate side-chains 232 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 93 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 145 ASN C 195 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.062544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.050609 restraints weight = 48819.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.052662 restraints weight = 21763.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.054062 restraints weight = 12996.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.054974 restraints weight = 9149.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.055655 restraints weight = 7198.072| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16790 Z= 0.225 Angle : 0.629 12.223 22830 Z= 0.328 Chirality : 0.048 0.189 2470 Planarity : 0.004 0.046 2900 Dihedral : 4.716 34.035 2200 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.28 % Allowed : 19.50 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.18), residues: 2040 helix: 3.55 (0.41), residues: 110 sheet: -0.98 (0.17), residues: 940 loop : -1.26 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 58 TYR 0.015 0.001 TYR G 125 PHE 0.016 0.001 PHE D 75 TRP 0.011 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00530 (16780) covalent geometry : angle 0.60977 (22810) SS BOND : bond 0.01221 ( 10) SS BOND : angle 5.19484 ( 20) hydrogen bonds : bond 0.03817 ( 495) hydrogen bonds : angle 5.89934 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9334 (t0) cc_final: 0.8869 (t0) REVERT: E 176 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8862 (mm) REVERT: E 203 GLN cc_start: 0.8730 (pt0) cc_final: 0.8051 (pt0) REVERT: A 186 ASN cc_start: 0.9287 (t0) cc_final: 0.8923 (t0) REVERT: B 91 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8590 (p) REVERT: B 195 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7620 (mp10) REVERT: C 60 ASP cc_start: 0.7678 (p0) cc_final: 0.7385 (p0) REVERT: C 186 ASN cc_start: 0.9454 (t0) cc_final: 0.9106 (t0) REVERT: C 195 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6925 (pp30) REVERT: D 14 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: D 49 TYR cc_start: 0.9380 (p90) cc_final: 0.9065 (p90) REVERT: D 203 GLN cc_start: 0.8954 (pt0) cc_final: 0.8562 (pt0) REVERT: F 23 LYS cc_start: 0.8839 (mptt) cc_final: 0.8415 (mmtt) REVERT: F 73 TYR cc_start: 0.9116 (m-80) cc_final: 0.8808 (m-80) REVERT: F 195 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8522 (mm-40) REVERT: G 195 GLN cc_start: 0.7652 (tp40) cc_final: 0.7304 (tp40) REVERT: I 6 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8628 (mmm-85) REVERT: I 125 TYR cc_start: 0.8727 (t80) cc_final: 0.8141 (t80) REVERT: J 161 MET cc_start: 0.8725 (ttm) cc_final: 0.8478 (ttm) REVERT: J 172 ASN cc_start: 0.9406 (t0) cc_final: 0.9191 (t0) REVERT: J 195 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7940 (mm-40) outliers start: 41 outliers final: 36 residues processed: 225 average time/residue: 0.1399 time to fit residues: 45.2850 Evaluate side-chains 229 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 170 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 195 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.052313 restraints weight = 48329.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.054403 restraints weight = 21521.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.055823 restraints weight = 12811.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.056776 restraints weight = 9004.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.057399 restraints weight = 7036.955| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16790 Z= 0.135 Angle : 0.596 12.699 22830 Z= 0.311 Chirality : 0.047 0.167 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.518 30.062 2200 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.11 % Allowed : 19.83 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.19), residues: 2040 helix: 3.73 (0.41), residues: 110 sheet: -0.85 (0.17), residues: 940 loop : -1.13 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 58 TYR 0.016 0.001 TYR H 54 PHE 0.015 0.001 PHE D 75 TRP 0.009 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00326 (16780) covalent geometry : angle 0.57633 (22810) SS BOND : bond 0.01263 ( 10) SS BOND : angle 5.20523 ( 20) hydrogen bonds : bond 0.03397 ( 495) hydrogen bonds : angle 5.87458 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: E 96 ILE cc_start: 0.9249 (pp) cc_final: 0.9017 (pp) REVERT: E 172 ASN cc_start: 0.9336 (t0) cc_final: 0.8820 (t0) REVERT: E 176 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8693 (mm) REVERT: E 203 GLN cc_start: 0.8692 (pt0) cc_final: 0.8205 (pt0) REVERT: A 70 ASP cc_start: 0.8008 (m-30) cc_final: 0.7569 (p0) REVERT: A 186 ASN cc_start: 0.9273 (t0) cc_final: 0.8905 (t0) REVERT: B 91 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8595 (p) REVERT: C 60 ASP cc_start: 0.7659 (p0) cc_final: 0.7354 (p0) REVERT: C 122 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8728 (mmtm) REVERT: C 186 ASN cc_start: 0.9414 (t0) cc_final: 0.8988 (t0) REVERT: D 14 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: D 49 TYR cc_start: 0.9377 (p90) cc_final: 0.9048 (p90) REVERT: D 203 GLN cc_start: 0.8860 (pt0) cc_final: 0.8489 (pt0) REVERT: F 23 LYS cc_start: 0.8816 (mptt) cc_final: 0.8399 (mmtt) REVERT: F 73 TYR cc_start: 0.9044 (m-80) cc_final: 0.8724 (m-80) REVERT: F 195 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8558 (mm-40) REVERT: G 195 GLN cc_start: 0.7597 (tp40) cc_final: 0.7225 (tp40) REVERT: I 6 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8517 (mmm-85) REVERT: I 125 TYR cc_start: 0.8695 (t80) cc_final: 0.8131 (t80) REVERT: J 161 MET cc_start: 0.8698 (ttm) cc_final: 0.8456 (ttm) REVERT: J 172 ASN cc_start: 0.9399 (t0) cc_final: 0.9179 (t0) REVERT: J 195 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8051 (mm-40) outliers start: 38 outliers final: 33 residues processed: 232 average time/residue: 0.1463 time to fit residues: 48.9142 Evaluate side-chains 232 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 25 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN B 195 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.063583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.051699 restraints weight = 48637.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.053770 restraints weight = 21802.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.055180 restraints weight = 13025.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.056138 restraints weight = 9171.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.056774 restraints weight = 7158.142| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16790 Z= 0.179 Angle : 0.632 19.102 22830 Z= 0.328 Chirality : 0.048 0.218 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.589 32.034 2200 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.22 % Allowed : 19.61 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.18), residues: 2040 helix: 3.67 (0.41), residues: 110 sheet: -0.87 (0.17), residues: 940 loop : -1.12 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 58 TYR 0.020 0.001 TYR A 192 PHE 0.015 0.001 PHE D 75 TRP 0.010 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00428 (16780) covalent geometry : angle 0.60932 (22810) SS BOND : bond 0.01392 ( 10) SS BOND : angle 5.65233 ( 20) hydrogen bonds : bond 0.03580 ( 495) hydrogen bonds : angle 5.86614 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.51 seconds wall clock time: 41 minutes 36.79 seconds (2496.79 seconds total)