Starting phenix.real_space_refine on Sat Jul 4 02:31:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0i_26260/07_2026/7u0i_26260.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0i_26260/07_2026/7u0i_26260.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/7u0i_26260/07_2026/7u0i_26260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0i_26260/07_2026/7u0i_26260.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0i_26260/07_2026/7u0i_26260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0i_26260/07_2026/7u0i_26260.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.139 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 298 5.49 5 S 38 5.16 5 C 9730 2.51 5 N 3038 2.21 5 O 3784 1.98 5 H 1220 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18108 Number of models: 1 Model: "" Number of chains: 14 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: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 664 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 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: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" 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: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3084 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3025 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "L" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1212 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1212 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1765 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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 Time building chain proxies: 3.32, per 1000 atoms: 0.18 Number of scatterers: 18108 At special positions: 0 Unit cell: (139.392, 124.608, 137.28, 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 38 16.00 P 298 15.00 O 3784 8.00 N 3038 7.00 C 9730 6.00 H 1220 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 246 " distance=2.03 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 491.2 milliseconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 23 sheets defined 51.4% alpha, 20.1% beta 129 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.502A 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 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.750A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 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 removed outlier: 3.530A pdb=" N THR D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.537A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.676A 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 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.526A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) 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 'L' and resid 141 through 161 removed outlier: 3.544A 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: 3.581A 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 removed outlier: 3.540A pdb=" N ILE M 184 " --> pdb=" O SER M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 212 Proline residue: M 202 - end of helix Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.501A pdb=" N ASP K 112 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 109 through 113' Processing helix chain 'K' and resid 237 through 241 removed outlier: 3.708A pdb=" N THR K 241 " --> pdb=" O SER K 238 " (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 84 through 87 removed outlier: 3.624A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.596A pdb=" N ASP N 112 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 113' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.539A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 237 through 241' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.984A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.684A 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 42 through 43 removed outlier: 7.139A pdb=" N ARG G 42 " --> 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 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.856A pdb=" N VAL K 101 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.391A pdb=" N GLU K 32 " --> pdb=" O THR K 139 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.391A pdb=" N GLU K 32 " --> pdb=" O THR K 139 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR K 131 " --> pdb=" O ARG K 120 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER K 122 " --> pdb=" O LEU K 129 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU K 129 " --> pdb=" O SER K 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 162 through 164 removed outlier: 4.098A pdb=" N PHE K 229 " --> pdb=" O CYS K 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.950A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.950A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.252A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.177A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 39 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 162 through 164 removed outlier: 4.187A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.730A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 168 through 171 659 hydrogen bonds defined for protein. 1848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 311 hydrogen bonds 622 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 2.27 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: 1225 1.03 - 1.23: 240 1.23 - 1.43: 7975 1.43 - 1.62: 9532 1.62 - 1.82: 59 Bond restraints: 19031 Sorted by residual: bond pdb=" C LYS B 59 " pdb=" O LYS B 59 " ideal model delta sigma weight residual 1.237 1.008 0.228 1.19e-02 7.06e+03 3.68e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.237 1.019 0.218 1.16e-02 7.43e+03 3.53e+02 bond pdb=" C MET G 51 " pdb=" O MET G 51 " ideal model delta sigma weight residual 1.237 1.013 0.223 1.19e-02 7.06e+03 3.52e+02 bond pdb=" C ARG D 93 " pdb=" O ARG D 93 " ideal model delta sigma weight residual 1.236 1.013 0.223 1.22e-02 6.72e+03 3.35e+02 bond pdb=" C ARG E 63 " pdb=" O ARG E 63 " ideal model delta sigma weight residual 1.234 1.031 0.203 1.27e-02 6.20e+03 2.55e+02 ... (remaining 19026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 27991 4.70 - 9.40: 112 9.40 - 14.10: 10 14.10 - 18.80: 4 18.80 - 23.51: 4 Bond angle restraints: 28121 Sorted by residual: angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 110.80 132.35 -21.55 2.13e+00 2.20e-01 1.02e+02 angle pdb=" CG ARG F 95 " pdb=" CD ARG F 95 " pdb=" NE ARG F 95 " ideal model delta sigma weight residual 112.00 90.95 21.05 2.20e+00 2.07e-01 9.16e+01 angle pdb=" CG MET C 51 " pdb=" SD MET C 51 " pdb=" CE MET C 51 " ideal model delta sigma weight residual 100.90 82.71 18.19 2.20e+00 2.07e-01 6.84e+01 angle pdb=" C MET C 51 " pdb=" CA MET C 51 " pdb=" CB MET C 51 " ideal model delta sigma weight residual 110.90 97.89 13.01 1.58e+00 4.01e-01 6.79e+01 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 89.19 23.51 3.00e+00 1.11e-01 6.14e+01 ... (remaining 28116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.20: 8540 32.20 - 64.40: 1808 64.40 - 96.60: 52 96.60 - 128.80: 1 128.80 - 161.00: 3 Dihedral angle restraints: 10404 sinusoidal: 6374 harmonic: 4030 Sorted by residual: dihedral pdb=" C MET C 51 " pdb=" N MET C 51 " pdb=" CA MET C 51 " pdb=" CB MET C 51 " ideal model delta harmonic sigma weight residual -122.60 -106.48 -16.12 0 2.50e+00 1.60e-01 4.16e+01 dihedral pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CA LYS C 13 " pdb=" CB LYS C 13 " ideal model delta harmonic sigma weight residual 122.80 136.47 -13.67 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" C LYS C 13 " pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" CB LYS C 13 " ideal model delta harmonic sigma weight residual -122.60 -136.23 13.63 0 2.50e+00 1.60e-01 2.97e+01 ... (remaining 10401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2838 0.145 - 0.290: 10 0.290 - 0.435: 9 0.435 - 0.580: 5 0.580 - 0.725: 1 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CA LYS C 13 " pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CB LYS C 13 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ARG B 92 " pdb=" N ARG B 92 " pdb=" C ARG B 92 " pdb=" CB ARG B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA MET G 51 " pdb=" N MET G 51 " pdb=" C MET G 51 " pdb=" CB MET G 51 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.81e+00 ... (remaining 2860 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET G 51 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" C MET G 51 " -0.099 2.00e-02 2.50e+03 pdb=" O MET G 51 " 0.038 2.00e-02 2.50e+03 pdb=" N ALA G 52 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " -0.027 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C GLU C 92 " 0.097 2.00e-02 2.50e+03 pdb=" O GLU C 92 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU C 93 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 51 " -0.025 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C MET C 51 " 0.084 2.00e-02 2.50e+03 pdb=" O MET C 51 " -0.032 2.00e-02 2.50e+03 pdb=" N ALA C 52 " -0.028 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 198 2.23 - 2.82: 9538 2.82 - 3.42: 22300 3.42 - 4.01: 44297 4.01 - 4.60: 61307 Nonbonded interactions: 137640 Sorted by model distance: nonbonded pdb=" HG LEU L 200 " pdb="HD12 LEU L 204 " model vdw 1.641 2.440 nonbonded pdb=" O ASP M 166 " pdb=" HG1 THR M 170 " model vdw 1.802 2.450 nonbonded pdb=" O GLN L 155 " pdb=" HG1 THR L 159 " model vdw 1.802 2.450 nonbonded pdb=" HE ARG L 157 " pdb=" OE2 GLU L 188 " model vdw 1.802 2.450 nonbonded pdb=" OP1 DT J 93 " pdb="HH12 ARG L 157 " model vdw 1.810 2.450 ... (remaining 137635 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 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) selection = (chain 'F' and ((resid 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 125) selection = (chain 'H' and (resid 31 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 'K' selection = (chain 'N' and (resid 23 through 264 or (resid 265 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.260 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 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 : 0.012 0.228 17815 Z= 0.857 Angle : 0.959 23.505 25345 Z= 0.713 Chirality : 0.055 0.725 2863 Planarity : 0.006 0.073 2164 Dihedral : 26.815 160.996 7468 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.88 % Favored : 95.97 % Rotamer: Outliers : 1.56 % Allowed : 20.83 % Favored : 77.61 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1340 helix: 0.86 (0.18), residues: 664 sheet: 0.20 (0.35), residues: 212 loop : -1.30 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 72 TYR 0.017 0.002 TYR A 41 PHE 0.010 0.001 PHE E 84 TRP 0.015 0.001 TRP K 199 HIS 0.016 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01218 / 0.86 (17811) covalent geometry : angle 0.95871 / 0.71 (25337) SS BOND : bond 0.00443 / 0.26 ( 4) SS BOND : angle 0.99945 / 0.51 ( 8) hydrogen bonds : bond 0.12132 / 8.21 ( 947) hydrogen bonds : angle 5.23287 / 3.69 ( 2470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.353 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 72 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: H 57 SER cc_start: 0.8947 (p) cc_final: 0.8705 (p) REVERT: N 237 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8568 (mp0) outliers start: 18 outliers final: 15 residues processed: 266 average time/residue: 0.6504 time to fit residues: 189.9398 Evaluate side-chains 247 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 230 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.0050 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 94 ASN C 104 GLN D 85 ASN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN H 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085636 restraints weight = 31499.288| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.92 r_work: 0.2899 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17815 Z= 0.260 Angle : 0.622 9.631 25345 Z= 0.356 Chirality : 0.042 0.210 2863 Planarity : 0.004 0.051 2164 Dihedral : 29.768 159.788 4876 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.54 % Allowed : 21.61 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.23), residues: 1340 helix: 1.92 (0.20), residues: 670 sheet: 0.34 (0.37), residues: 216 loop : -1.25 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 93 TYR 0.019 0.001 TYR C 50 PHE 0.015 0.001 PHE D 71 TRP 0.007 0.001 TRP N 132 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.26 (17811) covalent geometry : angle 0.62180 / 0.36 (25337) SS BOND : bond 0.00404 / 0.25 ( 4) SS BOND : angle 0.87678 / 0.44 ( 8) hydrogen bonds : bond 0.04860 / 3.21 ( 947) hydrogen bonds : angle 3.99386 / 2.93 ( 2470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.493 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 51 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8773 (tpp) REVERT: C 91 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8653 (tm-30) REVERT: G 87 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9052 (mt) REVERT: G 91 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8545 (tm-30) REVERT: K 162 MET cc_start: 0.9283 (mmp) cc_final: 0.9078 (mmp) REVERT: N 95 ASP cc_start: 0.8836 (t0) cc_final: 0.8385 (t0) outliers start: 41 outliers final: 28 residues processed: 234 average time/residue: 0.6687 time to fit residues: 171.3792 Evaluate side-chains 254 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 150 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 115 optimal weight: 0.0570 chunk 91 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087476 restraints weight = 31737.156| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.86 r_work: 0.2933 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17815 Z= 0.143 Angle : 0.552 9.562 25345 Z= 0.325 Chirality : 0.038 0.192 2863 Planarity : 0.004 0.044 2164 Dihedral : 29.759 158.564 4867 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.11 % Allowed : 22.21 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.23), residues: 1340 helix: 2.29 (0.20), residues: 675 sheet: 0.43 (0.36), residues: 214 loop : -1.14 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 TYR 0.012 0.001 TYR C 50 PHE 0.007 0.001 PHE F 61 TRP 0.005 0.001 TRP N 69 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (17811) covalent geometry : angle 0.55225 / 0.33 (25337) SS BOND : bond 0.00258 / 0.16 ( 4) SS BOND : angle 0.54092 / 0.24 ( 8) hydrogen bonds : bond 0.03997 / 2.62 ( 947) hydrogen bonds : angle 3.78824 / 2.79 ( 2470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.515 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 91 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8622 (tm-30) REVERT: G 91 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: H 72 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8455 (tm-30) REVERT: N 68 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8343 (pt0) REVERT: N 95 ASP cc_start: 0.8802 (t0) cc_final: 0.8286 (t0) REVERT: N 237 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8283 (mp0) REVERT: N 263 GLU cc_start: 0.8221 (tp30) cc_final: 0.7961 (tm-30) outliers start: 36 outliers final: 26 residues processed: 245 average time/residue: 0.7141 time to fit residues: 190.7788 Evaluate side-chains 254 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 176 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 95 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085778 restraints weight = 31787.198| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.91 r_work: 0.2908 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17815 Z= 0.176 Angle : 0.536 8.585 25345 Z= 0.317 Chirality : 0.037 0.199 2863 Planarity : 0.003 0.041 2164 Dihedral : 29.800 159.647 4864 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.89 % Allowed : 21.78 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1340 helix: 2.55 (0.20), residues: 675 sheet: 0.45 (0.35), residues: 238 loop : -1.02 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 176 TYR 0.010 0.001 TYR B 51 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (17811) covalent geometry : angle 0.53578 / 0.32 (25337) SS BOND : bond 0.00488 / 0.29 ( 4) SS BOND : angle 0.78434 / 0.38 ( 8) hydrogen bonds : bond 0.04037 / 2.66 ( 947) hydrogen bonds : angle 3.58348 / 2.65 ( 2470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.334 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: A 59 GLU cc_start: 0.8838 (pm20) cc_final: 0.8534 (pm20) REVERT: A 87 SER cc_start: 0.9135 (p) cc_final: 0.8873 (p) REVERT: C 91 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: G 74 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8734 (mtpp) REVERT: G 91 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: H 72 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8189 (tm-30) REVERT: H 87 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8607 (mtt90) REVERT: N 95 ASP cc_start: 0.8728 (t0) cc_final: 0.8180 (t0) outliers start: 45 outliers final: 29 residues processed: 245 average time/residue: 0.6722 time to fit residues: 180.3318 Evaluate side-chains 260 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 136 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 0.0570 chunk 89 optimal weight: 10.0000 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 108 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.142547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087910 restraints weight = 31530.906| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.86 r_work: 0.2947 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17815 Z= 0.114 Angle : 0.512 8.719 25345 Z= 0.306 Chirality : 0.036 0.189 2863 Planarity : 0.003 0.042 2164 Dihedral : 29.786 159.332 4856 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.37 % Allowed : 23.42 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.24), residues: 1340 helix: 2.71 (0.20), residues: 675 sheet: 0.47 (0.35), residues: 238 loop : -0.95 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 176 TYR 0.009 0.001 TYR B 51 PHE 0.005 0.001 PHE E 67 TRP 0.004 0.001 TRP N 58 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.11 (17811) covalent geometry : angle 0.51196 / 0.31 (25337) SS BOND : bond 0.00435 / 0.26 ( 4) SS BOND : angle 0.77232 / 0.38 ( 8) hydrogen bonds : bond 0.03622 / 2.38 ( 947) hydrogen bonds : angle 3.49510 / 2.59 ( 2470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.503 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: A 59 GLU cc_start: 0.8956 (pm20) cc_final: 0.8573 (pm20) REVERT: A 87 SER cc_start: 0.9176 (p) cc_final: 0.8922 (p) REVERT: C 91 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8496 (tp30) REVERT: E 49 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8355 (ptp90) REVERT: E 59 GLU cc_start: 0.8859 (pm20) cc_final: 0.8421 (pm20) REVERT: G 91 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: H 72 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8433 (tm-30) REVERT: K 93 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8602 (t) REVERT: N 95 ASP cc_start: 0.8708 (t0) cc_final: 0.8089 (t0) outliers start: 39 outliers final: 24 residues processed: 245 average time/residue: 0.6743 time to fit residues: 180.9717 Evaluate side-chains 259 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 176 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 chunk 108 optimal weight: 50.0000 chunk 95 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.086073 restraints weight = 31269.374| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.89 r_work: 0.2905 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17815 Z= 0.202 Angle : 0.545 8.511 25345 Z= 0.318 Chirality : 0.038 0.203 2863 Planarity : 0.003 0.040 2164 Dihedral : 29.876 160.162 4856 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.63 % Allowed : 22.99 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1340 helix: 2.66 (0.20), residues: 675 sheet: 0.41 (0.36), residues: 214 loop : -1.01 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 81 TYR 0.010 0.001 TYR D 41 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP N 132 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (17811) covalent geometry : angle 0.54498 / 0.32 (25337) SS BOND : bond 0.00519 / 0.31 ( 4) SS BOND : angle 0.69637 / 0.33 ( 8) hydrogen bonds : bond 0.04150 / 2.74 ( 947) hydrogen bonds : angle 3.49417 / 2.60 ( 2470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.475 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: A 59 GLU cc_start: 0.8978 (pm20) cc_final: 0.8589 (pm20) REVERT: A 87 SER cc_start: 0.9211 (p) cc_final: 0.8967 (p) REVERT: C 71 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8264 (ttm-80) REVERT: C 77 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8227 (ttp-110) REVERT: E 59 GLU cc_start: 0.8911 (pm20) cc_final: 0.8471 (pm20) REVERT: F 92 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8338 (ttp80) REVERT: G 91 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: H 72 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8463 (tm-30) REVERT: K 93 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8632 (t) REVERT: N 95 ASP cc_start: 0.8735 (t0) cc_final: 0.8134 (t0) REVERT: N 169 MET cc_start: 0.8860 (ptp) cc_final: 0.8607 (ptm) REVERT: N 237 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8249 (mp0) REVERT: N 263 GLU cc_start: 0.8256 (tp30) cc_final: 0.8007 (tm-30) outliers start: 42 outliers final: 26 residues processed: 247 average time/residue: 0.6663 time to fit residues: 180.0603 Evaluate side-chains 256 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 72 optimal weight: 50.0000 chunk 79 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 50.0000 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 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 = 0.3938 r_free = 0.3938 target = 0.141750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086955 restraints weight = 31498.221| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.85 r_work: 0.2928 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17815 Z= 0.140 Angle : 0.526 8.820 25345 Z= 0.311 Chirality : 0.037 0.195 2863 Planarity : 0.003 0.041 2164 Dihedral : 29.874 160.122 4856 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.89 % Allowed : 23.25 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1340 helix: 2.72 (0.20), residues: 675 sheet: 0.41 (0.36), residues: 214 loop : -1.01 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 176 TYR 0.009 0.001 TYR B 51 PHE 0.006 0.001 PHE A 67 TRP 0.004 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (17811) covalent geometry : angle 0.52569 / 0.31 (25337) SS BOND : bond 0.00447 / 0.26 ( 4) SS BOND : angle 0.80209 / 0.39 ( 8) hydrogen bonds : bond 0.03780 / 2.49 ( 947) hydrogen bonds : angle 3.46073 / 2.57 ( 2470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.330 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: A 59 GLU cc_start: 0.8967 (pm20) cc_final: 0.8570 (pm20) REVERT: A 87 SER cc_start: 0.9191 (p) cc_final: 0.8948 (p) REVERT: C 51 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8506 (tpt) REVERT: C 71 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8267 (ttm-80) REVERT: C 77 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8192 (ttp-110) REVERT: E 49 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8355 (ptp90) REVERT: E 59 GLU cc_start: 0.8938 (pm20) cc_final: 0.8469 (pm20) REVERT: G 91 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8509 (tm-30) REVERT: H 72 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8443 (tm-30) REVERT: K 93 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8666 (t) REVERT: N 95 ASP cc_start: 0.8709 (t0) cc_final: 0.8091 (t0) REVERT: N 103 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.7455 (tpt) REVERT: N 169 MET cc_start: 0.8854 (ptp) cc_final: 0.8615 (ptm) outliers start: 45 outliers final: 30 residues processed: 241 average time/residue: 0.6601 time to fit residues: 174.2072 Evaluate side-chains 264 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 176 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 108 optimal weight: 50.0000 chunk 140 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 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 = 0.3911 r_free = 0.3911 target = 0.139647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084459 restraints weight = 31740.581| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.91 r_work: 0.2869 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17815 Z= 0.292 Angle : 0.614 8.566 25345 Z= 0.347 Chirality : 0.041 0.216 2863 Planarity : 0.004 0.040 2164 Dihedral : 30.103 161.273 4856 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.58 % Allowed : 22.64 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1340 helix: 2.44 (0.20), residues: 675 sheet: 0.30 (0.36), residues: 216 loop : -1.19 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.012 0.002 TYR D 41 PHE 0.011 0.002 PHE F 100 TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.29 (17811) covalent geometry : angle 0.61380 / 0.35 (25337) SS BOND : bond 0.00623 / 0.38 ( 4) SS BOND : angle 0.80587 / 0.39 ( 8) hydrogen bonds : bond 0.04926 / 3.26 ( 947) hydrogen bonds : angle 3.61803 / 2.69 ( 2470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 0.503 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: A 59 GLU cc_start: 0.9021 (pm20) cc_final: 0.8618 (pm20) REVERT: C 51 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8515 (tpt) REVERT: C 71 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8280 (ttm-80) REVERT: C 77 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8252 (ttp-110) REVERT: E 49 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8386 (ptp90) REVERT: E 59 GLU cc_start: 0.8944 (pm20) cc_final: 0.8423 (pm20) REVERT: F 91 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8870 (ttpt) REVERT: F 92 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8211 (ttp80) REVERT: G 91 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: H 72 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8471 (tm-30) REVERT: K 41 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8428 (mmtm) REVERT: K 93 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8498 (p) REVERT: K 112 ASP cc_start: 0.8550 (m-30) cc_final: 0.8116 (m-30) REVERT: N 95 ASP cc_start: 0.8750 (t0) cc_final: 0.8147 (t0) REVERT: N 103 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.7248 (tpt) REVERT: N 169 MET cc_start: 0.8897 (ptp) cc_final: 0.8671 (ptm) REVERT: N 263 GLU cc_start: 0.8257 (tp30) cc_final: 0.8040 (tm-30) outliers start: 53 outliers final: 36 residues processed: 252 average time/residue: 0.6740 time to fit residues: 185.9086 Evaluate side-chains 268 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 0.0070 chunk 66 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 73 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 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 = 0.3942 r_free = 0.3942 target = 0.141996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087098 restraints weight = 31610.261| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.86 r_work: 0.2927 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17815 Z= 0.128 Angle : 0.526 7.929 25345 Z= 0.309 Chirality : 0.037 0.200 2863 Planarity : 0.003 0.039 2164 Dihedral : 29.981 161.521 4856 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.20 % Allowed : 24.46 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1340 helix: 2.82 (0.20), residues: 671 sheet: 0.51 (0.37), residues: 198 loop : -1.14 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 83 TYR 0.009 0.001 TYR N 72 PHE 0.006 0.001 PHE D 71 TRP 0.005 0.001 TRP N 69 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (17811) covalent geometry : angle 0.52554 / 0.31 (25337) SS BOND : bond 0.00475 / 0.28 ( 4) SS BOND : angle 0.89013 / 0.45 ( 8) hydrogen bonds : bond 0.03612 / 2.37 ( 947) hydrogen bonds : angle 3.42420 / 2.55 ( 2470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.382 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: A 59 GLU cc_start: 0.8987 (pm20) cc_final: 0.8578 (pm20) REVERT: A 87 SER cc_start: 0.9199 (p) cc_final: 0.8960 (p) REVERT: C 51 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8526 (tpt) REVERT: C 77 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8231 (ttp-110) REVERT: E 49 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8363 (ptp90) REVERT: E 59 GLU cc_start: 0.8956 (pm20) cc_final: 0.8429 (pm20) REVERT: G 91 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8509 (tm-30) REVERT: H 72 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8429 (tm-30) REVERT: N 95 ASP cc_start: 0.8670 (t0) cc_final: 0.8082 (t0) REVERT: N 103 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.7379 (tpt) REVERT: N 169 MET cc_start: 0.8814 (ptp) cc_final: 0.8603 (ptm) outliers start: 37 outliers final: 22 residues processed: 242 average time/residue: 0.6900 time to fit residues: 182.6538 Evaluate side-chains 263 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 123 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 141 optimal weight: 0.0370 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 65 optimal weight: 0.4980 chunk 105 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 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 = 0.3932 r_free = 0.3932 target = 0.141921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086056 restraints weight = 31354.771| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.89 r_work: 0.2891 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17815 Z= 0.113 Angle : 0.518 7.921 25345 Z= 0.306 Chirality : 0.036 0.194 2863 Planarity : 0.003 0.035 2164 Dihedral : 29.908 160.691 4856 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.59 % Allowed : 25.06 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1340 helix: 2.92 (0.20), residues: 671 sheet: 0.52 (0.37), residues: 198 loop : -1.09 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 124 TYR 0.009 0.001 TYR N 72 PHE 0.007 0.001 PHE D 71 TRP 0.005 0.001 TRP M 207 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.11 (17811) covalent geometry : angle 0.51762 / 0.31 (25337) SS BOND : bond 0.00447 / 0.26 ( 4) SS BOND : angle 0.92319 / 0.47 ( 8) hydrogen bonds : bond 0.03460 / 2.28 ( 947) hydrogen bonds : angle 3.37930 / 2.52 ( 2470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.497 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: A 59 GLU cc_start: 0.8988 (pm20) cc_final: 0.8577 (pm20) REVERT: A 87 SER cc_start: 0.9193 (p) cc_final: 0.8954 (p) REVERT: C 51 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8552 (tpt) REVERT: C 77 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8211 (ttp-110) REVERT: E 49 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8359 (ptp90) REVERT: E 59 GLU cc_start: 0.8937 (pm20) cc_final: 0.8428 (pm20) REVERT: G 91 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8478 (tm-30) REVERT: H 72 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8439 (tm-30) REVERT: N 95 ASP cc_start: 0.8637 (t0) cc_final: 0.8065 (t0) REVERT: N 103 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.7277 (tpt) REVERT: N 169 MET cc_start: 0.8780 (ptp) cc_final: 0.8572 (ptm) REVERT: N 237 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8283 (mp0) REVERT: N 263 GLU cc_start: 0.8234 (tp30) cc_final: 0.8022 (tm-30) outliers start: 30 outliers final: 21 residues processed: 246 average time/residue: 0.6866 time to fit residues: 184.3632 Evaluate side-chains 256 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 34 optimal weight: 0.0980 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 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 = 0.3917 r_free = 0.3917 target = 0.140805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084743 restraints weight = 31237.289| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.90 r_work: 0.2863 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17815 Z= 0.170 Angle : 0.526 7.624 25345 Z= 0.309 Chirality : 0.037 0.193 2863 Planarity : 0.003 0.036 2164 Dihedral : 29.898 160.318 4856 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.68 % Allowed : 24.72 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.24), residues: 1340 helix: 2.89 (0.20), residues: 671 sheet: 0.54 (0.37), residues: 198 loop : -1.11 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 40 TYR 0.010 0.001 TYR B 51 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (17811) covalent geometry : angle 0.52620 / 0.31 (25337) SS BOND : bond 0.00482 / 0.29 ( 4) SS BOND : angle 0.70194 / 0.34 ( 8) hydrogen bonds : bond 0.03757 / 2.47 ( 947) hydrogen bonds : angle 3.38310 / 2.52 ( 2470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7389.72 seconds wall clock time: 125 minutes 51.19 seconds (7551.19 seconds total)