Starting phenix.real_space_refine on Fri Jul 3 21:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv5_37865/07_2026/8wv5_37865.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv5_37865/07_2026/8wv5_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wv5_37865/07_2026/8wv5_37865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv5_37865/07_2026/8wv5_37865.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wv5_37865/07_2026/8wv5_37865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv5_37865/07_2026/8wv5_37865.map" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 3.69, per 1000 atoms: 0.23 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: 1.11 Conformation dependent library (CDL) restraints added in 739.5 milliseconds 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: 0.69 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: 2.61 Time building geometry restraints manager: 1.60 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 3.480 nonbonded pdb=" OE1 GLU H 147 " pdb="CA CA H 301 " model vdw 2.018 3.250 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 3.650 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: 0.01 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 are 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/Z covalent geometry : bond 0.00176 / 0.10 (16780) covalent geometry : angle 0.46831 / 0.29 (22810) SS BOND : bond 0.00643 / 0.37 ( 10) SS BOND : angle 2.18805 / 1.28 ( 20) hydrogen bonds : bond 0.28576 / 18.98 ( 495) hydrogen bonds : angle 10.99372 / 7.47 ( 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 : 0.632 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: 0.7600 (t) REVERT: D 195 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8077 (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: 0.7851 (tp-100) cc_final: 0.7450 (tp-100) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.1446 time to fit residues: 97.9346 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 : 0.620 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 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: 1.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** G 150 GLN ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.058509 restraints weight = 47454.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.060703 restraints weight = 20901.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.062187 restraints weight = 12198.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.063164 restraints weight = 8370.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.063853 restraints weight = 6414.604| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16790 Z= 0.149 Angle : 0.557 9.262 22830 Z= 0.297 Chirality : 0.047 0.148 2470 Planarity : 0.004 0.058 2900 Dihedral : 3.703 16.541 2200 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.28 % Allowed : 12.67 % Favored : 86.06 % 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 are not related in a simple way. whole: -2.70 (0.17), residues: 2040 helix: 2.71 (0.45), residues: 110 sheet: -1.92 (0.16), residues: 870 loop : -2.14 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 6 TYR 0.019 0.001 TYR H 54 PHE 0.018 0.001 PHE A 39 TRP 0.008 0.001 TRP H 67 HIS 0.006 0.002 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16780) covalent geometry : angle 0.54865 / 0.29 (22810) SS BOND : bond 0.00673 / 0.38 ( 10) SS BOND : angle 3.33544 / 2.03 ( 20) hydrogen bonds : bond 0.05014 / 3.39 ( 495) hydrogen bonds : angle 7.06483 / 4.79 ( 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 297 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.9203 (t80) cc_final: 0.8957 (t80) REVERT: E 101 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: E 172 ASN cc_start: 0.9392 (t0) cc_final: 0.8913 (t0) REVERT: E 176 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8680 (mm) REVERT: E 203 GLN cc_start: 0.8738 (pt0) cc_final: 0.8223 (pt0) REVERT: A 19 TYR cc_start: 0.8430 (p90) cc_final: 0.8051 (p90) REVERT: A 186 ASN cc_start: 0.9296 (t0) cc_final: 0.8891 (t0) REVERT: B 47 ARG cc_start: 0.8154 (ptt90) cc_final: 0.7890 (ptt-90) REVERT: B 91 VAL cc_start: 0.8839 (m) cc_final: 0.8569 (p) REVERT: C 60 ASP cc_start: 0.7376 (p0) cc_final: 0.7163 (p0) REVERT: C 122 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8823 (mmtt) REVERT: C 145 ASN cc_start: 0.8398 (m-40) cc_final: 0.8185 (m-40) REVERT: C 186 ASN cc_start: 0.9315 (t0) cc_final: 0.8819 (t0) REVERT: D 49 TYR cc_start: 0.9191 (p90) cc_final: 0.8942 (p90) REVERT: D 70 ASP cc_start: 0.8364 (t0) cc_final: 0.8138 (t0) REVERT: D 172 ASN cc_start: 0.9279 (t0) cc_final: 0.9032 (t0) REVERT: F 23 LYS cc_start: 0.8902 (mptt) cc_final: 0.8556 (mmtt) REVERT: F 195 GLN cc_start: 0.7741 (mt0) cc_final: 0.7527 (mt0) REVERT: G 4 MET cc_start: 0.8151 (mmt) cc_final: 0.7910 (mmt) REVERT: I 125 TYR cc_start: 0.8798 (t80) cc_final: 0.8558 (t80) REVERT: J 137 GLN cc_start: 0.8107 (mp10) cc_final: 0.7468 (mp10) REVERT: J 172 ASN cc_start: 0.9179 (t0) cc_final: 0.8966 (t0) REVERT: H 122 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8243 (mmtp) outliers start: 23 outliers final: 11 residues processed: 291 average time/residue: 0.1279 time to fit residues: 55.0634 Evaluate side-chains 240 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 227 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLU 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 Chi-restraints excluded: chain H residue 98 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: 10.0000 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 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 ** 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 145 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.059908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.048108 restraints weight = 50463.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.050111 restraints weight = 22539.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.051447 restraints weight = 13458.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.052392 restraints weight = 9516.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.053000 restraints weight = 7439.361| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.088 16790 Z= 0.479 Angle : 0.799 16.310 22830 Z= 0.418 Chirality : 0.052 0.215 2470 Planarity : 0.005 0.048 2900 Dihedral : 5.405 45.028 2200 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.78 % Allowed : 16.11 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.17), residues: 2040 helix: 2.76 (0.42), residues: 110 sheet: -1.84 (0.15), residues: 960 loop : -2.01 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 58 TYR 0.021 0.002 TYR G 175 PHE 0.022 0.003 PHE C 52 TRP 0.019 0.002 TRP F 110 HIS 0.009 0.003 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01108 / 0.48 (16780) covalent geometry : angle 0.78339 / 0.41 (22810) SS BOND : bond 0.01607 / 1.13 ( 10) SS BOND : angle 5.38046 / 3.41 ( 20) hydrogen bonds : bond 0.05331 / 3.61 ( 495) hydrogen bonds : angle 6.56088 / 4.37 ( 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 251 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9439 (t0) cc_final: 0.9069 (t0) REVERT: E 176 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8961 (mm) REVERT: E 203 GLN cc_start: 0.8983 (pt0) cc_final: 0.8566 (pt0) REVERT: B 91 VAL cc_start: 0.8927 (m) cc_final: 0.8592 (p) REVERT: C 60 ASP cc_start: 0.7631 (p0) cc_final: 0.7348 (p0) REVERT: C 94 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9139 (p) REVERT: C 145 ASN cc_start: 0.8486 (m110) cc_final: 0.8135 (m110) REVERT: C 186 ASN cc_start: 0.9462 (t0) cc_final: 0.9190 (t0) REVERT: D 49 TYR cc_start: 0.9354 (p90) cc_final: 0.9135 (p90) REVERT: I 6 ARG cc_start: 0.9138 (mmm-85) cc_final: 0.8416 (mmm-85) REVERT: I 203 GLN cc_start: 0.9071 (pt0) cc_final: 0.8728 (pm20) REVERT: J 172 ASN cc_start: 0.9381 (t0) cc_final: 0.9168 (t0) REVERT: J 191 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8953 (ttpp) REVERT: H 6 ARG cc_start: 0.8700 (mmm160) cc_final: 0.8460 (mmm160) outliers start: 50 outliers final: 27 residues processed: 242 average time/residue: 0.1331 time to fit residues: 47.1891 Evaluate side-chains 204 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 20 VAL 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 I residue 112 ASP 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 J residue 191 LYS 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: 0.0570 chunk 6 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 HIS ** 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 F 158 ASN ** G 95 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.064642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.052997 restraints weight = 48615.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.055046 restraints weight = 21240.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.056474 restraints weight = 12471.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.057416 restraints weight = 8621.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.058106 restraints weight = 6663.634| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16790 Z= 0.114 Angle : 0.565 13.170 22830 Z= 0.296 Chirality : 0.048 0.183 2470 Planarity : 0.004 0.046 2900 Dihedral : 4.575 34.990 2200 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.72 % Allowed : 17.67 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.18), residues: 2040 helix: 3.50 (0.41), residues: 110 sheet: -1.40 (0.16), residues: 910 loop : -1.79 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 58 TYR 0.016 0.001 TYR D 54 PHE 0.012 0.001 PHE A 39 TRP 0.012 0.001 TRP D 110 HIS 0.007 0.002 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (16780) covalent geometry : angle 0.55208 / 0.29 (22810) SS BOND : bond 0.01130 / 0.71 ( 10) SS BOND : angle 4.16065 / 2.53 ( 20) hydrogen bonds : bond 0.03680 / 2.43 ( 495) hydrogen bonds : angle 6.20942 / 4.17 ( 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 258 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9381 (t0) cc_final: 0.8817 (t0) REVERT: E 176 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8793 (mm) REVERT: E 203 GLN cc_start: 0.8782 (pt0) cc_final: 0.8483 (pt0) REVERT: A 112 ASP cc_start: 0.9167 (m-30) cc_final: 0.8955 (m-30) REVERT: A 186 ASN cc_start: 0.9211 (t0) cc_final: 0.8859 (t0) REVERT: A 194 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8940 (t) REVERT: B 91 VAL cc_start: 0.8821 (m) cc_final: 0.8550 (p) REVERT: C 60 ASP cc_start: 0.7645 (p0) cc_final: 0.7281 (p0) REVERT: C 145 ASN cc_start: 0.8404 (m110) cc_final: 0.8165 (m-40) REVERT: C 186 ASN cc_start: 0.9465 (t0) cc_final: 0.9137 (t0) REVERT: D 49 TYR cc_start: 0.9325 (p90) cc_final: 0.8965 (p90) REVERT: F 172 ASN cc_start: 0.8861 (t0) cc_final: 0.8241 (t0) REVERT: F 192 TYR cc_start: 0.8950 (p90) cc_final: 0.8717 (p90) REVERT: I 6 ARG cc_start: 0.9022 (mmm-85) cc_final: 0.8168 (mmm-85) REVERT: I 125 TYR cc_start: 0.8641 (t80) cc_final: 0.7922 (t80) REVERT: I 203 GLN cc_start: 0.8982 (pt0) cc_final: 0.8696 (pm20) REVERT: J 172 ASN cc_start: 0.9346 (t0) cc_final: 0.9139 (t0) REVERT: J 175 TYR cc_start: 0.9491 (t80) cc_final: 0.9190 (t80) REVERT: H 83 LEU cc_start: 0.9205 (mm) cc_final: 0.8947 (mm) REVERT: H 122 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8212 (mmtp) outliers start: 31 outliers final: 18 residues processed: 252 average time/residue: 0.1394 time to fit residues: 51.0163 Evaluate side-chains 217 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 194 VAL Chi-restraints excluded: chain B residue 35 VAL 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 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 36 CYS 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 J residue 96 ILE Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR 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: 9.9990 chunk 116 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 HIS ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 HIS 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 = 0.2964 r_free = 0.2964 target = 0.063969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.052217 restraints weight = 48086.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054288 restraints weight = 21365.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055700 restraints weight = 12607.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.056642 restraints weight = 8803.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.057349 restraints weight = 6843.989| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16790 Z= 0.147 Angle : 0.563 11.659 22830 Z= 0.294 Chirality : 0.047 0.161 2470 Planarity : 0.004 0.046 2900 Dihedral : 4.436 32.826 2200 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.44 % Allowed : 18.17 % 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 are not related in a simple way. whole: -1.71 (0.18), residues: 2040 helix: 3.67 (0.41), residues: 110 sheet: -1.29 (0.16), residues: 980 loop : -1.43 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 188 TYR 0.022 0.001 TYR G 125 PHE 0.014 0.001 PHE C 146 TRP 0.010 0.001 TRP C 100 HIS 0.006 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (16780) covalent geometry : angle 0.54867 / 0.29 (22810) SS BOND : bond 0.01077 / 0.66 ( 10) SS BOND : angle 4.23563 / 2.64 ( 20) hydrogen bonds : bond 0.03648 / 2.42 ( 495) hydrogen bonds : angle 6.03263 / 4.05 ( 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 251 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9383 (t0) cc_final: 0.8824 (t0) REVERT: E 176 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8805 (mm) REVERT: E 203 GLN cc_start: 0.8790 (pt0) cc_final: 0.8492 (pt0) REVERT: A 112 ASP cc_start: 0.9169 (m-30) cc_final: 0.8949 (m-30) REVERT: A 186 ASN cc_start: 0.9268 (t0) cc_final: 0.8934 (t0) REVERT: B 91 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8544 (p) REVERT: C 60 ASP cc_start: 0.7650 (p0) cc_final: 0.7362 (p0) REVERT: C 145 ASN cc_start: 0.8433 (m110) cc_final: 0.7952 (m-40) REVERT: C 186 ASN cc_start: 0.9454 (t0) cc_final: 0.9119 (t0) REVERT: D 49 TYR cc_start: 0.9347 (p90) cc_final: 0.9012 (p90) REVERT: I 6 ARG cc_start: 0.9025 (mmm-85) cc_final: 0.8214 (mmm-85) REVERT: I 125 TYR cc_start: 0.8692 (t80) cc_final: 0.7962 (t80) REVERT: I 203 GLN cc_start: 0.8998 (pt0) cc_final: 0.8744 (pm20) REVERT: J 49 TYR cc_start: 0.9288 (p90) cc_final: 0.8905 (p90) REVERT: J 172 ASN cc_start: 0.9372 (t0) cc_final: 0.9146 (t0) REVERT: J 195 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7822 (mm-40) REVERT: H 83 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8913 (mm) outliers start: 44 outliers final: 30 residues processed: 244 average time/residue: 0.1301 time to fit residues: 46.9143 Evaluate side-chains 223 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 91 VAL Chi-restraints excluded: chain C residue 91 VAL 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 I residue 36 CYS 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 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 96 ILE Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 CYS 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: 10.0000 chunk 11 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 195 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.050532 restraints weight = 48826.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.052569 restraints weight = 21623.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.053961 restraints weight = 12790.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.054868 restraints weight = 8940.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.055559 restraints weight = 6991.249| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 16790 Z= 0.247 Angle : 0.624 11.866 22830 Z= 0.325 Chirality : 0.048 0.192 2470 Planarity : 0.004 0.047 2900 Dihedral : 4.733 36.962 2200 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.78 % Allowed : 18.33 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.18), residues: 2040 helix: 3.52 (0.41), residues: 110 sheet: -1.18 (0.16), residues: 960 loop : -1.44 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 58 TYR 0.019 0.001 TYR G 125 PHE 0.017 0.001 PHE D 180 TRP 0.012 0.001 TRP C 100 HIS 0.008 0.002 HIS J 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (16780) covalent geometry : angle 0.60790 / 0.32 (22810) SS BOND : bond 0.01190 / 0.69 ( 10) SS BOND : angle 4.72259 / 3.03 ( 20) hydrogen bonds : bond 0.03983 / 2.68 ( 495) hydrogen bonds : angle 6.01942 / 4.04 ( 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 247 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9379 (t0) cc_final: 0.8858 (t0) REVERT: E 176 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8848 (mm) REVERT: E 203 GLN cc_start: 0.8781 (pt0) cc_final: 0.8257 (pt0) REVERT: A 186 ASN cc_start: 0.9280 (t0) cc_final: 0.8890 (t0) REVERT: B 91 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8594 (p) REVERT: C 60 ASP cc_start: 0.7704 (p0) cc_final: 0.7406 (p0) REVERT: C 145 ASN cc_start: 0.8171 (m110) cc_final: 0.7938 (m-40) REVERT: C 186 ASN cc_start: 0.9467 (t0) cc_final: 0.9118 (t0) REVERT: D 49 TYR cc_start: 0.9354 (p90) cc_final: 0.9059 (p90) REVERT: F 195 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8461 (mm-40) REVERT: G 203 GLN cc_start: 0.9022 (pt0) cc_final: 0.8767 (pt0) REVERT: I 6 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8252 (mmm-85) REVERT: I 125 TYR cc_start: 0.8703 (t80) cc_final: 0.8031 (t80) REVERT: I 203 GLN cc_start: 0.8990 (pt0) cc_final: 0.8682 (pm20) REVERT: J 49 TYR cc_start: 0.9295 (p90) cc_final: 0.8891 (p90) REVERT: J 172 ASN cc_start: 0.9397 (t0) cc_final: 0.9179 (t0) REVERT: J 195 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7900 (mm-40) REVERT: H 83 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8967 (mm) outliers start: 50 outliers final: 38 residues processed: 240 average time/residue: 0.1406 time to fit residues: 49.2705 Evaluate side-chains 227 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR 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 60 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 27 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 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 161 MET 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 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 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 17 THR Chi-restraints excluded: chain H residue 83 LEU 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: 10.0000 chunk 184 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** C 195 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** J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.061277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.049520 restraints weight = 49075.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.051539 restraints weight = 21949.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.052925 restraints weight = 13121.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.053870 restraints weight = 9219.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.054424 restraints weight = 7193.842| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 16790 Z= 0.292 Angle : 0.657 12.251 22830 Z= 0.342 Chirality : 0.048 0.205 2470 Planarity : 0.004 0.047 2900 Dihedral : 4.994 43.223 2200 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.72 % Allowed : 18.89 % Favored : 78.39 % 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 are not related in a simple way. whole: -1.64 (0.18), residues: 2040 helix: 3.34 (0.42), residues: 110 sheet: -1.17 (0.16), residues: 960 loop : -1.44 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 58 TYR 0.018 0.001 TYR G 125 PHE 0.015 0.002 PHE C 52 TRP 0.013 0.001 TRP C 100 HIS 0.007 0.002 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.29 (16780) covalent geometry : angle 0.63811 / 0.33 (22810) SS BOND : bond 0.01145 / 0.67 ( 10) SS BOND : angle 5.28386 / 3.43 ( 20) hydrogen bonds : bond 0.04136 / 2.79 ( 495) hydrogen bonds : angle 6.04854 / 4.06 ( 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 239 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9371 (t0) cc_final: 0.8876 (t0) REVERT: E 176 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8907 (mm) REVERT: E 203 GLN cc_start: 0.8761 (pt0) cc_final: 0.8240 (pt0) REVERT: A 186 ASN cc_start: 0.9275 (t0) cc_final: 0.8890 (t0) REVERT: B 91 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8595 (p) REVERT: B 195 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7641 (mm-40) REVERT: C 60 ASP cc_start: 0.7820 (p0) cc_final: 0.7530 (p0) REVERT: C 137 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8314 (mm-40) REVERT: C 145 ASN cc_start: 0.8090 (m110) cc_final: 0.7862 (m-40) REVERT: C 186 ASN cc_start: 0.9482 (t0) cc_final: 0.9140 (t0) REVERT: D 49 TYR cc_start: 0.9370 (p90) cc_final: 0.9097 (p90) REVERT: D 203 GLN cc_start: 0.9030 (pt0) cc_final: 0.8620 (pt0) REVERT: F 73 TYR cc_start: 0.9147 (m-80) cc_final: 0.8899 (m-80) REVERT: F 195 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8528 (mm-40) REVERT: G 203 GLN cc_start: 0.9110 (pt0) cc_final: 0.8873 (pt0) REVERT: I 6 ARG cc_start: 0.8990 (mmm-85) cc_final: 0.8294 (mmm-85) REVERT: I 125 TYR cc_start: 0.8757 (t80) cc_final: 0.8167 (t80) REVERT: I 203 GLN cc_start: 0.8988 (pt0) cc_final: 0.8694 (pm20) REVERT: J 108 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: J 172 ASN cc_start: 0.9421 (t0) cc_final: 0.9211 (t0) REVERT: J 195 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8017 (mm-40) outliers start: 49 outliers final: 40 residues processed: 231 average time/residue: 0.1386 time to fit residues: 47.2713 Evaluate side-chains 227 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR 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 60 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 27 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 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 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 96 ILE 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 96 ILE Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 108 GLU 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: 1.9990 chunk 139 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN B 203 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.051019 restraints weight = 48170.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.053084 restraints weight = 21397.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.054499 restraints weight = 12666.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.055466 restraints weight = 8831.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.056084 restraints weight = 6844.079| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16790 Z= 0.165 Angle : 0.598 11.727 22830 Z= 0.312 Chirality : 0.047 0.185 2470 Planarity : 0.004 0.048 2900 Dihedral : 4.782 41.616 2200 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.28 % Allowed : 19.61 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.18), residues: 2040 helix: 3.48 (0.42), residues: 110 sheet: -1.07 (0.17), residues: 960 loop : -1.31 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 58 TYR 0.017 0.001 TYR H 54 PHE 0.013 0.001 PHE J 39 TRP 0.011 0.001 TRP C 100 HIS 0.007 0.002 HIS J 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (16780) covalent geometry : angle 0.57837 / 0.30 (22810) SS BOND : bond 0.01292 / 0.80 ( 10) SS BOND : angle 5.15558 / 3.32 ( 20) hydrogen bonds : bond 0.03664 / 2.45 ( 495) hydrogen bonds : angle 5.98956 / 4.03 ( 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 246 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9373 (t0) cc_final: 0.8845 (t0) REVERT: E 176 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8867 (mm) REVERT: E 203 GLN cc_start: 0.8712 (pt0) cc_final: 0.8176 (pt0) REVERT: A 186 ASN cc_start: 0.9272 (t0) cc_final: 0.8904 (t0) REVERT: B 91 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8551 (p) REVERT: B 195 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7494 (mp10) REVERT: C 60 ASP cc_start: 0.7904 (p0) cc_final: 0.7673 (p0) REVERT: C 145 ASN cc_start: 0.7997 (m110) cc_final: 0.7774 (m110) REVERT: C 186 ASN cc_start: 0.9467 (t0) cc_final: 0.9095 (t0) REVERT: D 14 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: D 49 TYR cc_start: 0.9382 (p90) cc_final: 0.9090 (p90) REVERT: D 203 GLN cc_start: 0.8968 (pt0) cc_final: 0.8546 (pt0) REVERT: F 73 TYR cc_start: 0.9116 (m-80) cc_final: 0.8866 (m-80) REVERT: F 195 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8525 (mm-40) REVERT: I 6 ARG cc_start: 0.8980 (mmm-85) cc_final: 0.8278 (mmm-85) REVERT: I 125 TYR cc_start: 0.8702 (t80) cc_final: 0.8101 (t80) REVERT: I 203 GLN cc_start: 0.8969 (pt0) cc_final: 0.8686 (pm20) REVERT: J 195 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7951 (mm-40) outliers start: 41 outliers final: 32 residues processed: 237 average time/residue: 0.1365 time to fit residues: 47.5852 Evaluate side-chains 229 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 91 VAL 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 20 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 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 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: 9.9990 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 196 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN H 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.062075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.050566 restraints weight = 49026.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.052547 restraints weight = 21630.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.053903 restraints weight = 12871.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.054847 restraints weight = 9021.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.055456 restraints weight = 7007.076| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 16790 Z= 0.252 Angle : 0.649 12.526 22830 Z= 0.338 Chirality : 0.048 0.202 2470 Planarity : 0.004 0.048 2900 Dihedral : 4.955 43.654 2200 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.44 % Allowed : 19.83 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.18), residues: 2040 helix: 3.40 (0.42), residues: 110 sheet: -1.11 (0.16), residues: 960 loop : -1.35 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 58 TYR 0.029 0.002 TYR G 125 PHE 0.014 0.001 PHE C 52 TRP 0.012 0.001 TRP C 100 HIS 0.007 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (16780) covalent geometry : angle 0.62888 / 0.33 (22810) SS BOND : bond 0.01257 / 0.75 ( 10) SS BOND : angle 5.45871 / 3.51 ( 20) hydrogen bonds : bond 0.03963 / 2.67 ( 495) hydrogen bonds : angle 5.96824 / 4.01 ( 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 240 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9374 (t0) cc_final: 0.8873 (t0) REVERT: E 176 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8892 (mm) REVERT: E 203 GLN cc_start: 0.8709 (pt0) cc_final: 0.8060 (pt0) REVERT: A 186 ASN cc_start: 0.9268 (t0) cc_final: 0.8887 (t0) REVERT: B 91 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8574 (p) REVERT: B 195 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7635 (mm-40) REVERT: C 60 ASP cc_start: 0.7940 (p0) cc_final: 0.7706 (p0) REVERT: C 145 ASN cc_start: 0.8053 (m110) cc_final: 0.7837 (m-40) REVERT: C 186 ASN cc_start: 0.9467 (t0) cc_final: 0.9108 (t0) REVERT: C 195 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6594 (pp30) REVERT: D 14 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: D 49 TYR cc_start: 0.9394 (p90) cc_final: 0.9121 (p90) REVERT: D 203 GLN cc_start: 0.9019 (pt0) cc_final: 0.8591 (pt0) REVERT: F 73 TYR cc_start: 0.9126 (m-80) cc_final: 0.8873 (m-80) REVERT: F 195 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8488 (mm-40) REVERT: G 203 GLN cc_start: 0.9093 (pt0) cc_final: 0.8838 (pt0) REVERT: I 6 ARG cc_start: 0.8946 (mmm-85) cc_final: 0.8233 (mmm-85) REVERT: I 125 TYR cc_start: 0.8760 (t80) cc_final: 0.8199 (t80) REVERT: I 203 GLN cc_start: 0.8965 (pt0) cc_final: 0.8688 (pm20) REVERT: J 38 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.7799 (t-90) REVERT: J 108 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: J 195 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8009 (mm-40) REVERT: H 38 HIS cc_start: 0.9077 (OUTLIER) cc_final: 0.8815 (m-70) outliers start: 44 outliers final: 35 residues processed: 229 average time/residue: 0.1225 time to fit residues: 41.8176 Evaluate side-chains 230 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 91 VAL 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 20 VAL 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 I residue 21 SER 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 35 VAL Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 108 GLU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 38 HIS 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: 2.9990 chunk 171 optimal weight: 0.8980 chunk 192 optimal weight: 0.0040 chunk 149 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 132 optimal weight: 3.9990 chunk 136 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN ** 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** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.064868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.053149 restraints weight = 47576.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.055250 restraints weight = 21083.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.056667 restraints weight = 12452.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.057655 restraints weight = 8711.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058292 restraints weight = 6713.911| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 16790 Z= 0.109 Angle : 0.599 12.685 22830 Z= 0.313 Chirality : 0.048 0.162 2470 Planarity : 0.004 0.047 2900 Dihedral : 4.590 36.940 2200 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.72 % Allowed : 20.39 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.18), residues: 2040 helix: 3.66 (0.42), residues: 110 sheet: -0.89 (0.17), residues: 970 loop : -1.24 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 58 TYR 0.019 0.001 TYR H 54 PHE 0.016 0.001 PHE C 146 TRP 0.013 0.001 TRP D 110 HIS 0.006 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (16780) covalent geometry : angle 0.57925 / 0.30 (22810) SS BOND : bond 0.01436 / 0.90 ( 10) SS BOND : angle 5.22653 / 3.36 ( 20) hydrogen bonds : bond 0.03317 / 2.19 ( 495) hydrogen bonds : angle 5.93192 / 4.00 ( 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 246 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 LEU cc_start: 0.9457 (pt) cc_final: 0.9049 (pp) REVERT: E 172 ASN cc_start: 0.9371 (t0) cc_final: 0.8819 (t0) REVERT: E 176 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8663 (mm) REVERT: E 203 GLN cc_start: 0.8636 (pt0) cc_final: 0.8054 (pt0) REVERT: A 70 ASP cc_start: 0.8110 (m-30) cc_final: 0.7730 (p0) REVERT: A 186 ASN cc_start: 0.9315 (t0) cc_final: 0.8938 (t0) REVERT: B 91 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8545 (p) REVERT: B 195 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7535 (mp10) REVERT: C 186 ASN cc_start: 0.9419 (t0) cc_final: 0.9019 (t0) REVERT: D 14 GLU cc_start: 0.8087 (pt0) cc_final: 0.7493 (tt0) REVERT: D 49 TYR cc_start: 0.9383 (p90) cc_final: 0.9073 (p90) REVERT: D 203 GLN cc_start: 0.8846 (pt0) cc_final: 0.8433 (pt0) REVERT: F 73 TYR cc_start: 0.9018 (m-80) cc_final: 0.8744 (m-80) REVERT: I 6 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8130 (mmm-85) REVERT: I 98 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7850 (t) REVERT: I 125 TYR cc_start: 0.8667 (t80) cc_final: 0.8103 (t80) REVERT: J 38 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.7599 (t-90) REVERT: J 137 GLN cc_start: 0.8612 (mp10) cc_final: 0.8109 (mp10) REVERT: J 195 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7825 (mm-40) REVERT: H 38 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8725 (m-70) outliers start: 31 outliers final: 22 residues processed: 238 average time/residue: 0.1401 time to fit residues: 48.4015 Evaluate side-chains 228 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 B residue 91 VAL 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 91 VAL Chi-restraints excluded: chain I residue 21 SER 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 I residue 117 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 38 HIS 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: 10.0000 chunk 60 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 38 HIS ** 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 = 0.2906 r_free = 0.2906 target = 0.061289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.049543 restraints weight = 48912.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.051563 restraints weight = 21832.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.052945 restraints weight = 13024.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.053898 restraints weight = 9164.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.054513 restraints weight = 7140.279| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 16790 Z= 0.316 Angle : 0.697 13.380 22830 Z= 0.364 Chirality : 0.049 0.240 2470 Planarity : 0.004 0.048 2900 Dihedral : 5.032 40.649 2200 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.67 % Allowed : 20.67 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 2040 helix: 3.36 (0.42), residues: 110 sheet: -1.09 (0.16), residues: 960 loop : -1.28 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 58 TYR 0.017 0.002 TYR G 125 PHE 0.017 0.002 PHE C 52 TRP 0.012 0.001 TRP C 187 HIS 0.007 0.002 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.32 (16780) covalent geometry : angle 0.67615 / 0.35 (22810) SS BOND : bond 0.01311 / 0.78 ( 10) SS BOND : angle 5.80904 / 3.77 ( 20) hydrogen bonds : bond 0.04151 / 2.82 ( 495) hydrogen bonds : angle 5.90556 / 3.97 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.86 seconds wall clock time: 41 minutes 58.50 seconds (2518.50 seconds total)