Starting phenix.real_space_refine on Thu Mar 5 00:45:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0i_26260/03_2026/7u0i_26260.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0i_26260/03_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_26260/03_2026/7u0i_26260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0i_26260/03_2026/7u0i_26260.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0i_26260/03_2026/7u0i_26260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0i_26260/03_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-5986/lib/python3.9/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: 3.61, per 1000 atoms: 0.20 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: 1.58 Conformation dependent library (CDL) restraints added in 537.1 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: 2.65 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: 3.89 Time building geometry restraints manager: 2.12 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: 27993 4.70 - 9.40: 110 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: 2842 0.145 - 0.290: 6 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: 1.270 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: 0.080 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.070 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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= 0.748 Angle : 0.863 23.505 25345 Z= 0.487 Chirality : 0.049 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 covalent geometry : bond 0.01164 (17811) covalent geometry : angle 0.86269 (25337) SS BOND : bond 0.00443 ( 4) SS BOND : angle 0.99945 ( 8) hydrogen bonds : bond 0.12132 ( 947) hydrogen bonds : angle 5.23287 ( 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 : 0.535 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: 0.8066 time to fit residues: 233.7997 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 : 0.536 ------------------------------------------------------------------------------- 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: 7.9990 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: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0050 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 94 ASN C 104 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN H 96 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085709 restraints weight = 31625.417| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.90 r_work: 0.2897 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 17815 Z= 0.261 Angle : 0.549 8.342 25345 Z= 0.325 Chirality : 0.035 0.122 2863 Planarity : 0.004 0.052 2164 Dihedral : 29.674 157.377 4876 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.80 % Allowed : 21.26 % Favored : 74.94 % 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: 1.17 (0.23), residues: 1340 helix: 2.09 (0.20), residues: 671 sheet: 0.43 (0.35), residues: 238 loop : -1.17 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 TYR 0.012 0.001 TYR C 57 PHE 0.014 0.001 PHE D 71 TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00591 (17811) covalent geometry : angle 0.54917 (25337) SS BOND : bond 0.00572 ( 4) SS BOND : angle 0.76301 ( 8) hydrogen bonds : bond 0.04383 ( 947) hydrogen bonds : angle 3.74538 ( 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 270 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.555 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: A 87 SER cc_start: 0.9251 (p) cc_final: 0.8981 (p) REVERT: C 91 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8677 (tm-30) REVERT: G 87 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9076 (mt) REVERT: G 91 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: H 72 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8442 (tm-30) REVERT: N 95 ASP cc_start: 0.8795 (t0) cc_final: 0.8271 (t0) REVERT: N 169 MET cc_start: 0.8844 (ptp) cc_final: 0.8510 (ptm) outliers start: 44 outliers final: 26 residues processed: 239 average time/residue: 0.8142 time to fit residues: 212.0036 Evaluate side-chains 255 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU 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 D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 19 SER 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 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 40 VAL 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 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: 0.5980 chunk 156 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3922 r_free = 0.3922 target = 0.140514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085526 restraints weight = 31753.204| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.89 r_work: 0.2891 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 17815 Z= 0.251 Angle : 0.536 9.152 25345 Z= 0.317 Chirality : 0.034 0.132 2863 Planarity : 0.004 0.047 2164 Dihedral : 29.755 160.196 4860 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.80 % Allowed : 21.95 % Favored : 74.24 % 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: 1.45 (0.24), residues: 1340 helix: 2.39 (0.20), residues: 675 sheet: 0.40 (0.34), residues: 238 loop : -1.09 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 81 TYR 0.011 0.001 TYR C 57 PHE 0.008 0.001 PHE F 100 TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00569 (17811) covalent geometry : angle 0.53580 (25337) SS BOND : bond 0.00522 ( 4) SS BOND : angle 0.81961 ( 8) hydrogen bonds : bond 0.04109 ( 947) hydrogen bonds : angle 3.54233 ( 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 273 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 0.537 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 87 SER cc_start: 0.9255 (p) cc_final: 0.9013 (p) REVERT: A 90 MET cc_start: 0.8918 (mmp) cc_final: 0.8678 (mmp) REVERT: C 71 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8257 (ttm-80) REVERT: C 91 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8674 (tm-30) REVERT: G 91 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8586 (tm-30) REVERT: H 72 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8473 (tm-30) REVERT: H 87 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8698 (mtt90) REVERT: K 237 GLU cc_start: 0.7668 (mp0) cc_final: 0.7465 (mp0) REVERT: N 95 ASP cc_start: 0.8743 (t0) cc_final: 0.8156 (t0) outliers start: 44 outliers final: 29 residues processed: 242 average time/residue: 0.8217 time to fit residues: 217.1313 Evaluate side-chains 255 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG 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 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU 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 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 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 95 ASP Chi-restraints excluded: chain K residue 176 ARG 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 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 95 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 114 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3927 r_free = 0.3927 target = 0.140983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.086134 restraints weight = 31620.949| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.85 r_work: 0.2901 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17815 Z= 0.183 Angle : 0.519 8.992 25345 Z= 0.309 Chirality : 0.033 0.121 2863 Planarity : 0.003 0.043 2164 Dihedral : 29.771 159.935 4856 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.98 % Allowed : 22.39 % Favored : 73.64 % 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: 1.57 (0.24), residues: 1340 helix: 2.50 (0.20), residues: 675 sheet: 0.44 (0.35), residues: 238 loop : -1.06 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.010 0.001 TYR B 51 PHE 0.007 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 covalent geometry : bond 0.00408 (17811) covalent geometry : angle 0.51907 (25337) SS BOND : bond 0.00514 ( 4) SS BOND : angle 0.89457 ( 8) hydrogen bonds : bond 0.03815 ( 947) hydrogen bonds : angle 3.51396 ( 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: 46 poor density : 227 time to evaluate : 0.377 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 87 SER cc_start: 0.9222 (p) cc_final: 0.8974 (p) REVERT: A 90 MET cc_start: 0.8839 (mmp) cc_final: 0.8603 (mmp) REVERT: C 77 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8273 (ttp-110) REVERT: C 91 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8633 (tm-30) REVERT: E 49 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8418 (ptp90) REVERT: G 91 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8526 (tm-30) REVERT: H 72 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8438 (tm-30) REVERT: H 87 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8677 (mtt90) REVERT: K 93 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8636 (t) REVERT: K 237 GLU cc_start: 0.7587 (mp0) cc_final: 0.7298 (mp0) REVERT: N 95 ASP cc_start: 0.8699 (t0) cc_final: 0.8115 (t0) REVERT: N 103 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.7393 (tpt) outliers start: 46 outliers final: 31 residues processed: 240 average time/residue: 0.8184 time to fit residues: 214.1084 Evaluate side-chains 269 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 77 ARG 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 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG 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 79 LYS 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 87 ARG Chi-restraints excluded: chain H residue 106 GLU 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 40 VAL Chi-restraints excluded: chain K residue 93 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 103 MET Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 136 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 118 optimal weight: 0.0000 chunk 89 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.141792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.087016 restraints weight = 31485.655| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.86 r_work: 0.2926 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17815 Z= 0.145 Angle : 0.500 9.047 25345 Z= 0.299 Chirality : 0.032 0.120 2863 Planarity : 0.003 0.040 2164 Dihedral : 29.745 159.503 4856 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.63 % Allowed : 22.47 % Favored : 73.90 % 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: 1.72 (0.24), residues: 1340 helix: 2.64 (0.20), residues: 675 sheet: 0.46 (0.35), residues: 238 loop : -0.98 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 69 TYR 0.009 0.001 TYR B 51 PHE 0.005 0.001 PHE A 67 TRP 0.004 0.001 TRP N 58 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00315 (17811) covalent geometry : angle 0.50010 (25337) SS BOND : bond 0.00466 ( 4) SS BOND : angle 0.92849 ( 8) hydrogen bonds : bond 0.03513 ( 947) hydrogen bonds : angle 3.44717 ( 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 276 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.535 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 87 SER cc_start: 0.9205 (p) cc_final: 0.8962 (p) REVERT: A 90 MET cc_start: 0.8830 (mmp) cc_final: 0.8596 (mmp) REVERT: C 77 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8261 (ttp-110) REVERT: E 49 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8436 (ptp90) REVERT: E 59 GLU cc_start: 0.8802 (pm20) cc_final: 0.8409 (pm20) REVERT: G 91 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: H 72 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8421 (tm-30) REVERT: H 87 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8630 (mtt90) REVERT: K 93 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8644 (t) REVERT: K 112 ASP cc_start: 0.8467 (m-30) cc_final: 0.8234 (m-30) REVERT: N 95 ASP cc_start: 0.8651 (t0) cc_final: 0.8045 (t0) REVERT: N 103 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.7614 (tpt) outliers start: 42 outliers final: 29 residues processed: 247 average time/residue: 0.8233 time to fit residues: 222.0825 Evaluate side-chains 264 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET 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 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 H residue 87 ARG Chi-restraints excluded: chain H residue 106 GLU 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 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 103 MET Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 108 optimal weight: 50.0000 chunk 95 optimal weight: 4.9990 chunk 148 optimal weight: 0.0970 chunk 144 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3924 r_free = 0.3924 target = 0.140566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.085439 restraints weight = 31298.152| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.88 r_work: 0.2890 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17815 Z= 0.236 Angle : 0.522 8.540 25345 Z= 0.310 Chirality : 0.034 0.122 2863 Planarity : 0.003 0.040 2164 Dihedral : 29.739 159.823 4856 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.98 % Allowed : 22.39 % Favored : 73.64 % 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: 1.72 (0.24), residues: 1340 helix: 2.68 (0.20), residues: 671 sheet: 0.62 (0.36), residues: 222 loop : -1.08 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.011 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 covalent geometry : bond 0.00533 (17811) covalent geometry : angle 0.52221 (25337) SS BOND : bond 0.00527 ( 4) SS BOND : angle 0.73946 ( 8) hydrogen bonds : bond 0.03928 ( 947) hydrogen bonds : angle 3.45309 ( 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 273 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 0.489 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: 0.8984 (pm20) cc_final: 0.8629 (pm20) REVERT: A 87 SER cc_start: 0.9224 (p) cc_final: 0.8990 (p) REVERT: A 90 MET cc_start: 0.8876 (mmp) cc_final: 0.8639 (mmp) REVERT: C 77 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8260 (ttp-110) REVERT: D 77 GLU cc_start: 0.9176 (tp30) cc_final: 0.8969 (tp30) REVERT: E 49 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8471 (ptp90) REVERT: E 59 GLU cc_start: 0.8904 (pm20) cc_final: 0.8494 (pm20) REVERT: G 91 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: H 72 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8446 (tm-30) REVERT: K 93 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8606 (t) REVERT: K 112 ASP cc_start: 0.8532 (m-30) cc_final: 0.8111 (m-30) REVERT: K 237 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: N 95 ASP cc_start: 0.8687 (t0) cc_final: 0.8148 (t0) REVERT: N 103 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.7511 (tpt) outliers start: 46 outliers final: 31 residues processed: 243 average time/residue: 0.8205 time to fit residues: 217.3000 Evaluate side-chains 265 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 B residue 84 MET 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 60 MET 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 F residue 22 LEU 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 38 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 237 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 72 optimal weight: 50.0000 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 50.0000 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086353 restraints weight = 31459.685| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.85 r_work: 0.2907 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17815 Z= 0.183 Angle : 0.507 8.533 25345 Z= 0.302 Chirality : 0.032 0.123 2863 Planarity : 0.003 0.039 2164 Dihedral : 29.718 159.768 4856 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.80 % Allowed : 22.90 % Favored : 73.29 % 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: 1.75 (0.24), residues: 1340 helix: 2.76 (0.20), residues: 671 sheet: 0.61 (0.37), residues: 198 loop : -1.05 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.010 0.001 TYR B 51 PHE 0.007 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 covalent geometry : bond 0.00407 (17811) covalent geometry : angle 0.50677 (25337) SS BOND : bond 0.00489 ( 4) SS BOND : angle 0.78263 ( 8) hydrogen bonds : bond 0.03623 ( 947) hydrogen bonds : angle 3.41137 ( 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 273 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 0.524 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: 0.8993 (pm20) cc_final: 0.8643 (pm20) REVERT: A 87 SER cc_start: 0.9230 (p) cc_final: 0.9002 (p) REVERT: A 90 MET cc_start: 0.8792 (mmp) cc_final: 0.8569 (mmp) REVERT: C 51 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8519 (tpt) REVERT: C 77 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8265 (ttp-110) REVERT: D 77 GLU cc_start: 0.9203 (tp30) cc_final: 0.8990 (tp30) REVERT: E 49 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8517 (ptp90) REVERT: E 59 GLU cc_start: 0.8948 (pm20) cc_final: 0.8544 (pm20) REVERT: F 92 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8341 (ttp80) REVERT: G 91 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: H 72 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8455 (tm-30) REVERT: K 93 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8549 (p) REVERT: N 95 ASP cc_start: 0.8700 (t0) cc_final: 0.8143 (t0) REVERT: N 103 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.7587 (tpt) REVERT: N 169 MET cc_start: 0.8863 (ptm) cc_final: 0.8658 (ptp) outliers start: 44 outliers final: 31 residues processed: 244 average time/residue: 0.8068 time to fit residues: 214.6894 Evaluate side-chains 263 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 B residue 84 MET 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 C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET 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 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 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 38 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 140 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 96 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 148 optimal weight: 0.3980 chunk 108 optimal weight: 50.0000 chunk 140 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 30.0000 chunk 116 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086373 restraints weight = 31664.341| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.86 r_work: 0.2908 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17815 Z= 0.194 Angle : 0.507 8.250 25345 Z= 0.301 Chirality : 0.033 0.123 2863 Planarity : 0.003 0.040 2164 Dihedral : 29.661 159.264 4856 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.98 % Allowed : 22.99 % Favored : 73.03 % 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: 1.79 (0.24), residues: 1340 helix: 2.80 (0.20), residues: 671 sheet: 0.61 (0.37), residues: 198 loop : -1.03 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 83 TYR 0.010 0.001 TYR B 51 PHE 0.007 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 covalent geometry : bond 0.00434 (17811) covalent geometry : angle 0.50652 (25337) SS BOND : bond 0.00459 ( 4) SS BOND : angle 0.71598 ( 8) hydrogen bonds : bond 0.03566 ( 947) hydrogen bonds : angle 3.38024 ( 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 272 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.514 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: 0.8968 (pm20) cc_final: 0.8603 (pm20) REVERT: A 87 SER cc_start: 0.9200 (p) cc_final: 0.8960 (p) REVERT: A 90 MET cc_start: 0.8781 (mmp) cc_final: 0.8541 (mmp) REVERT: C 51 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8530 (tpt) REVERT: C 77 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8238 (ttp-110) REVERT: D 77 GLU cc_start: 0.9193 (tp30) cc_final: 0.8975 (tp30) REVERT: E 49 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8458 (ptp90) REVERT: E 59 GLU cc_start: 0.8940 (pm20) cc_final: 0.8502 (pm20) REVERT: F 92 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8328 (ttp80) REVERT: G 91 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8526 (tm-30) REVERT: H 72 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8432 (tm-30) REVERT: K 93 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8514 (p) REVERT: N 95 ASP cc_start: 0.8659 (t0) cc_final: 0.8121 (t0) REVERT: N 103 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.7557 (tpt) outliers start: 46 outliers final: 34 residues processed: 243 average time/residue: 0.7909 time to fit residues: 209.8129 Evaluate side-chains 268 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 B residue 84 MET 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 C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET 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 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 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 H residue 106 GLU 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 93 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 140 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS N 235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.086801 restraints weight = 31538.698| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.85 r_work: 0.2924 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17815 Z= 0.165 Angle : 0.503 8.391 25345 Z= 0.300 Chirality : 0.032 0.124 2863 Planarity : 0.003 0.040 2164 Dihedral : 29.661 159.217 4856 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.98 % Allowed : 22.99 % Favored : 73.03 % 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: 2.83 (0.20), residues: 671 sheet: 0.62 (0.37), residues: 198 loop : -1.01 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.010 0.001 TYR B 51 PHE 0.006 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 covalent geometry : bond 0.00365 (17811) covalent geometry : angle 0.50271 (25337) SS BOND : bond 0.00463 ( 4) SS BOND : angle 0.80401 ( 8) hydrogen bonds : bond 0.03471 ( 947) hydrogen bonds : angle 3.37077 ( 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 270 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 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: A 59 GLU cc_start: 0.8984 (pm20) cc_final: 0.8623 (pm20) REVERT: A 87 SER cc_start: 0.9210 (p) cc_final: 0.8975 (p) REVERT: A 90 MET cc_start: 0.8815 (mmp) cc_final: 0.8578 (mmp) REVERT: C 51 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8525 (tpt) REVERT: C 77 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8252 (ttp-110) REVERT: D 72 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: E 49 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8501 (ptp90) REVERT: E 59 GLU cc_start: 0.8973 (pm20) cc_final: 0.8542 (pm20) REVERT: F 92 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8334 (ttp80) REVERT: G 91 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: H 72 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8430 (tm-30) REVERT: K 93 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8532 (p) REVERT: N 95 ASP cc_start: 0.8673 (t0) cc_final: 0.8129 (t0) REVERT: N 103 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.7572 (tpt) outliers start: 46 outliers final: 32 residues processed: 242 average time/residue: 0.8433 time to fit residues: 222.3974 Evaluate side-chains 264 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 B residue 84 MET 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 C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET 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 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 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 H residue 106 GLU 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 93 THR Chi-restraints excluded: chain K residue 139 THR 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: 4.9990 chunk 154 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 141 optimal weight: 0.0870 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087388 restraints weight = 31493.864| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.85 r_work: 0.2934 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17815 Z= 0.134 Angle : 0.497 8.493 25345 Z= 0.297 Chirality : 0.031 0.133 2863 Planarity : 0.003 0.039 2164 Dihedral : 29.657 159.144 4856 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.46 % Allowed : 23.42 % Favored : 73.12 % 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: 1.90 (0.24), residues: 1340 helix: 2.89 (0.20), residues: 671 sheet: 0.63 (0.37), residues: 198 loop : -0.98 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.010 0.001 TYR D 41 PHE 0.006 0.001 PHE A 67 TRP 0.004 0.001 TRP N 58 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00290 (17811) covalent geometry : angle 0.49732 (25337) SS BOND : bond 0.00446 ( 4) SS BOND : angle 0.87274 ( 8) hydrogen bonds : bond 0.03319 ( 947) hydrogen bonds : angle 3.35279 ( 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: 40 poor density : 228 time to evaluate : 0.537 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: 0.8976 (pm20) cc_final: 0.8613 (pm20) REVERT: A 87 SER cc_start: 0.9206 (p) cc_final: 0.8970 (p) REVERT: A 90 MET cc_start: 0.8788 (mmp) cc_final: 0.8551 (mmp) REVERT: C 51 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8497 (tpt) REVERT: C 77 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8239 (ttp-110) REVERT: D 72 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: E 49 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8501 (ptp90) REVERT: E 59 GLU cc_start: 0.8975 (pm20) cc_final: 0.8541 (pm20) REVERT: F 92 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8345 (ttp80) REVERT: G 91 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: H 72 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8424 (tm-30) REVERT: K 93 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8534 (p) REVERT: K 104 GLU cc_start: 0.8432 (tp30) cc_final: 0.8090 (mm-30) REVERT: N 95 ASP cc_start: 0.8656 (t0) cc_final: 0.8138 (t0) REVERT: N 103 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.7665 (tpt) outliers start: 40 outliers final: 27 residues processed: 241 average time/residue: 0.8019 time to fit residues: 210.6812 Evaluate side-chains 261 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 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 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 H residue 106 GLU 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 93 THR Chi-restraints excluded: chain K residue 139 THR 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 34 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS 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 = 0.142172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.087432 restraints weight = 31479.341| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.85 r_work: 0.2935 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17815 Z= 0.148 Angle : 0.494 8.208 25345 Z= 0.295 Chirality : 0.031 0.121 2863 Planarity : 0.003 0.037 2164 Dihedral : 29.612 158.860 4856 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.20 % Allowed : 23.85 % Favored : 72.95 % 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: 1.94 (0.24), residues: 1340 helix: 2.94 (0.20), residues: 671 sheet: 0.63 (0.37), residues: 198 loop : -0.98 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 87 TYR 0.009 0.001 TYR B 51 PHE 0.005 0.001 PHE A 67 TRP 0.005 0.001 TRP N 132 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00326 (17811) covalent geometry : angle 0.49401 (25337) SS BOND : bond 0.00430 ( 4) SS BOND : angle 0.77600 ( 8) hydrogen bonds : bond 0.03313 ( 947) hydrogen bonds : angle 3.32594 ( 2470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9477.09 seconds wall clock time: 161 minutes 3.47 seconds (9663.47 seconds total)