Starting phenix.real_space_refine on Thu Mar 5 01:51:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0g_26258/03_2026/7u0g_26258.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0g_26258/03_2026/7u0g_26258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u0g_26258/03_2026/7u0g_26258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0g_26258/03_2026/7u0g_26258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u0g_26258/03_2026/7u0g_26258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0g_26258/03_2026/7u0g_26258.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.067 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: 6 Type Number sf(0) Gaussians P 266 5.49 5 S 43 5.16 5 C 10110 2.51 5 N 3125 2.21 5 O 3783 1.98 5 H 1244 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18571 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 101} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 747 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2758 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2695 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "K" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1012 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "L" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1228 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "M" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1228 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "O" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 3.80, per 1000 atoms: 0.20 Number of scatterers: 18571 At special positions: 0 Unit cell: (138.336, 116.16, 159.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 43 16.00 P 266 15.00 O 3783 8.00 N 3125 7.00 C 10110 6.00 H 1244 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Simple disulfide: pdb=" SG CYS O 44 " - pdb=" SG CYS O 118 " distance=2.03 Simple disulfide: pdb=" SG CYS O 181 " - pdb=" SG CYS O 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 595.7 milliseconds 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2818 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 24 sheets defined 53.2% alpha, 17.7% beta 121 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.510A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.752A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.554A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.733A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 141 through 161 Processing helix chain 'K' and resid 163 through 176 removed outlier: 3.952A pdb=" N GLY K 172 " --> pdb=" O GLY K 168 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 190 Processing helix chain 'K' and resid 193 through 214 Proline residue: K 202 - end of helix removed outlier: 3.556A pdb=" N GLU K 209 " --> pdb=" O GLN K 205 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN K 213 " --> pdb=" O GLU K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 247 Processing helix chain 'K' and resid 255 through 268 removed outlier: 3.586A pdb=" N HIS K 262 " --> pdb=" O GLN K 258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN K 265 " --> pdb=" O SER K 261 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN K 266 " --> pdb=" O HIS K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 287 Processing helix chain 'L' and resid 141 through 161 removed outlier: 3.934A pdb=" N GLU L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 176 Processing helix chain 'L' and resid 180 through 189 Processing helix chain 'L' and resid 193 through 212 Proline residue: L 202 - end of helix Processing helix chain 'M' and resid 141 through 161 removed outlier: 3.937A pdb=" N GLU M 145 " --> pdb=" O ALA M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 176 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 193 through 214 Proline residue: M 202 - end of helix removed outlier: 4.009A pdb=" N ASN M 213 " --> pdb=" O GLU M 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 4.052A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.738A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 52 No H-bonds generated for 'chain 'O' and resid 50 through 52' Processing helix chain 'O' and resid 84 through 87 removed outlier: 3.552A pdb=" N LYS O 87 " --> pdb=" O GLU O 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 84 through 87' Processing helix chain 'O' and resid 109 through 113 removed outlier: 3.691A pdb=" N ASP O 112 " --> pdb=" O THR O 109 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER O 113 " --> pdb=" O SER O 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 109 through 113' Processing helix chain 'O' and resid 237 through 241 removed outlier: 3.717A pdb=" N THR O 241 " --> pdb=" O SER O 238 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.884A pdb=" N ARG A 83 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.204A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.570A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.939A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB3, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.507A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.059A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AB6, first strand: chain 'N' and resid 162 through 164 removed outlier: 4.088A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 168 through 171 removed outlier: 4.360A pdb=" N GLU N 263 " --> pdb=" O MET N 169 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA N 171 " --> pdb=" O GLU N 263 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 168 through 171 removed outlier: 4.360A pdb=" N GLU N 263 " --> pdb=" O MET N 169 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA N 171 " --> pdb=" O GLU N 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 25 through 27 Processing sheet with id=AC1, first strand: chain 'O' and resid 32 through 34 removed outlier: 6.509A pdb=" N GLU O 32 " --> pdb=" O THR O 139 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS O 60 " --> pdb=" O TRP O 69 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TRP O 69 " --> pdb=" O LYS O 60 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR O 62 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU O 67 " --> pdb=" O THR O 62 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 32 through 34 removed outlier: 6.509A pdb=" N GLU O 32 " --> pdb=" O THR O 139 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR O 131 " --> pdb=" O ARG O 120 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER O 122 " --> pdb=" O LEU O 129 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU O 129 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 39 through 43 Processing sheet with id=AC4, first strand: chain 'O' and resid 162 through 164 removed outlier: 4.389A pdb=" N PHE O 229 " --> pdb=" O CYS O 181 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP O 228 " --> pdb=" O SER O 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 168 through 171 removed outlier: 4.099A pdb=" N GLU O 263 " --> pdb=" O MET O 169 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA O 171 " --> pdb=" O GLU O 263 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU O 191 " --> pdb=" O TYR O 207 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR O 207 " --> pdb=" O LEU O 191 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP O 193 " --> pdb=" O LEU O 205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 168 through 171 removed outlier: 4.099A pdb=" N GLU O 263 " --> pdb=" O MET O 169 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA O 171 " --> pdb=" O GLU O 263 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR O 255 " --> pdb=" O GLN O 248 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 294 hydrogen bonds 588 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1244 1.03 - 1.23: 284 1.23 - 1.43: 7952 1.43 - 1.62: 9882 1.62 - 1.82: 66 Bond restraints: 19428 Sorted by residual: bond pdb=" C MET C 52 " pdb=" O MET C 52 " ideal model delta sigma weight residual 1.236 1.123 0.114 1.15e-02 7.56e+03 9.75e+01 bond pdb=" C MET G 52 " pdb=" O MET G 52 " ideal model delta sigma weight residual 1.237 1.133 0.104 1.19e-02 7.06e+03 7.62e+01 bond pdb=" C ARG E 63 " pdb=" O ARG E 63 " ideal model delta sigma weight residual 1.234 1.125 0.109 1.27e-02 6.20e+03 7.42e+01 bond pdb=" C ARG B 93 " pdb=" O ARG B 93 " ideal model delta sigma weight residual 1.236 1.134 0.102 1.32e-02 5.74e+03 6.00e+01 bond pdb=" N MET G 52 " pdb=" CA MET G 52 " ideal model delta sigma weight residual 1.459 1.373 0.086 1.23e-02 6.61e+03 4.87e+01 ... (remaining 19423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 28407 4.29 - 8.58: 100 8.58 - 12.87: 17 12.87 - 17.16: 2 17.16 - 21.45: 3 Bond angle restraints: 28529 Sorted by residual: angle pdb=" CB MET G 52 " pdb=" CG MET G 52 " pdb=" SD MET G 52 " ideal model delta sigma weight residual 112.70 91.25 21.45 3.00e+00 1.11e-01 5.11e+01 angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 91.40 21.30 3.00e+00 1.11e-01 5.04e+01 angle pdb=" C MET C 52 " pdb=" CA MET C 52 " pdb=" CB MET C 52 " ideal model delta sigma weight residual 110.88 100.04 10.84 1.57e+00 4.06e-01 4.77e+01 angle pdb=" CA LEU K 153 " pdb=" CB LEU K 153 " pdb=" CG LEU K 153 " ideal model delta sigma weight residual 116.30 137.75 -21.45 3.50e+00 8.16e-02 3.76e+01 angle pdb=" CB GLU O 111 " pdb=" CG GLU O 111 " pdb=" CD GLU O 111 " ideal model delta sigma weight residual 112.60 122.73 -10.13 1.70e+00 3.46e-01 3.55e+01 ... (remaining 28524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.16: 9043 32.16 - 64.31: 1636 64.31 - 96.47: 49 96.47 - 128.62: 1 128.62 - 160.78: 4 Dihedral angle restraints: 10733 sinusoidal: 6294 harmonic: 4439 Sorted by residual: dihedral pdb=" C MET C 52 " pdb=" N MET C 52 " pdb=" CA MET C 52 " pdb=" CB MET C 52 " ideal model delta harmonic sigma weight residual -122.60 -106.97 -15.63 0 2.50e+00 1.60e-01 3.91e+01 dihedral pdb=" N MET C 52 " pdb=" C MET C 52 " pdb=" CA MET C 52 " pdb=" CB MET C 52 " ideal model delta harmonic sigma weight residual 122.80 109.12 13.68 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" N ARG F 95 " pdb=" C ARG F 95 " pdb=" CA ARG F 95 " pdb=" CB ARG F 95 " ideal model delta harmonic sigma weight residual 122.80 111.61 11.19 0 2.50e+00 1.60e-01 2.00e+01 ... (remaining 10730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2706 0.067 - 0.135: 182 0.135 - 0.202: 13 0.202 - 0.270: 2 0.270 - 0.337: 2 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA MET G 52 " pdb=" N MET G 52 " pdb=" C MET G 52 " pdb=" CB MET G 52 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CG LEU A 60 " pdb=" CB LEU A 60 " pdb=" CD1 LEU A 60 " pdb=" CD2 LEU A 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ARG E 53 " pdb=" N ARG E 53 " pdb=" C ARG E 53 " pdb=" CB ARG E 53 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2902 not shown) Planarity restraints: 2470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 181 " 0.079 2.00e-02 2.50e+03 8.79e-02 1.16e+02 pdb=" CD GLN L 181 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN L 181 " -0.081 2.00e-02 2.50e+03 pdb=" NE2 GLN L 181 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN L 181 " 0.129 2.00e-02 2.50e+03 pdb="HE22 GLN L 181 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU O 111 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C GLU O 111 " 0.075 2.00e-02 2.50e+03 pdb=" O GLU O 111 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP O 112 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 111 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C GLU N 111 " -0.073 2.00e-02 2.50e+03 pdb=" O GLU N 111 " 0.028 2.00e-02 2.50e+03 pdb=" N ASP N 112 " 0.024 2.00e-02 2.50e+03 ... (remaining 2467 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 733 2.36 - 2.92: 11589 2.92 - 3.48: 23797 3.48 - 4.04: 43656 4.04 - 4.60: 59583 Nonbonded interactions: 139358 Sorted by model distance: nonbonded pdb=" OP2 DA J 8 " pdb=" H GLN M 164 " model vdw 1.796 2.450 nonbonded pdb=" O ASP M 166 " pdb=" HG1 THR M 170 " model vdw 1.797 2.450 nonbonded pdb=" OP2 DG I 150 " pdb="HD22 ASN M 196 " model vdw 1.798 2.450 nonbonded pdb=" O GLN M 155 " pdb=" HG1 THR M 159 " model vdw 1.806 2.450 nonbonded pdb=" OE2 GLU M 145 " pdb="HH12 ARG M 201 " model vdw 1.820 2.450 ... (remaining 139353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 119)) } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and ((resid 32 and (name N or name CA or name C or name O or name CB \ )) or resid 33 through 34 or (resid 35 and (name N or name CA or name C or name \ O or name CB )) or resid 36 through 125)) } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.480 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.006 0.126 18188 Z= 0.333 Angle : 0.778 21.452 25699 Z= 0.419 Chirality : 0.037 0.337 2905 Planarity : 0.005 0.045 2324 Dihedral : 25.564 160.781 7525 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 0.87 % Allowed : 21.76 % Favored : 77.37 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1478 helix: 1.02 (0.17), residues: 769 sheet: 0.09 (0.35), residues: 232 loop : -1.09 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.022 0.001 TYR F 88 PHE 0.012 0.001 PHE K 149 TRP 0.013 0.001 TRP O 199 HIS 0.004 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00582 (18184) covalent geometry : angle 0.77765 (25691) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.96962 ( 8) hydrogen bonds : bond 0.11223 ( 993) hydrogen bonds : angle 4.97772 ( 2631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 263 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8354 (mtm-85) REVERT: C 72 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7980 (ttp80) REVERT: C 78 ARG cc_start: 0.8283 (ttt90) cc_final: 0.8051 (ttt-90) REVERT: C 92 GLU cc_start: 0.8258 (tt0) cc_final: 0.7984 (tt0) REVERT: N 237 GLU cc_start: 0.7937 (tt0) cc_final: 0.7556 (tm-30) REVERT: O 32 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8091 (mp0) outliers start: 11 outliers final: 14 residues processed: 272 average time/residue: 0.8297 time to fit residues: 246.3751 Evaluate side-chains 257 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 237 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 ASN N 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085770 restraints weight = 30462.224| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.85 r_work: 0.2836 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 18188 Z= 0.259 Angle : 0.552 7.515 25699 Z= 0.321 Chirality : 0.036 0.126 2905 Planarity : 0.003 0.042 2324 Dihedral : 28.358 159.459 4669 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 3.16 % Allowed : 22.55 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1478 helix: 2.25 (0.18), residues: 776 sheet: 0.70 (0.38), residues: 196 loop : -1.14 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.018 0.002 TYR C 58 PHE 0.014 0.002 PHE E 67 TRP 0.014 0.001 TRP N 132 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00582 (18184) covalent geometry : angle 0.55208 (25691) SS BOND : bond 0.00699 ( 4) SS BOND : angle 0.97158 ( 8) hydrogen bonds : bond 0.04349 ( 993) hydrogen bonds : angle 3.81400 ( 2631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ARG cc_start: 0.8679 (ttm110) cc_final: 0.8478 (ttp80) REVERT: C 78 ARG cc_start: 0.8660 (ttt90) cc_final: 0.8136 (ttt-90) REVERT: D 69 ASP cc_start: 0.9441 (t0) cc_final: 0.9197 (t0) REVERT: K 153 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8510 (pt) REVERT: K 233 LYS cc_start: 0.5242 (tptp) cc_final: 0.4932 (mmmt) REVERT: N 95 ASP cc_start: 0.8642 (t0) cc_final: 0.8248 (t0) REVERT: N 104 GLU cc_start: 0.8297 (tp30) cc_final: 0.8029 (tp30) REVERT: N 237 GLU cc_start: 0.8068 (tt0) cc_final: 0.7452 (tm-30) REVERT: O 23 GLU cc_start: 0.7550 (tp30) cc_final: 0.7286 (tp30) REVERT: O 32 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8054 (mm-30) REVERT: O 103 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7417 (tpp) REVERT: O 111 GLU cc_start: 0.8030 (pp20) cc_final: 0.7817 (pp20) REVERT: O 176 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7659 (ttm-80) outliers start: 40 outliers final: 24 residues processed: 263 average time/residue: 0.8103 time to fit residues: 233.0529 Evaluate side-chains 269 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 168 SER Chi-restraints excluded: chain O residue 177 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 105 GLN ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.146799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095770 restraints weight = 33025.281| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.85 r_work: 0.3087 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18188 Z= 0.136 Angle : 0.472 10.096 25699 Z= 0.278 Chirality : 0.031 0.154 2905 Planarity : 0.003 0.039 2324 Dihedral : 27.981 158.188 4652 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.45 % Allowed : 23.81 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.23), residues: 1478 helix: 2.83 (0.18), residues: 781 sheet: 0.48 (0.37), residues: 220 loop : -0.83 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 188 TYR 0.010 0.001 TYR C 58 PHE 0.007 0.001 PHE E 67 TRP 0.008 0.001 TRP N 132 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00292 (18184) covalent geometry : angle 0.47150 (25691) SS BOND : bond 0.00366 ( 4) SS BOND : angle 0.76654 ( 8) hydrogen bonds : bond 0.03188 ( 993) hydrogen bonds : angle 3.42392 ( 2631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ARG cc_start: 0.8650 (ttm110) cc_final: 0.8441 (ttp80) REVERT: C 78 ARG cc_start: 0.8561 (ttt90) cc_final: 0.8200 (ttt-90) REVERT: N 33 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8728 (mm) REVERT: N 95 ASP cc_start: 0.8668 (t0) cc_final: 0.8296 (t0) REVERT: N 104 GLU cc_start: 0.8234 (tp30) cc_final: 0.7967 (tp30) REVERT: N 237 GLU cc_start: 0.8119 (tt0) cc_final: 0.7606 (tm-30) REVERT: O 103 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.7439 (tpp) REVERT: O 112 ASP cc_start: 0.8588 (m-30) cc_final: 0.8388 (m-30) REVERT: O 176 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7540 (ttm-80) outliers start: 31 outliers final: 18 residues processed: 260 average time/residue: 0.7728 time to fit residues: 220.1860 Evaluate side-chains 266 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 168 SER Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 236 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 0.0040 chunk 87 optimal weight: 8.9990 chunk 108 optimal weight: 50.0000 chunk 48 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.145848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094706 restraints weight = 32971.917| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.84 r_work: 0.3058 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18188 Z= 0.152 Angle : 0.482 10.212 25699 Z= 0.282 Chirality : 0.032 0.133 2905 Planarity : 0.003 0.035 2324 Dihedral : 28.023 159.216 4648 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.16 % Allowed : 23.73 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.23), residues: 1478 helix: 3.03 (0.19), residues: 778 sheet: 0.56 (0.37), residues: 220 loop : -0.75 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 124 TYR 0.012 0.001 TYR C 58 PHE 0.011 0.001 PHE E 67 TRP 0.009 0.001 TRP N 132 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00332 (18184) covalent geometry : angle 0.48165 (25691) SS BOND : bond 0.00449 ( 4) SS BOND : angle 0.80830 ( 8) hydrogen bonds : bond 0.03223 ( 993) hydrogen bonds : angle 3.35766 ( 2631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8445 (ttp80) REVERT: K 233 LYS cc_start: 0.5831 (mppt) cc_final: 0.5320 (mmmt) REVERT: N 95 ASP cc_start: 0.8690 (t0) cc_final: 0.8317 (t0) REVERT: N 104 GLU cc_start: 0.8238 (tp30) cc_final: 0.7946 (tp30) REVERT: N 237 GLU cc_start: 0.8188 (tt0) cc_final: 0.7629 (tm-30) REVERT: O 103 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7437 (tpp) REVERT: O 176 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7443 (ttm-80) REVERT: O 237 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6673 (mp0) outliers start: 40 outliers final: 30 residues processed: 263 average time/residue: 0.7536 time to fit residues: 217.4160 Evaluate side-chains 271 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 168 SER Chi-restraints excluded: chain O residue 169 MET Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 237 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 26 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 118 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 163 optimal weight: 0.0670 chunk 108 optimal weight: 50.0000 chunk 80 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 25 GLN O 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.145043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093836 restraints weight = 32446.309| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.83 r_work: 0.3044 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18188 Z= 0.171 Angle : 0.491 9.895 25699 Z= 0.287 Chirality : 0.032 0.128 2905 Planarity : 0.003 0.038 2324 Dihedral : 28.098 160.144 4648 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.32 % Allowed : 23.89 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.23), residues: 1478 helix: 3.04 (0.19), residues: 778 sheet: 0.56 (0.37), residues: 220 loop : -0.77 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 275 TYR 0.012 0.001 TYR C 58 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP N 132 HIS 0.003 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00379 (18184) covalent geometry : angle 0.49125 (25691) SS BOND : bond 0.00489 ( 4) SS BOND : angle 0.80109 ( 8) hydrogen bonds : bond 0.03342 ( 993) hydrogen bonds : angle 3.34727 ( 2631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 92 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: K 204 LEU cc_start: 0.8698 (mm) cc_final: 0.8338 (pp) REVERT: K 233 LYS cc_start: 0.5849 (mppt) cc_final: 0.5384 (mmmt) REVERT: N 45 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8613 (tppt) REVERT: N 95 ASP cc_start: 0.8682 (t0) cc_final: 0.8311 (t0) REVERT: N 103 MET cc_start: 0.8577 (ttt) cc_final: 0.8347 (ttm) REVERT: N 104 GLU cc_start: 0.8263 (tp30) cc_final: 0.7917 (tp30) REVERT: N 237 GLU cc_start: 0.8189 (tt0) cc_final: 0.7642 (tm-30) REVERT: O 103 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7452 (tpp) REVERT: O 176 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7436 (ttm-80) outliers start: 42 outliers final: 32 residues processed: 255 average time/residue: 0.8298 time to fit residues: 231.2345 Evaluate side-chains 273 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 197 MET Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 168 SER Chi-restraints excluded: chain O residue 169 MET Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 236 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 ASN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.140440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086747 restraints weight = 30378.792| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.83 r_work: 0.2887 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18188 Z= 0.209 Angle : 0.516 10.457 25699 Z= 0.300 Chirality : 0.034 0.131 2905 Planarity : 0.003 0.040 2324 Dihedral : 28.287 163.414 4648 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.48 % Allowed : 24.21 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.23), residues: 1478 helix: 2.97 (0.18), residues: 775 sheet: 0.93 (0.38), residues: 200 loop : -0.91 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.014 0.001 TYR C 58 PHE 0.014 0.001 PHE E 67 TRP 0.010 0.001 TRP N 132 HIS 0.004 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00468 (18184) covalent geometry : angle 0.51585 (25691) SS BOND : bond 0.00580 ( 4) SS BOND : angle 0.84843 ( 8) hydrogen bonds : bond 0.03651 ( 993) hydrogen bonds : angle 3.40722 ( 2631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 92 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: H 94 GLU cc_start: 0.9176 (mp0) cc_final: 0.8882 (mp0) REVERT: K 204 LEU cc_start: 0.8677 (mm) cc_final: 0.8316 (pp) REVERT: K 233 LYS cc_start: 0.5916 (mppt) cc_final: 0.5707 (mppt) REVERT: N 45 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8722 (tppt) REVERT: N 95 ASP cc_start: 0.8742 (t0) cc_final: 0.8391 (t0) REVERT: N 104 GLU cc_start: 0.8298 (tp30) cc_final: 0.8049 (tp30) REVERT: N 237 GLU cc_start: 0.8233 (tt0) cc_final: 0.7712 (tm-30) REVERT: O 103 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.7454 (tpp) REVERT: O 176 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7433 (ttm-80) outliers start: 44 outliers final: 33 residues processed: 261 average time/residue: 0.7543 time to fit residues: 215.9194 Evaluate side-chains 275 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 168 SER Chi-restraints excluded: chain O residue 169 MET Chi-restraints excluded: chain O residue 236 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 25 GLN O 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087708 restraints weight = 30508.879| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.86 r_work: 0.2860 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18188 Z= 0.138 Angle : 0.486 11.435 25699 Z= 0.285 Chirality : 0.032 0.158 2905 Planarity : 0.002 0.037 2324 Dihedral : 28.210 161.649 4648 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.40 % Allowed : 24.13 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.23), residues: 1478 helix: 3.12 (0.19), residues: 778 sheet: 0.57 (0.37), residues: 220 loop : -0.74 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 188 TYR 0.011 0.001 TYR C 58 PHE 0.009 0.001 PHE K 149 TRP 0.007 0.001 TRP N 132 HIS 0.003 0.001 HIS O 170 Details of bonding type rmsd covalent geometry : bond 0.00298 (18184) covalent geometry : angle 0.48604 (25691) SS BOND : bond 0.00446 ( 4) SS BOND : angle 0.89762 ( 8) hydrogen bonds : bond 0.03190 ( 993) hydrogen bonds : angle 3.32688 ( 2631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8437 (mtp180) REVERT: H 94 GLU cc_start: 0.9193 (mp0) cc_final: 0.8873 (mp0) REVERT: K 204 LEU cc_start: 0.8657 (mm) cc_final: 0.8281 (pp) REVERT: N 45 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8616 (tppt) REVERT: N 81 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8382 (ttpt) REVERT: N 95 ASP cc_start: 0.8669 (t0) cc_final: 0.8272 (t0) REVERT: N 104 GLU cc_start: 0.8232 (tp30) cc_final: 0.7935 (tp30) REVERT: N 237 GLU cc_start: 0.8124 (tt0) cc_final: 0.7588 (tm-30) REVERT: O 103 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.7398 (tpp) REVERT: O 176 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7446 (ttm-80) outliers start: 43 outliers final: 31 residues processed: 262 average time/residue: 0.8093 time to fit residues: 232.5724 Evaluate side-chains 266 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 168 SER Chi-restraints excluded: chain O residue 169 MET Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 236 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 130 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.139579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084933 restraints weight = 30254.920| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.86 r_work: 0.2811 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 18188 Z= 0.247 Angle : 0.533 9.666 25699 Z= 0.310 Chirality : 0.035 0.163 2905 Planarity : 0.003 0.041 2324 Dihedral : 28.350 163.717 4648 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.24 % Allowed : 24.68 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.23), residues: 1478 helix: 2.95 (0.19), residues: 775 sheet: 0.91 (0.38), residues: 200 loop : -0.94 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 72 TYR 0.015 0.001 TYR C 58 PHE 0.015 0.001 PHE E 67 TRP 0.010 0.001 TRP N 132 HIS 0.004 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00555 (18184) covalent geometry : angle 0.53319 (25691) SS BOND : bond 0.00666 ( 4) SS BOND : angle 0.84342 ( 8) hydrogen bonds : bond 0.03902 ( 993) hydrogen bonds : angle 3.43833 ( 2631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.8438 (mtp180) REVERT: G 92 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: H 94 GLU cc_start: 0.9204 (mp0) cc_final: 0.8872 (mp0) REVERT: K 204 LEU cc_start: 0.8711 (mm) cc_final: 0.8326 (pp) REVERT: K 233 LYS cc_start: 0.5402 (mppt) cc_final: 0.5131 (mmmt) REVERT: N 45 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8633 (tppt) REVERT: N 95 ASP cc_start: 0.8684 (t0) cc_final: 0.8274 (t0) REVERT: N 104 GLU cc_start: 0.8325 (tp30) cc_final: 0.8027 (tp30) REVERT: N 237 GLU cc_start: 0.8125 (tt0) cc_final: 0.7575 (tm-30) REVERT: O 103 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7343 (tpp) outliers start: 41 outliers final: 32 residues processed: 261 average time/residue: 0.7714 time to fit residues: 220.9176 Evaluate side-chains 268 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 168 SER Chi-restraints excluded: chain O residue 169 MET Chi-restraints excluded: chain O residue 191 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 159 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087243 restraints weight = 30259.853| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.85 r_work: 0.2850 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18188 Z= 0.132 Angle : 0.498 9.878 25699 Z= 0.292 Chirality : 0.032 0.163 2905 Planarity : 0.003 0.037 2324 Dihedral : 28.317 162.960 4648 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.93 % Allowed : 24.68 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.23), residues: 1478 helix: 3.06 (0.19), residues: 778 sheet: 0.54 (0.37), residues: 220 loop : -0.74 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.011 0.001 TYR C 58 PHE 0.009 0.001 PHE K 149 TRP 0.007 0.001 TRP N 132 HIS 0.003 0.001 HIS O 170 Details of bonding type rmsd covalent geometry : bond 0.00281 (18184) covalent geometry : angle 0.49784 (25691) SS BOND : bond 0.00469 ( 4) SS BOND : angle 1.00215 ( 8) hydrogen bonds : bond 0.03285 ( 993) hydrogen bonds : angle 3.36783 ( 2631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.8438 (mtp180) REVERT: G 92 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: H 94 GLU cc_start: 0.9187 (mp0) cc_final: 0.8873 (mp0) REVERT: K 204 LEU cc_start: 0.8700 (mm) cc_final: 0.8319 (pp) REVERT: K 233 LYS cc_start: 0.5411 (mppt) cc_final: 0.5135 (mmmt) REVERT: N 81 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8403 (ttpt) REVERT: N 95 ASP cc_start: 0.8676 (t0) cc_final: 0.8285 (t0) REVERT: N 104 GLU cc_start: 0.8311 (tp30) cc_final: 0.7997 (tp30) REVERT: N 237 GLU cc_start: 0.8129 (tt0) cc_final: 0.7606 (tm-30) REVERT: O 176 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7588 (ttm110) outliers start: 37 outliers final: 32 residues processed: 258 average time/residue: 0.7321 time to fit residues: 207.3829 Evaluate side-chains 268 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 168 SER Chi-restraints excluded: chain O residue 169 MET Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 125 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 131 optimal weight: 0.0980 chunk 132 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 ASN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086781 restraints weight = 30457.491| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.87 r_work: 0.2852 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18188 Z= 0.170 Angle : 0.496 9.477 25699 Z= 0.290 Chirality : 0.032 0.159 2905 Planarity : 0.003 0.034 2324 Dihedral : 28.181 160.850 4648 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.69 % Allowed : 25.00 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.23), residues: 1478 helix: 3.12 (0.19), residues: 778 sheet: 0.54 (0.37), residues: 220 loop : -0.75 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 72 TYR 0.012 0.001 TYR C 58 PHE 0.011 0.001 PHE E 67 TRP 0.009 0.001 TRP N 132 HIS 0.003 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00375 (18184) covalent geometry : angle 0.49614 (25691) SS BOND : bond 0.00495 ( 4) SS BOND : angle 0.81438 ( 8) hydrogen bonds : bond 0.03311 ( 993) hydrogen bonds : angle 3.29144 ( 2631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8485 (mtp180) REVERT: G 92 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: H 94 GLU cc_start: 0.9202 (mp0) cc_final: 0.8893 (mp0) REVERT: K 204 LEU cc_start: 0.8712 (mm) cc_final: 0.8319 (pp) REVERT: K 233 LYS cc_start: 0.5603 (mppt) cc_final: 0.5325 (mmmt) REVERT: N 95 ASP cc_start: 0.8680 (t0) cc_final: 0.8288 (t0) REVERT: N 104 GLU cc_start: 0.8320 (tp30) cc_final: 0.8005 (tp30) REVERT: N 237 GLU cc_start: 0.8111 (tt0) cc_final: 0.7575 (tm-30) REVERT: O 176 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7408 (ttm-80) outliers start: 34 outliers final: 30 residues processed: 254 average time/residue: 0.8148 time to fit residues: 226.6504 Evaluate side-chains 270 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 169 MET Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.138948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.084043 restraints weight = 30609.912| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.90 r_work: 0.2792 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 18188 Z= 0.298 Angle : 0.563 9.428 25699 Z= 0.326 Chirality : 0.037 0.164 2905 Planarity : 0.003 0.038 2324 Dihedral : 28.475 165.552 4648 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.85 % Allowed : 24.92 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.23), residues: 1478 helix: 2.85 (0.19), residues: 773 sheet: 0.85 (0.38), residues: 200 loop : -1.00 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.017 0.002 TYR C 58 PHE 0.016 0.002 PHE E 67 TRP 0.010 0.001 TRP N 132 HIS 0.006 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00677 (18184) covalent geometry : angle 0.56267 (25691) SS BOND : bond 0.00772 ( 4) SS BOND : angle 0.89803 ( 8) hydrogen bonds : bond 0.04224 ( 993) hydrogen bonds : angle 3.50275 ( 2631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10131.72 seconds wall clock time: 172 minutes 17.19 seconds (10337.19 seconds total)