Starting phenix.real_space_refine on Mon Jun 16 05:15:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0g_26258/06_2025/7u0g_26258.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0g_26258/06_2025/7u0g_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u0g_26258/06_2025/7u0g_26258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0g_26258/06_2025/7u0g_26258.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0g_26258/06_2025/7u0g_26258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0g_26258/06_2025/7u0g_26258.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.85, per 1000 atoms: 0.58 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: 4.57 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 7.68 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: 7.60 Time building geometry restraints manager: 5.52 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.430 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 49.300 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.100 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.013 0.001 TRP O 199 HIS 0.004 0.001 HIS N 249 PHE 0.012 0.001 PHE K 149 TYR 0.022 0.001 TYR F 88 ARG 0.007 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.11223 ( 993) hydrogen bonds : angle 4.97772 ( 2631) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.96962 ( 8) covalent geometry : bond 0.00582 (18184) covalent geometry : angle 0.77765 (25691) *********************** 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 : 1.522 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: 0.8377 (mm-30) cc_final: 0.8091 (mp0) outliers start: 11 outliers final: 14 residues processed: 272 average time/residue: 1.6243 time to fit residues: 484.2454 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 : 1.683 ------------------------------------------------------------------------------- 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 143 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086748 restraints weight = 30442.291| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.83 r_work: 0.2855 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 18188 Z= 0.224 Angle : 0.531 7.327 25699 Z= 0.310 Chirality : 0.035 0.125 2905 Planarity : 0.003 0.040 2324 Dihedral : 28.238 158.117 4669 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 3.09 % Allowed : 22.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1478 helix: 2.33 (0.18), residues: 776 sheet: 0.74 (0.38), residues: 196 loop : -1.11 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 132 HIS 0.004 0.001 HIS O 249 PHE 0.012 0.001 PHE E 67 TYR 0.016 0.001 TYR C 58 ARG 0.002 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 993) hydrogen bonds : angle 3.76137 ( 2631) SS BOND : bond 0.00636 ( 4) SS BOND : angle 0.93249 ( 8) covalent geometry : bond 0.00501 (18184) covalent geometry : angle 0.53093 (25691) *********************** 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 288 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 1.646 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: 0.8678 (ttm110) cc_final: 0.8473 (ttp80) REVERT: D 69 ASP cc_start: 0.9417 (t0) cc_final: 0.9169 (t0) REVERT: K 153 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8542 (pt) REVERT: K 233 LYS cc_start: 0.5324 (tptp) cc_final: 0.5028 (mmmt) REVERT: N 95 ASP cc_start: 0.8631 (t0) cc_final: 0.8219 (t0) REVERT: N 104 GLU cc_start: 0.8254 (tp30) cc_final: 0.7942 (tp30) REVERT: N 237 GLU cc_start: 0.8056 (tt0) cc_final: 0.7437 (tm-30) REVERT: O 32 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8020 (mm-30) REVERT: O 103 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.7470 (tpp) REVERT: O 176 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7609 (ttm-80) outliers start: 39 outliers final: 24 residues processed: 262 average time/residue: 1.5716 time to fit residues: 453.4094 Evaluate side-chains 261 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 85 MET 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 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 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 Chi-restraints excluded: chain O residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 105 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 86 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.3702 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.141919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088170 restraints weight = 30543.757| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.83 r_work: 0.2880 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18188 Z= 0.166 Angle : 0.490 10.351 25699 Z= 0.288 Chirality : 0.032 0.140 2905 Planarity : 0.003 0.044 2324 Dihedral : 28.130 160.467 4650 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.09 % Allowed : 23.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.23), residues: 1478 helix: 2.76 (0.18), residues: 778 sheet: 0.46 (0.37), residues: 220 loop : -0.82 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 132 HIS 0.003 0.001 HIS O 249 PHE 0.010 0.001 PHE E 67 TYR 0.012 0.001 TYR C 58 ARG 0.002 0.000 ARG N 124 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 993) hydrogen bonds : angle 3.52151 ( 2631) SS BOND : bond 0.00473 ( 4) SS BOND : angle 0.79840 ( 8) covalent geometry : bond 0.00363 (18184) covalent geometry : angle 0.48978 (25691) *********************** 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 282 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 1.608 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: 0.8683 (ttm110) cc_final: 0.8481 (ttp80) REVERT: D 69 ASP cc_start: 0.9422 (t0) cc_final: 0.9163 (t0) REVERT: K 153 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8426 (pt) REVERT: K 233 LYS cc_start: 0.5410 (tptp) cc_final: 0.5198 (mppt) REVERT: N 33 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8730 (mm) REVERT: N 95 ASP cc_start: 0.8677 (t0) cc_final: 0.8320 (t0) REVERT: N 104 GLU cc_start: 0.8265 (tp30) cc_final: 0.7954 (tp30) REVERT: N 237 GLU cc_start: 0.8156 (tt0) cc_final: 0.7596 (tm-30) REVERT: O 103 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7455 (tpp) REVERT: O 176 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7562 (ttm-80) outliers start: 39 outliers final: 28 residues processed: 255 average time/residue: 1.6045 time to fit residues: 449.5960 Evaluate side-chains 269 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 111 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 59 LYS 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 124 SER Chi-restraints excluded: chain K residue 153 LEU 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 M residue 197 MET 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 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 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 26 optimal weight: 0.0170 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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** G 111 ASN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.142909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089076 restraints weight = 30752.741| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.86 r_work: 0.2899 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18188 Z= 0.127 Angle : 0.482 11.115 25699 Z= 0.283 Chirality : 0.031 0.130 2905 Planarity : 0.003 0.036 2324 Dihedral : 28.102 159.955 4650 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.45 % Allowed : 24.60 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.23), residues: 1478 helix: 2.89 (0.19), residues: 781 sheet: 0.52 (0.37), residues: 220 loop : -0.76 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.003 0.001 HIS N 170 PHE 0.009 0.001 PHE K 149 TYR 0.009 0.001 TYR C 58 ARG 0.002 0.000 ARG N 124 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 993) hydrogen bonds : angle 3.47059 ( 2631) SS BOND : bond 0.00392 ( 4) SS BOND : angle 0.85286 ( 8) covalent geometry : bond 0.00272 (18184) covalent geometry : angle 0.48225 (25691) *********************** 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 279 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 1.527 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: D 69 ASP cc_start: 0.9370 (t0) cc_final: 0.9139 (t0) REVERT: G 92 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: H 94 GLU cc_start: 0.9177 (mp0) cc_final: 0.8904 (mp0) REVERT: K 233 LYS cc_start: 0.5435 (tptp) cc_final: 0.5222 (mppt) REVERT: N 95 ASP cc_start: 0.8679 (t0) cc_final: 0.8312 (t0) REVERT: N 104 GLU cc_start: 0.8187 (tp30) cc_final: 0.7899 (tp30) REVERT: N 237 GLU cc_start: 0.8186 (tt0) cc_final: 0.7609 (tm-30) REVERT: O 32 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8092 (mm-30) REVERT: O 34 VAL cc_start: 0.8944 (m) cc_final: 0.8725 (p) REVERT: O 176 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7606 (ttm-80) outliers start: 31 outliers final: 26 residues processed: 259 average time/residue: 1.6159 time to fit residues: 459.6983 Evaluate side-chains 264 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 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 H residue 44 LYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 40 VAL 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 118 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 122 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084932 restraints weight = 30631.441| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.88 r_work: 0.2821 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 18188 Z= 0.285 Angle : 0.552 7.499 25699 Z= 0.321 Chirality : 0.037 0.129 2905 Planarity : 0.003 0.045 2324 Dihedral : 28.450 164.707 4650 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.88 % Allowed : 23.50 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1478 helix: 2.73 (0.19), residues: 773 sheet: 0.65 (0.37), residues: 212 loop : -0.90 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 132 HIS 0.005 0.001 HIS O 249 PHE 0.017 0.002 PHE E 67 TYR 0.017 0.002 TYR C 58 ARG 0.003 0.000 ARG N 124 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 993) hydrogen bonds : angle 3.61353 ( 2631) SS BOND : bond 0.00777 ( 4) SS BOND : angle 0.85076 ( 8) covalent geometry : bond 0.00646 (18184) covalent geometry : angle 0.55141 (25691) *********************** 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 292 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 1.699 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: D 120 THR cc_start: 0.9651 (OUTLIER) cc_final: 0.9440 (m) REVERT: E 131 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.8394 (mtp180) REVERT: G 92 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: H 94 GLU cc_start: 0.9212 (mp0) cc_final: 0.8868 (mp0) REVERT: K 153 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8399 (pt) REVERT: N 33 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8745 (mm) REVERT: N 45 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8669 (tppt) REVERT: N 81 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8263 (ttpt) REVERT: N 95 ASP cc_start: 0.8727 (t0) cc_final: 0.8310 (t0) REVERT: N 237 GLU cc_start: 0.8249 (tt0) cc_final: 0.7700 (tm-30) REVERT: O 103 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7386 (tpp) REVERT: O 176 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7578 (ttm-80) REVERT: O 237 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6747 (mp0) outliers start: 49 outliers final: 30 residues processed: 262 average time/residue: 1.5833 time to fit residues: 456.0020 Evaluate side-chains 269 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 60 LYS Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 120 THR 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 52 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain L residue 142 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 33 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 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 236 LEU Chi-restraints excluded: chain O residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 14 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087142 restraints weight = 30635.835| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.82 r_work: 0.2856 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18188 Z= 0.144 Angle : 0.510 7.406 25699 Z= 0.300 Chirality : 0.033 0.129 2905 Planarity : 0.003 0.050 2324 Dihedral : 28.456 163.911 4650 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.77 % Allowed : 24.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.23), residues: 1478 helix: 2.78 (0.19), residues: 778 sheet: 0.93 (0.38), residues: 200 loop : -0.93 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS O 170 PHE 0.010 0.001 PHE E 67 TYR 0.011 0.001 TYR C 58 ARG 0.003 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 993) hydrogen bonds : angle 3.53441 ( 2631) SS BOND : bond 0.00602 ( 4) SS BOND : angle 1.03031 ( 8) covalent geometry : bond 0.00313 (18184) covalent geometry : angle 0.50941 (25691) *********************** 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 282 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 1.672 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: D 120 THR cc_start: 0.9643 (OUTLIER) cc_final: 0.9438 (m) REVERT: E 131 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8369 (mtp180) REVERT: G 92 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: H 94 GLU cc_start: 0.9178 (mp0) cc_final: 0.8861 (mp0) REVERT: K 233 LYS cc_start: 0.5662 (mppt) cc_final: 0.5174 (mmmt) REVERT: N 33 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8719 (mm) REVERT: N 81 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8431 (ttpt) REVERT: N 95 ASP cc_start: 0.8700 (t0) cc_final: 0.8318 (t0) REVERT: N 104 GLU cc_start: 0.8292 (tp30) cc_final: 0.7978 (tp30) REVERT: N 237 GLU cc_start: 0.8271 (tt0) cc_final: 0.7792 (tm-30) REVERT: O 34 VAL cc_start: 0.8952 (m) cc_final: 0.8747 (p) REVERT: O 176 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7554 (ttm-80) outliers start: 35 outliers final: 25 residues processed: 263 average time/residue: 1.5489 time to fit residues: 448.7157 Evaluate side-chains 266 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 120 THR 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 K residue 153 LEU Chi-restraints excluded: chain L residue 204 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 33 LEU Chi-restraints excluded: chain N residue 40 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 111 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091588 restraints weight = 32444.396| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.85 r_work: 0.3001 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18188 Z= 0.236 Angle : 0.524 7.027 25699 Z= 0.307 Chirality : 0.035 0.137 2905 Planarity : 0.003 0.039 2324 Dihedral : 28.433 163.638 4650 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.80 % Allowed : 23.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1478 helix: 2.79 (0.18), residues: 773 sheet: 0.90 (0.38), residues: 200 loop : -1.01 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 132 HIS 0.004 0.001 HIS O 249 PHE 0.014 0.001 PHE E 67 TYR 0.014 0.001 TYR C 58 ARG 0.003 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 993) hydrogen bonds : angle 3.50784 ( 2631) SS BOND : bond 0.00653 ( 4) SS BOND : angle 0.88575 ( 8) covalent geometry : bond 0.00532 (18184) covalent geometry : angle 0.52411 (25691) *********************** 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 291 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 1.471 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: 0.8667 (ttp80) cc_final: 0.8425 (ttp80) REVERT: D 120 THR cc_start: 0.9639 (OUTLIER) cc_final: 0.9420 (m) REVERT: E 131 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8428 (mtp180) REVERT: G 92 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: G 96 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8791 (tttp) REVERT: H 94 GLU cc_start: 0.9196 (mp0) cc_final: 0.8841 (mp0) REVERT: K 153 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8409 (pt) REVERT: K 233 LYS cc_start: 0.5824 (mppt) cc_final: 0.5350 (mmmt) REVERT: N 45 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8660 (tppt) REVERT: N 81 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8381 (ttpt) REVERT: N 95 ASP cc_start: 0.8710 (t0) cc_final: 0.8333 (t0) REVERT: O 176 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7423 (ttm-80) outliers start: 48 outliers final: 30 residues processed: 261 average time/residue: 1.6233 time to fit residues: 464.8680 Evaluate side-chains 276 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 120 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 59 LYS 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 96 LYS 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 K residue 153 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 200 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 57 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 chunk 83 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093027 restraints weight = 32510.861| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.84 r_work: 0.3023 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18188 Z= 0.143 Angle : 0.506 7.260 25699 Z= 0.298 Chirality : 0.032 0.133 2905 Planarity : 0.003 0.034 2324 Dihedral : 28.428 163.335 4650 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.77 % Allowed : 24.60 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.23), residues: 1478 helix: 2.83 (0.19), residues: 778 sheet: 0.92 (0.38), residues: 200 loop : -0.95 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.005 0.001 HIS N 170 PHE 0.010 0.001 PHE E 67 TYR 0.011 0.001 TYR C 58 ARG 0.003 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 993) hydrogen bonds : angle 3.46453 ( 2631) SS BOND : bond 0.00500 ( 4) SS BOND : angle 1.10248 ( 8) covalent geometry : bond 0.00312 (18184) covalent geometry : angle 0.50577 (25691) *********************** 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 271 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 1.582 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 72 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8425 (ttp80) REVERT: D 120 THR cc_start: 0.9633 (OUTLIER) cc_final: 0.9420 (m) REVERT: G 92 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: G 96 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8786 (tttp) REVERT: H 94 GLU cc_start: 0.9185 (mp0) cc_final: 0.8840 (mp0) REVERT: K 153 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8394 (pt) REVERT: K 204 LEU cc_start: 0.8678 (mm) cc_final: 0.8313 (pp) REVERT: K 233 LYS cc_start: 0.5760 (mppt) cc_final: 0.5299 (mmmt) REVERT: N 81 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8379 (ttpt) REVERT: N 95 ASP cc_start: 0.8706 (t0) cc_final: 0.8334 (t0) REVERT: O 176 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7610 (ttm110) outliers start: 35 outliers final: 25 residues processed: 251 average time/residue: 1.5232 time to fit residues: 421.6484 Evaluate side-chains 265 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 THR 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 96 LYS Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain L residue 142 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 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 138 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 161 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.089768 restraints weight = 32735.951| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.87 r_work: 0.2963 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 18188 Z= 0.395 Angle : 0.619 8.797 25699 Z= 0.357 Chirality : 0.042 0.141 2905 Planarity : 0.004 0.039 2324 Dihedral : 28.783 169.508 4650 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.85 % Allowed : 24.60 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1478 helix: 2.53 (0.19), residues: 771 sheet: 0.49 (0.37), residues: 214 loop : -1.13 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 132 HIS 0.006 0.001 HIS O 249 PHE 0.018 0.002 PHE E 67 TYR 0.018 0.002 TYR C 58 ARG 0.005 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 993) hydrogen bonds : angle 3.73034 ( 2631) SS BOND : bond 0.00942 ( 4) SS BOND : angle 0.97338 ( 8) covalent geometry : bond 0.00902 (18184) covalent geometry : angle 0.61918 (25691) *********************** 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 268 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 1.707 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: 0.9406 (OUTLIER) cc_final: 0.8501 (mtp180) REVERT: G 92 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: G 96 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8777 (tttp) REVERT: H 94 GLU cc_start: 0.9201 (mp0) cc_final: 0.8806 (mp0) REVERT: K 153 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8291 (pt) REVERT: K 204 LEU cc_start: 0.8704 (mm) cc_final: 0.8327 (pp) REVERT: N 95 ASP cc_start: 0.8739 (t0) cc_final: 0.8307 (t0) outliers start: 36 outliers final: 25 residues processed: 246 average time/residue: 1.4930 time to fit residues: 405.7515 Evaluate side-chains 252 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 120 THR 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 96 LYS 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 K residue 153 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 144 LYS 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 87 LYS Chi-restraints excluded: chain N residue 138 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 155 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.144669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093580 restraints weight = 32907.927| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.83 r_work: 0.3033 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18188 Z= 0.133 Angle : 0.517 9.247 25699 Z= 0.303 Chirality : 0.033 0.227 2905 Planarity : 0.003 0.059 2324 Dihedral : 28.619 165.642 4650 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.90 % Allowed : 25.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.23), residues: 1478 helix: 2.84 (0.19), residues: 778 sheet: 0.89 (0.38), residues: 196 loop : -1.05 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS N 170 PHE 0.009 0.001 PHE K 149 TYR 0.010 0.001 TYR C 58 ARG 0.005 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 993) hydrogen bonds : angle 3.50615 ( 2631) SS BOND : bond 0.00485 ( 4) SS BOND : angle 1.11151 ( 8) covalent geometry : bond 0.00283 (18184) covalent geometry : angle 0.51627 (25691) ********************** 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 261 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 1.706 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: E 131 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8425 (mtp180) REVERT: G 96 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8753 (tttp) REVERT: H 94 GLU cc_start: 0.9177 (mp0) cc_final: 0.8836 (mp0) REVERT: K 153 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8258 (pt) REVERT: K 204 LEU cc_start: 0.8678 (mm) cc_final: 0.8321 (pp) REVERT: N 81 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8342 (ttpt) REVERT: N 95 ASP cc_start: 0.8686 (t0) cc_final: 0.8289 (t0) REVERT: N 104 GLU cc_start: 0.8445 (tp30) cc_final: 0.8145 (tp30) REVERT: O 237 GLU cc_start: 0.6869 (mp0) cc_final: 0.6609 (mp0) outliers start: 24 outliers final: 17 residues processed: 247 average time/residue: 2.0825 time to fit residues: 570.2663 Evaluate side-chains 248 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 LYS Chi-restraints excluded: chain H residue 62 ILE 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 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 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 168 SER Chi-restraints excluded: chain O residue 169 MET 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 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091867 restraints weight = 32677.588| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.83 r_work: 0.2980 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18188 Z= 0.224 Angle : 0.530 8.771 25699 Z= 0.310 Chirality : 0.034 0.133 2905 Planarity : 0.003 0.025 2324 Dihedral : 28.496 163.855 4650 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.06 % Allowed : 25.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1478 helix: 2.83 (0.19), residues: 773 sheet: 0.61 (0.37), residues: 212 loop : -0.97 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 132 HIS 0.004 0.001 HIS N 170 PHE 0.014 0.001 PHE E 67 TYR 0.014 0.001 TYR C 58 ARG 0.005 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 993) hydrogen bonds : angle 3.49195 ( 2631) SS BOND : bond 0.00630 ( 4) SS BOND : angle 0.88782 ( 8) covalent geometry : bond 0.00503 (18184) covalent geometry : angle 0.52959 (25691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20437.43 seconds wall clock time: 352 minutes 57.51 seconds (21177.51 seconds total)