Starting phenix.real_space_refine on Sat Jun 14 16:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv5_37865/06_2025/8wv5_37865.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv5_37865/06_2025/8wv5_37865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wv5_37865/06_2025/8wv5_37865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv5_37865/06_2025/8wv5_37865.map" model { file = "/net/cci-nas-00/data/ceres_data/8wv5_37865/06_2025/8wv5_37865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv5_37865/06_2025/8wv5_37865.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16340 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "F" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "H" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.34, per 1000 atoms: 0.63 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: 3.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.99 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: 5.67 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5080 1.35 - 1.47: 4492 1.47 - 1.59: 7148 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 16780 Sorted by residual: bond pdb=" N VAL F 86 " pdb=" CA VAL F 86 " ideal model delta sigma weight residual 1.454 1.462 -0.007 7.70e-03 1.69e+04 9.32e-01 bond pdb=" N VAL C 86 " pdb=" CA VAL C 86 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 7.71e-01 bond pdb=" N GLY I 178 " pdb=" CA GLY I 178 " ideal model delta sigma weight residual 1.434 1.444 -0.010 1.22e-02 6.72e+03 6.92e-01 bond pdb=" N SER C 181 " pdb=" CA SER C 181 " ideal model delta sigma weight residual 1.463 1.455 0.007 8.80e-03 1.29e+04 6.87e-01 bond pdb=" C VAL E 153 " pdb=" N GLY E 154 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 6.85e-01 ... (remaining 16775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 22020 1.08 - 2.15: 601 2.15 - 3.23: 167 3.23 - 4.31: 14 4.31 - 5.38: 8 Bond angle restraints: 22810 Sorted by residual: angle pdb=" N THR G 17 " pdb=" CA THR G 17 " pdb=" C THR G 17 " ideal model delta sigma weight residual 114.31 109.95 4.36 1.29e+00 6.01e-01 1.14e+01 angle pdb=" N THR E 17 " pdb=" CA THR E 17 " pdb=" C THR E 17 " ideal model delta sigma weight residual 114.31 110.46 3.85 1.29e+00 6.01e-01 8.91e+00 angle pdb=" N THR D 17 " pdb=" CA THR D 17 " pdb=" C THR D 17 " ideal model delta sigma weight residual 114.31 110.55 3.76 1.29e+00 6.01e-01 8.49e+00 angle pdb=" N THR H 17 " pdb=" CA THR H 17 " pdb=" C THR H 17 " ideal model delta sigma weight residual 114.31 110.65 3.66 1.29e+00 6.01e-01 8.06e+00 angle pdb=" N THR A 17 " pdb=" CA THR A 17 " pdb=" C THR A 17 " ideal model delta sigma weight residual 114.56 110.95 3.61 1.27e+00 6.20e-01 8.06e+00 ... (remaining 22805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9084 17.80 - 35.59: 573 35.59 - 53.39: 90 53.39 - 71.19: 33 71.19 - 88.98: 10 Dihedral angle restraints: 9790 sinusoidal: 3880 harmonic: 5910 Sorted by residual: dihedral pdb=" CB CYS I 36 " pdb=" SG CYS I 36 " pdb=" SG CYS I 97 " pdb=" CB CYS I 97 " ideal model delta sinusoidal sigma weight residual 93.00 14.18 78.82 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS D 36 " pdb=" SG CYS D 36 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual -86.00 -40.91 -45.09 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS E 36 " pdb=" SG CYS E 36 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual -86.00 -44.00 -42.00 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 9787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1400 0.026 - 0.051: 610 0.051 - 0.077: 182 0.077 - 0.103: 160 0.103 - 0.129: 118 Chirality restraints: 2470 Sorted by residual: chirality pdb=" CA ILE A 63 " pdb=" N ILE A 63 " pdb=" C ILE A 63 " pdb=" CB ILE A 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE F 63 " pdb=" N ILE F 63 " pdb=" C ILE F 63 " pdb=" CB ILE F 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE C 63 " pdb=" N ILE C 63 " pdb=" C ILE C 63 " pdb=" CB ILE C 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 2467 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 167 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO D 168 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 168 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 35 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C VAL C 35 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL C 35 " 0.008 2.00e-02 2.50e+03 pdb=" N CYS C 36 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 167 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO E 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.016 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 138 2.43 - 3.05: 9726 3.05 - 3.66: 24069 3.66 - 4.28: 36448 4.28 - 4.90: 62114 Nonbonded interactions: 132495 Sorted by model distance: nonbonded pdb=" CD GLU H 147 " pdb="CA CA H 301 " model vdw 1.812 2.740 nonbonded pdb=" OE1 GLU H 147 " pdb="CA CA H 301 " model vdw 2.018 2.510 nonbonded pdb=" OG1 THR I 98 " pdb=" O GLU I 108 " model vdw 2.207 3.040 nonbonded pdb=" CG GLU I 147 " pdb="CA CA I 301 " model vdw 2.221 2.910 nonbonded pdb=" OG1 THR J 98 " pdb=" O GLU J 108 " model vdw 2.231 3.040 ... (remaining 132490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 1.470 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 40.510 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16790 Z= 0.104 Angle : 0.473 5.760 22830 Z= 0.291 Chirality : 0.043 0.129 2470 Planarity : 0.003 0.032 2900 Dihedral : 12.215 88.982 5980 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.000 TRP J 100 HIS 0.002 0.001 HIS J 38 PHE 0.006 0.001 PHE J 199 TYR 0.006 0.001 TYR F 54 ARG 0.002 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.28576 ( 495) hydrogen bonds : angle 10.99372 ( 1224) SS BOND : bond 0.00643 ( 10) SS BOND : angle 2.18805 ( 20) covalent geometry : bond 0.00176 (16780) covalent geometry : angle 0.46831 (22810) *********************** 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 : 1.814 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: 0.7852 (tp-100) cc_final: 0.7450 (tp-100) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.3515 time to fit residues: 234.3882 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 : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN B 195 GLN ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN 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** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 ASN ** 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 = 0.2956 r_free = 0.2956 target = 0.063757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.051661 restraints weight = 48637.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.053711 restraints weight = 22047.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.055119 restraints weight = 13217.718| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16790 Z= 0.306 Angle : 0.691 13.272 22830 Z= 0.365 Chirality : 0.050 0.176 2470 Planarity : 0.005 0.071 2900 Dihedral : 4.630 26.338 2200 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.11 % Allowed : 13.72 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.17), residues: 2040 helix: 2.44 (0.44), residues: 110 sheet: -1.95 (0.16), residues: 860 loop : -2.17 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 100 HIS 0.009 0.002 HIS B 38 PHE 0.021 0.002 PHE A 39 TYR 0.017 0.002 TYR G 175 ARG 0.005 0.001 ARG E 58 Details of bonding type rmsd hydrogen bonds : bond 0.05155 ( 495) hydrogen bonds : angle 6.64084 ( 1224) SS BOND : bond 0.01008 ( 10) SS BOND : angle 4.58518 ( 20) covalent geometry : bond 0.00700 (16780) covalent geometry : angle 0.67745 (22810) *********************** 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 261 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 130 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8165 (tm-30) REVERT: E 172 ASN cc_start: 0.9466 (t0) cc_final: 0.8923 (t0) REVERT: E 176 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.8887 (mm) REVERT: E 203 GLN cc_start: 0.8728 (pt0) cc_final: 0.8047 (pt0) REVERT: A 147 GLU cc_start: 0.6995 (mp0) cc_final: 0.6736 (mp0) REVERT: A 186 ASN cc_start: 0.9297 (t0) cc_final: 0.9013 (t0) REVERT: A 195 GLN cc_start: 0.7512 (mp10) cc_final: 0.7012 (mp10) REVERT: B 91 VAL cc_start: 0.8892 (m) cc_final: 0.8614 (p) REVERT: B 94 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.9029 (p) REVERT: C 60 ASP cc_start: 0.7319 (p0) cc_final: 0.7100 (p0) REVERT: C 122 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8853 (mmtt) REVERT: C 137 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8483 (mm-40) REVERT: C 145 ASN cc_start: 0.8251 (m110) cc_final: 0.7953 (m110) REVERT: C 186 ASN cc_start: 0.9428 (t0) cc_final: 0.9079 (t0) REVERT: D 49 TYR cc_start: 0.9373 (p90) cc_final: 0.9138 (p90) REVERT: D 172 ASN cc_start: 0.9357 (t0) cc_final: 0.9109 (t0) REVERT: F 23 LYS cc_start: 0.8869 (mptt) cc_final: 0.8502 (mmtt) REVERT: I 6 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8295 (mmm-85) REVERT: I 125 TYR cc_start: 0.8874 (t80) cc_final: 0.8653 (t80) REVERT: J 4 MET cc_start: 0.8864 (mmm) cc_final: 0.8552 (mmm) REVERT: J 172 ASN cc_start: 0.9286 (t0) cc_final: 0.9064 (t0) outliers start: 38 outliers final: 19 residues processed: 257 average time/residue: 0.3151 time to fit residues: 117.9864 Evaluate side-chains 217 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 94 VAL 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 94 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain 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 188 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 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** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS J 145 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.062938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.050908 restraints weight = 48301.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.052940 restraints weight = 21944.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.054341 restraints weight = 13221.646| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 16790 Z= 0.267 Angle : 0.626 14.244 22830 Z= 0.330 Chirality : 0.048 0.203 2470 Planarity : 0.004 0.047 2900 Dihedral : 4.760 36.352 2200 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.33 % Allowed : 15.61 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.18), residues: 2040 helix: 3.09 (0.41), residues: 110 sheet: -1.64 (0.17), residues: 860 loop : -1.85 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 100 HIS 0.007 0.002 HIS C 38 PHE 0.016 0.002 PHE C 52 TYR 0.021 0.001 TYR F 192 ARG 0.006 0.001 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 495) hydrogen bonds : angle 6.37449 ( 1224) SS BOND : bond 0.01316 ( 10) SS BOND : angle 4.65894 ( 20) covalent geometry : bond 0.00622 (16780) covalent geometry : angle 0.61073 (22810) *********************** 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 250 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9389 (t0) cc_final: 0.8856 (t0) REVERT: E 176 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8811 (mm) REVERT: E 203 GLN cc_start: 0.8840 (pt0) cc_final: 0.8379 (pt0) REVERT: A 186 ASN cc_start: 0.9276 (t0) cc_final: 0.8969 (t0) REVERT: B 91 VAL cc_start: 0.8923 (m) cc_final: 0.8632 (p) REVERT: C 60 ASP cc_start: 0.7604 (p0) cc_final: 0.7275 (p0) REVERT: C 122 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8872 (mmtt) REVERT: C 145 ASN cc_start: 0.8025 (m110) cc_final: 0.7822 (m-40) REVERT: C 186 ASN cc_start: 0.9433 (t0) cc_final: 0.9125 (t0) REVERT: D 49 TYR cc_start: 0.9366 (p90) cc_final: 0.9048 (p90) REVERT: D 197 GLU cc_start: 0.8184 (pm20) cc_final: 0.7772 (pm20) REVERT: F 23 LYS cc_start: 0.8848 (mptt) cc_final: 0.8489 (mmtt) REVERT: G 195 GLN cc_start: 0.7737 (tp40) cc_final: 0.7462 (tp40) REVERT: J 49 TYR cc_start: 0.9299 (p90) cc_final: 0.8953 (p90) REVERT: J 163 ASP cc_start: 0.8988 (p0) cc_final: 0.8623 (p0) REVERT: J 172 ASN cc_start: 0.9369 (t0) cc_final: 0.9155 (t0) outliers start: 42 outliers final: 27 residues processed: 244 average time/residue: 0.3106 time to fit residues: 110.5029 Evaluate side-chains 217 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 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 D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 8 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS F 95 HIS F 158 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.063254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.051209 restraints weight = 48026.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.053266 restraints weight = 21771.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.054660 restraints weight = 13047.287| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16790 Z= 0.203 Angle : 0.589 13.403 22830 Z= 0.311 Chirality : 0.047 0.203 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.680 36.910 2200 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.33 % Allowed : 17.33 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.18), residues: 2040 helix: 3.36 (0.41), residues: 110 sheet: -1.57 (0.16), residues: 980 loop : -1.63 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 100 HIS 0.007 0.002 HIS J 38 PHE 0.013 0.001 PHE C 146 TYR 0.031 0.001 TYR G 125 ARG 0.006 0.001 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 495) hydrogen bonds : angle 6.12476 ( 1224) SS BOND : bond 0.01112 ( 10) SS BOND : angle 4.52594 ( 20) covalent geometry : bond 0.00475 (16780) covalent geometry : angle 0.57395 (22810) *********************** 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 238 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9395 (t0) cc_final: 0.8851 (t0) REVERT: E 176 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8871 (mm) REVERT: E 203 GLN cc_start: 0.8786 (pt0) cc_final: 0.8311 (pt0) REVERT: A 186 ASN cc_start: 0.9265 (t0) cc_final: 0.8963 (t0) REVERT: B 91 VAL cc_start: 0.8864 (m) cc_final: 0.8581 (p) REVERT: C 60 ASP cc_start: 0.7717 (p0) cc_final: 0.7445 (p0) REVERT: C 122 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8838 (mmtt) REVERT: C 145 ASN cc_start: 0.8032 (m110) cc_final: 0.7820 (m-40) REVERT: C 186 ASN cc_start: 0.9443 (t0) cc_final: 0.9141 (t0) REVERT: D 49 TYR cc_start: 0.9377 (p90) cc_final: 0.9047 (p90) REVERT: D 197 GLU cc_start: 0.8197 (pm20) cc_final: 0.7711 (pm20) REVERT: D 203 GLN cc_start: 0.8933 (pt0) cc_final: 0.8619 (pt0) REVERT: F 23 LYS cc_start: 0.8840 (mptt) cc_final: 0.8436 (mmtt) REVERT: G 195 GLN cc_start: 0.7675 (tp40) cc_final: 0.7393 (tp40) REVERT: I 6 ARG cc_start: 0.8939 (mmm-85) cc_final: 0.8495 (mmm-85) REVERT: I 161 MET cc_start: 0.8729 (tpp) cc_final: 0.8486 (ttt) REVERT: J 49 TYR cc_start: 0.9311 (p90) cc_final: 0.8938 (p90) REVERT: J 172 ASN cc_start: 0.9374 (t0) cc_final: 0.9156 (t0) REVERT: J 195 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7770 (mm-40) outliers start: 42 outliers final: 35 residues processed: 232 average time/residue: 0.3173 time to fit residues: 106.1765 Evaluate side-chains 225 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR 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 D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL 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 J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 114 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 87 optimal weight: 0.0870 chunk 90 optimal weight: 5.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.050688 restraints weight = 48986.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.052742 restraints weight = 21996.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054151 restraints weight = 13166.921| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16790 Z= 0.221 Angle : 0.595 12.432 22830 Z= 0.313 Chirality : 0.047 0.184 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.748 41.309 2200 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.17 % Allowed : 17.39 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 2040 helix: 3.48 (0.41), residues: 110 sheet: -1.44 (0.16), residues: 980 loop : -1.45 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 PHE 0.014 0.001 PHE C 52 TYR 0.027 0.001 TYR G 125 ARG 0.006 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 495) hydrogen bonds : angle 6.04408 ( 1224) SS BOND : bond 0.01101 ( 10) SS BOND : angle 4.58930 ( 20) covalent geometry : bond 0.00517 (16780) covalent geometry : angle 0.57922 (22810) *********************** 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 254 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 197 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9370 (t0) cc_final: 0.8846 (t0) REVERT: E 176 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8874 (mm) REVERT: E 203 GLN cc_start: 0.8724 (pt0) cc_final: 0.8202 (pt0) REVERT: A 186 ASN cc_start: 0.9274 (t0) cc_final: 0.8953 (t0) REVERT: B 91 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8597 (p) REVERT: B 195 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7554 (mm-40) REVERT: C 60 ASP cc_start: 0.7701 (p0) cc_final: 0.7426 (p0) REVERT: C 122 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8906 (mmtt) REVERT: C 145 ASN cc_start: 0.8001 (m110) cc_final: 0.7786 (m-40) REVERT: C 186 ASN cc_start: 0.9455 (t0) cc_final: 0.9142 (t0) REVERT: D 49 TYR cc_start: 0.9386 (p90) cc_final: 0.9063 (p90) REVERT: D 197 GLU cc_start: 0.8284 (pm20) cc_final: 0.7877 (pm20) REVERT: D 203 GLN cc_start: 0.8992 (pt0) cc_final: 0.8625 (pt0) REVERT: F 23 LYS cc_start: 0.8873 (mptt) cc_final: 0.8327 (mmtt) REVERT: I 6 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8554 (mmm-85) REVERT: I 125 TYR cc_start: 0.8669 (t80) cc_final: 0.8102 (t80) REVERT: I 161 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8495 (ttt) REVERT: J 108 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: J 172 ASN cc_start: 0.9390 (t0) cc_final: 0.9182 (t0) REVERT: J 195 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7824 (mm-40) REVERT: H 83 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9039 (mm) outliers start: 57 outliers final: 39 residues processed: 245 average time/residue: 0.3104 time to fit residues: 110.9835 Evaluate side-chains 231 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 2 THR 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 D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL 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 G residue 96 ILE Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 VAL 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 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 170 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 169 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN C 160 ASN ** 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** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.063810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.051776 restraints weight = 48105.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.053856 restraints weight = 21636.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.055284 restraints weight = 12962.612| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16790 Z= 0.144 Angle : 0.556 11.263 22830 Z= 0.292 Chirality : 0.047 0.171 2470 Planarity : 0.004 0.043 2900 Dihedral : 4.553 38.736 2200 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.72 % Allowed : 18.72 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2040 helix: 3.72 (0.41), residues: 110 sheet: -1.17 (0.17), residues: 910 loop : -1.49 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 100 HIS 0.005 0.001 HIS C 38 PHE 0.015 0.001 PHE D 180 TYR 0.021 0.001 TYR G 125 ARG 0.006 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 495) hydrogen bonds : angle 5.92320 ( 1224) SS BOND : bond 0.01033 ( 10) SS BOND : angle 4.29578 ( 20) covalent geometry : bond 0.00343 (16780) covalent geometry : angle 0.54143 (22810) *********************** 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 259 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 CYS cc_start: 0.6386 (m) cc_final: 0.6184 (m) REVERT: E 54 TYR cc_start: 0.9175 (t80) cc_final: 0.8894 (t80) REVERT: E 172 ASN cc_start: 0.9375 (t0) cc_final: 0.8808 (t0) REVERT: E 176 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8823 (mm) REVERT: E 203 GLN cc_start: 0.8640 (pt0) cc_final: 0.8007 (pt0) REVERT: A 186 ASN cc_start: 0.9252 (t0) cc_final: 0.8907 (t0) REVERT: B 91 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8578 (p) REVERT: B 195 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7588 (mm-40) REVERT: C 60 ASP cc_start: 0.7645 (p0) cc_final: 0.7354 (p0) REVERT: C 122 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8827 (mmtt) REVERT: C 186 ASN cc_start: 0.9430 (t0) cc_final: 0.9052 (t0) REVERT: D 49 TYR cc_start: 0.9377 (p90) cc_final: 0.9026 (p90) REVERT: D 197 GLU cc_start: 0.8255 (pm20) cc_final: 0.7876 (pm20) REVERT: D 203 GLN cc_start: 0.8927 (pt0) cc_final: 0.8567 (pt0) REVERT: F 23 LYS cc_start: 0.8889 (mptt) cc_final: 0.8333 (mmtt) REVERT: I 6 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8533 (mmm-85) REVERT: I 125 TYR cc_start: 0.8707 (t80) cc_final: 0.8122 (t80) REVERT: I 161 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8574 (ttt) REVERT: J 108 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6852 (mm-30) REVERT: J 195 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7903 (mm-40) REVERT: H 83 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9001 (mm) REVERT: H 122 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8454 (mmtp) outliers start: 49 outliers final: 34 residues processed: 248 average time/residue: 0.3178 time to fit residues: 114.2315 Evaluate side-chains 232 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 98 THR 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 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR 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 D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 161 MET 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 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 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 10 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 ASN ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 145 ASN C 160 ASN ** C 195 GLN ** 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** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.062201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.050191 restraints weight = 48391.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.052240 restraints weight = 21877.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.053631 restraints weight = 13152.912| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 16790 Z= 0.264 Angle : 0.624 12.077 22830 Z= 0.328 Chirality : 0.048 0.197 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.870 43.121 2200 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.00 % Allowed : 19.17 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2040 helix: 3.54 (0.42), residues: 110 sheet: -1.23 (0.16), residues: 960 loop : -1.37 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 PHE 0.014 0.001 PHE C 52 TYR 0.022 0.001 TYR G 125 ARG 0.007 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 495) hydrogen bonds : angle 5.95022 ( 1224) SS BOND : bond 0.01081 ( 10) SS BOND : angle 4.66992 ( 20) covalent geometry : bond 0.00617 (16780) covalent geometry : angle 0.60865 (22810) *********************** 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 245 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9373 (t0) cc_final: 0.8786 (t0) REVERT: E 176 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8871 (mm) REVERT: E 203 GLN cc_start: 0.8612 (pt0) cc_final: 0.7938 (pt0) REVERT: A 186 ASN cc_start: 0.9258 (t0) cc_final: 0.8911 (t0) REVERT: B 91 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 195 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7720 (mm-40) REVERT: C 60 ASP cc_start: 0.7701 (p0) cc_final: 0.7417 (p0) REVERT: C 160 ASN cc_start: 0.8973 (m-40) cc_final: 0.8764 (m-40) REVERT: C 186 ASN cc_start: 0.9431 (t0) cc_final: 0.9148 (t0) REVERT: D 49 TYR cc_start: 0.9389 (p90) cc_final: 0.9082 (p90) REVERT: D 203 GLN cc_start: 0.9046 (pt0) cc_final: 0.8604 (pt0) REVERT: F 23 LYS cc_start: 0.8878 (mptt) cc_final: 0.8318 (mmtt) REVERT: F 73 TYR cc_start: 0.9163 (m-80) cc_final: 0.8863 (m-80) REVERT: G 203 GLN cc_start: 0.9097 (pt0) cc_final: 0.8874 (pt0) REVERT: I 6 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8641 (mmm-85) REVERT: I 125 TYR cc_start: 0.8688 (t80) cc_final: 0.8195 (t80) REVERT: J 108 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: J 195 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8008 (mm-40) REVERT: H 83 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9054 (mm) outliers start: 54 outliers final: 44 residues processed: 232 average time/residue: 0.3044 time to fit residues: 103.2318 Evaluate side-chains 232 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 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 91 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 2 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 94 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain 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 J residue 108 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 193 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** C 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** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.063475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.051516 restraints weight = 47769.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.053593 restraints weight = 21517.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.055006 restraints weight = 12891.378| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16790 Z= 0.163 Angle : 0.587 11.398 22830 Z= 0.308 Chirality : 0.047 0.179 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.684 41.138 2200 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.61 % Allowed : 19.83 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2040 helix: 3.73 (0.42), residues: 110 sheet: -1.11 (0.16), residues: 960 loop : -1.25 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 100 HIS 0.005 0.001 HIS H 38 PHE 0.011 0.001 PHE C 52 TYR 0.019 0.001 TYR G 125 ARG 0.008 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 495) hydrogen bonds : angle 5.89323 ( 1224) SS BOND : bond 0.01141 ( 10) SS BOND : angle 4.49699 ( 20) covalent geometry : bond 0.00386 (16780) covalent geometry : angle 0.57155 (22810) *********************** 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 252 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.9178 (t80) cc_final: 0.8910 (t80) REVERT: E 172 ASN cc_start: 0.9379 (t0) cc_final: 0.8829 (t0) REVERT: E 176 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8839 (mm) REVERT: E 203 GLN cc_start: 0.8582 (pt0) cc_final: 0.7890 (pt0) REVERT: A 186 ASN cc_start: 0.9246 (t0) cc_final: 0.8904 (t0) REVERT: B 91 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 195 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7713 (mm-40) REVERT: C 60 ASP cc_start: 0.7687 (p0) cc_final: 0.7418 (p0) REVERT: C 160 ASN cc_start: 0.8869 (m-40) cc_final: 0.8643 (m-40) REVERT: C 186 ASN cc_start: 0.9401 (t0) cc_final: 0.9120 (t0) REVERT: D 14 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: D 49 TYR cc_start: 0.9398 (p90) cc_final: 0.9082 (p90) REVERT: D 203 GLN cc_start: 0.8980 (pt0) cc_final: 0.8523 (pt0) REVERT: F 23 LYS cc_start: 0.8878 (mptt) cc_final: 0.8299 (mmtt) REVERT: F 73 TYR cc_start: 0.9132 (m-80) cc_final: 0.8816 (m-80) REVERT: G 203 GLN cc_start: 0.9041 (pt0) cc_final: 0.8806 (pt0) REVERT: I 6 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8581 (mmm-85) REVERT: I 125 TYR cc_start: 0.8679 (t80) cc_final: 0.8183 (t80) REVERT: J 49 TYR cc_start: 0.9361 (p90) cc_final: 0.8865 (p90) REVERT: J 108 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: J 195 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7774 (mm-40) REVERT: H 83 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9009 (mm) outliers start: 47 outliers final: 35 residues processed: 243 average time/residue: 0.3162 time to fit residues: 111.2203 Evaluate side-chains 233 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 B residue 35 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 2 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 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain 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 J residue 108 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 183 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN C 195 GLN ** 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** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS H 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.065686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.053718 restraints weight = 47582.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.055852 restraints weight = 21403.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.057302 restraints weight = 12816.505| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16790 Z= 0.107 Angle : 0.565 10.182 22830 Z= 0.296 Chirality : 0.047 0.162 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.354 32.132 2200 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.89 % Allowed : 20.72 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 2040 helix: 3.98 (0.42), residues: 110 sheet: -0.94 (0.17), residues: 960 loop : -1.12 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 110 HIS 0.004 0.001 HIS C 38 PHE 0.012 0.001 PHE C 146 TYR 0.016 0.001 TYR H 54 ARG 0.007 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 495) hydrogen bonds : angle 5.78341 ( 1224) SS BOND : bond 0.01068 ( 10) SS BOND : angle 3.91361 ( 20) covalent geometry : bond 0.00257 (16780) covalent geometry : angle 0.55282 (22810) *********************** 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 254 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.9154 (t80) cc_final: 0.8877 (t80) REVERT: E 172 ASN cc_start: 0.9380 (t0) cc_final: 0.8910 (t0) REVERT: E 176 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8846 (mm) REVERT: E 203 GLN cc_start: 0.8512 (pt0) cc_final: 0.7627 (pt0) REVERT: A 70 ASP cc_start: 0.8121 (m-30) cc_final: 0.7715 (p0) REVERT: A 186 ASN cc_start: 0.9223 (t0) cc_final: 0.8858 (t0) REVERT: B 91 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8585 (p) REVERT: B 195 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7687 (mp10) REVERT: C 60 ASP cc_start: 0.7641 (p0) cc_final: 0.7323 (p0) REVERT: C 186 ASN cc_start: 0.9363 (t0) cc_final: 0.8984 (t0) REVERT: D 14 GLU cc_start: 0.8096 (pt0) cc_final: 0.7447 (tt0) REVERT: D 49 TYR cc_start: 0.9383 (p90) cc_final: 0.9044 (p90) REVERT: D 203 GLN cc_start: 0.8851 (pt0) cc_final: 0.8420 (pt0) REVERT: F 23 LYS cc_start: 0.8865 (mptt) cc_final: 0.8338 (mmtt) REVERT: F 73 TYR cc_start: 0.9041 (m-80) cc_final: 0.8676 (m-80) REVERT: I 98 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7762 (t) REVERT: I 125 TYR cc_start: 0.8657 (t80) cc_final: 0.8182 (t80) REVERT: J 49 TYR cc_start: 0.9311 (p90) cc_final: 0.8884 (p90) REVERT: J 137 GLN cc_start: 0.8580 (mp10) cc_final: 0.8217 (mp10) REVERT: J 163 ASP cc_start: 0.8868 (p0) cc_final: 0.8573 (p0) REVERT: J 195 GLN cc_start: 0.8416 (mm-40) cc_final: 0.7938 (mm-40) REVERT: H 70 ASP cc_start: 0.8278 (m-30) cc_final: 0.7966 (m-30) REVERT: H 83 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8999 (mm) outliers start: 34 outliers final: 23 residues processed: 244 average time/residue: 0.3182 time to fit residues: 112.4296 Evaluate side-chains 230 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 16 ASP 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 98 THR Chi-restraints excluded: chain I residue 117 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 H residue 83 LEU 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 166 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 0.0670 chunk 136 optimal weight: 0.9980 chunk 158 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** 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 = 0.2987 r_free = 0.2987 target = 0.065168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.053363 restraints weight = 48263.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.055456 restraints weight = 21348.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.056888 restraints weight = 12735.847| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16790 Z= 0.114 Angle : 0.581 11.865 22830 Z= 0.301 Chirality : 0.047 0.172 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.278 27.581 2200 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.61 % Allowed : 20.94 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 2040 helix: 4.06 (0.41), residues: 110 sheet: -0.89 (0.17), residues: 960 loop : -1.06 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 67 HIS 0.005 0.001 HIS B 38 PHE 0.012 0.001 PHE J 66 TYR 0.015 0.001 TYR H 54 ARG 0.007 0.001 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 495) hydrogen bonds : angle 5.72316 ( 1224) SS BOND : bond 0.01060 ( 10) SS BOND : angle 3.92159 ( 20) covalent geometry : bond 0.00274 (16780) covalent geometry : angle 0.56923 (22810) ********************** 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 235 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.9156 (t80) cc_final: 0.8891 (t80) REVERT: E 172 ASN cc_start: 0.9374 (t0) cc_final: 0.8919 (t0) REVERT: E 176 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8873 (mm) REVERT: E 203 GLN cc_start: 0.8570 (pt0) cc_final: 0.8043 (pt0) REVERT: A 70 ASP cc_start: 0.8111 (m-30) cc_final: 0.7671 (p0) REVERT: A 186 ASN cc_start: 0.9243 (t0) cc_final: 0.8881 (t0) REVERT: B 91 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8638 (p) REVERT: B 195 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7690 (mp10) REVERT: C 60 ASP cc_start: 0.7700 (p0) cc_final: 0.7372 (p0) REVERT: C 125 TYR cc_start: 0.8951 (t80) cc_final: 0.8742 (t80) REVERT: C 186 ASN cc_start: 0.9413 (t0) cc_final: 0.9000 (t0) REVERT: D 14 GLU cc_start: 0.8114 (pt0) cc_final: 0.7445 (tt0) REVERT: D 49 TYR cc_start: 0.9378 (p90) cc_final: 0.9039 (p90) REVERT: D 203 GLN cc_start: 0.8841 (pt0) cc_final: 0.8390 (pt0) REVERT: F 23 LYS cc_start: 0.8877 (mptt) cc_final: 0.8358 (mmtt) REVERT: I 98 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7615 (t) REVERT: I 125 TYR cc_start: 0.8671 (t80) cc_final: 0.8200 (t80) REVERT: J 49 TYR cc_start: 0.9283 (p90) cc_final: 0.8873 (p90) REVERT: J 137 GLN cc_start: 0.8599 (mp10) cc_final: 0.8213 (mp10) REVERT: J 195 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7956 (mm-40) REVERT: H 70 ASP cc_start: 0.8319 (m-30) cc_final: 0.8033 (m-30) REVERT: H 83 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9008 (mm) outliers start: 29 outliers final: 22 residues processed: 227 average time/residue: 0.3163 time to fit residues: 104.0183 Evaluate side-chains 227 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 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 B residue 91 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain 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 J residue 38 HIS Chi-restraints excluded: chain J residue 90 THR 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 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 192 optimal weight: 0.0770 chunk 191 optimal weight: 2.9990 overall best weight: 0.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 195 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.065723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.053868 restraints weight = 48435.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.055997 restraints weight = 21583.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.057428 restraints weight = 12859.764| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16790 Z= 0.107 Angle : 0.574 11.122 22830 Z= 0.298 Chirality : 0.047 0.163 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.200 23.668 2200 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 21.17 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 2040 helix: 4.06 (0.41), residues: 110 sheet: -0.83 (0.17), residues: 960 loop : -1.00 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 110 HIS 0.004 0.001 HIS G 38 PHE 0.020 0.001 PHE J 39 TYR 0.015 0.001 TYR H 54 ARG 0.007 0.001 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 495) hydrogen bonds : angle 5.68414 ( 1224) SS BOND : bond 0.01076 ( 10) SS BOND : angle 3.74351 ( 20) covalent geometry : bond 0.00257 (16780) covalent geometry : angle 0.56375 (22810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4793.36 seconds wall clock time: 84 minutes 21.47 seconds (5061.47 seconds total)