Starting phenix.real_space_refine on Sat Sep 12 19:03:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0i_26260/09_2026/7u0i_26260.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0i_26260/09_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_26260/09_2026/7u0i_26260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0i_26260/09_2026/7u0i_26260.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0i_26260/09_2026/7u0i_26260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0i_26260/09_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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18108 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 664 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3084 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3025 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "L" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1212 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1212 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1765 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 3.59, 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: 1.96 Conformation dependent library (CDL) restraints added in 586.5 milliseconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 23 sheets defined 51.4% alpha, 20.1% beta 129 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.502A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.750A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 removed outlier: 3.530A pdb=" N THR D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.537A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.676A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.526A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'L' and resid 141 through 161 removed outlier: 3.544A pdb=" N GLU L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 176 Processing helix chain 'L' and resid 180 through 189 Processing helix chain 'L' and resid 193 through 212 Proline residue: L 202 - end of helix Processing helix chain 'M' and resid 141 through 161 removed outlier: 3.581A pdb=" N GLU M 145 " --> pdb=" O ALA M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 176 Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.540A pdb=" N ILE M 184 " --> pdb=" O SER M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 212 Proline residue: M 202 - end of helix Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.501A pdb=" N ASP K 112 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 109 through 113' Processing helix chain 'K' and resid 237 through 241 removed outlier: 3.708A pdb=" N THR K 241 " --> pdb=" O SER K 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.624A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.596A pdb=" N ASP N 112 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 113' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.539A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 237 through 241' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.984A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.684A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.139A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.856A pdb=" N VAL K 101 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.391A pdb=" N GLU K 32 " --> pdb=" O THR K 139 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.391A pdb=" N GLU K 32 " --> pdb=" O THR K 139 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR K 131 " --> pdb=" O ARG K 120 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER K 122 " --> pdb=" O LEU K 129 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU K 129 " --> pdb=" O SER K 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 162 through 164 removed outlier: 4.098A pdb=" N PHE K 229 " --> pdb=" O CYS K 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.950A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.950A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.252A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.177A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 39 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 162 through 164 removed outlier: 4.187A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.730A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 168 through 171 659 hydrogen bonds defined for protein. 1848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 311 hydrogen bonds 622 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1225 1.03 - 1.23: 240 1.23 - 1.43: 7975 1.43 - 1.62: 9532 1.62 - 1.82: 59 Bond restraints: 19031 Sorted by residual: bond pdb=" C LYS B 59 " pdb=" O LYS B 59 " ideal model delta sigma weight residual 1.237 1.008 0.228 1.19e-02 7.06e+03 3.68e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.237 1.019 0.218 1.16e-02 7.43e+03 3.53e+02 bond pdb=" C MET G 51 " pdb=" O MET G 51 " ideal model delta sigma weight residual 1.237 1.013 0.223 1.19e-02 7.06e+03 3.52e+02 bond pdb=" C ARG D 93 " pdb=" O ARG D 93 " ideal model delta sigma weight residual 1.236 1.013 0.223 1.22e-02 6.72e+03 3.35e+02 bond pdb=" C ARG E 63 " pdb=" O ARG E 63 " ideal model delta sigma weight residual 1.234 1.031 0.203 1.27e-02 6.20e+03 2.55e+02 ... (remaining 19026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 27991 4.70 - 9.40: 112 9.40 - 14.10: 10 14.10 - 18.80: 4 18.80 - 23.51: 4 Bond angle restraints: 28121 Sorted by residual: angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 110.80 132.35 -21.55 2.13e+00 2.20e-01 1.02e+02 angle pdb=" CG ARG F 95 " pdb=" CD ARG F 95 " pdb=" NE ARG F 95 " ideal model delta sigma weight residual 112.00 90.95 21.05 2.20e+00 2.07e-01 9.16e+01 angle pdb=" CG MET C 51 " pdb=" SD MET C 51 " pdb=" CE MET C 51 " ideal model delta sigma weight residual 100.90 82.71 18.19 2.20e+00 2.07e-01 6.84e+01 angle pdb=" C MET C 51 " pdb=" CA MET C 51 " pdb=" CB MET C 51 " ideal model delta sigma weight residual 110.90 97.89 13.01 1.58e+00 4.01e-01 6.79e+01 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 89.19 23.51 3.00e+00 1.11e-01 6.14e+01 ... (remaining 28116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.20: 8540 32.20 - 64.40: 1808 64.40 - 96.60: 52 96.60 - 128.80: 1 128.80 - 161.00: 3 Dihedral angle restraints: 10404 sinusoidal: 6374 harmonic: 4030 Sorted by residual: dihedral pdb=" C MET C 51 " pdb=" N MET C 51 " pdb=" CA MET C 51 " pdb=" CB MET C 51 " ideal model delta harmonic sigma weight residual -122.60 -106.48 -16.12 0 2.50e+00 1.60e-01 4.16e+01 dihedral pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CA LYS C 13 " pdb=" CB LYS C 13 " ideal model delta harmonic sigma weight residual 122.80 136.47 -13.67 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" C LYS C 13 " pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" CB LYS C 13 " ideal model delta harmonic sigma weight residual -122.60 -136.23 13.63 0 2.50e+00 1.60e-01 2.97e+01 ... (remaining 10401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2838 0.145 - 0.290: 10 0.290 - 0.435: 9 0.435 - 0.580: 5 0.580 - 0.725: 1 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CA LYS C 13 " pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CB LYS C 13 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ARG B 92 " pdb=" N ARG B 92 " pdb=" C ARG B 92 " pdb=" CB ARG B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA MET G 51 " pdb=" N MET G 51 " pdb=" C MET G 51 " pdb=" CB MET G 51 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.81e+00 ... (remaining 2860 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET G 51 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" C MET G 51 " -0.099 2.00e-02 2.50e+03 pdb=" O MET G 51 " 0.038 2.00e-02 2.50e+03 pdb=" N ALA G 52 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " -0.027 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C GLU C 92 " 0.097 2.00e-02 2.50e+03 pdb=" O GLU C 92 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU C 93 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 51 " -0.025 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C MET C 51 " 0.084 2.00e-02 2.50e+03 pdb=" O MET C 51 " -0.032 2.00e-02 2.50e+03 pdb=" N ALA C 52 " -0.028 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 198 2.23 - 2.82: 9538 2.82 - 3.42: 22300 3.42 - 4.01: 44297 4.01 - 4.60: 61307 Nonbonded interactions: 137640 Sorted by model distance: nonbonded pdb=" HG LEU L 200 " pdb="HD12 LEU L 204 " model vdw 1.641 2.440 nonbonded pdb=" O ASP M 166 " pdb=" HG1 THR M 170 " model vdw 1.802 2.450 nonbonded pdb=" O GLN L 155 " pdb=" HG1 THR L 159 " model vdw 1.802 2.450 nonbonded pdb=" HE ARG L 157 " pdb=" OE2 GLU L 188 " model vdw 1.802 2.450 nonbonded pdb=" OP1 DT J 93 " pdb="HH12 ARG L 157 " model vdw 1.810 2.450 ... (remaining 137635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and ((resid 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) selection = (chain 'F' and ((resid 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 125) selection = (chain 'H' and (resid 31 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 125)) } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 23 through 264 or (resid 265 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.780 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.228 17815 Z= 0.858 Angle : 0.962 23.505 25345 Z= 0.716 Chirality : 0.055 0.725 2863 Planarity : 0.006 0.073 2164 Dihedral : 26.815 160.996 7468 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.88 % Favored : 95.97 % Rotamer: Outliers : 1.56 % Allowed : 20.83 % Favored : 77.61 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1340 helix: 0.86 (0.18), residues: 664 sheet: 0.20 (0.35), residues: 212 loop : -1.30 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 72 TYR 0.017 0.002 TYR A 41 PHE 0.010 0.001 PHE E 84 TRP 0.015 0.001 TRP K 199 HIS 0.016 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01218 / 0.86 (17811) covalent geometry : angle 0.96243 / 0.72 (25337) SS BOND : bond 0.00443 / 0.26 ( 4) SS BOND : angle 0.99945 / 0.51 ( 8) hydrogen bonds : bond 0.12132 / 8.21 ( 947) hydrogen bonds : angle 5.23287 / 3.69 ( 2470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.419 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: 0.8139 time to fit residues: 237.2117 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 : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 230 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.0050 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 94 ASN C 104 GLN D 85 ASN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN H 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.140847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085876 restraints weight = 31487.937| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.86 r_work: 0.2889 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17815 Z= 0.259 Angle : 0.631 9.106 25345 Z= 0.358 Chirality : 0.043 0.219 2863 Planarity : 0.004 0.051 2164 Dihedral : 29.720 159.859 4876 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.54 % Allowed : 21.43 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.23), residues: 1340 helix: 1.94 (0.20), residues: 670 sheet: 0.34 (0.37), residues: 216 loop : -1.24 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 95 TYR 0.020 0.002 TYR C 50 PHE 0.016 0.002 PHE D 71 TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.26 (17811) covalent geometry : angle 0.63105 / 0.36 (25337) SS BOND : bond 0.00450 / 0.28 ( 4) SS BOND : angle 0.85656 / 0.42 ( 8) hydrogen bonds : bond 0.04875 / 3.22 ( 947) hydrogen bonds : angle 3.97976 / 2.92 ( 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 264 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8799 (tpp) REVERT: C 91 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: G 87 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9053 (mt) REVERT: G 91 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: N 95 ASP cc_start: 0.8844 (t0) cc_final: 0.8373 (t0) outliers start: 41 outliers final: 28 residues processed: 235 average time/residue: 0.8092 time to fit residues: 208.2510 Evaluate side-chains 255 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 150 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 142 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 115 optimal weight: 0.0030 chunk 91 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087057 restraints weight = 31677.621| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.86 r_work: 0.2930 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0955 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= 0.144 Angle : 0.559 9.902 25345 Z= 0.328 Chirality : 0.039 0.195 2863 Planarity : 0.004 0.045 2164 Dihedral : 29.716 158.642 4867 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.03 % Allowed : 22.90 % Favored : 74.07 % 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: 1.29 (0.23), residues: 1340 helix: 2.28 (0.20), residues: 675 sheet: 0.36 (0.36), residues: 216 loop : -1.16 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 63 TYR 0.011 0.001 TYR C 50 PHE 0.006 0.001 PHE F 61 TRP 0.004 0.001 TRP N 69 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (17811) covalent geometry : angle 0.55937 / 0.33 (25337) SS BOND : bond 0.00371 / 0.23 ( 4) SS BOND : angle 0.55153 / 0.25 ( 8) hydrogen bonds : bond 0.04041 / 2.65 ( 947) hydrogen bonds : angle 3.79535 / 2.79 ( 2470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8629 (tm-30) REVERT: G 87 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9041 (mt) REVERT: G 91 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: N 68 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: N 95 ASP cc_start: 0.8802 (t0) cc_final: 0.8289 (t0) REVERT: N 237 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8300 (mp0) REVERT: N 263 GLU cc_start: 0.8205 (tp30) cc_final: 0.7951 (tm-30) outliers start: 35 outliers final: 25 residues processed: 245 average time/residue: 0.8759 time to fit residues: 233.7722 Evaluate side-chains 252 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 176 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 95 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 114 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN H 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.087777 restraints weight = 31665.881| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.86 r_work: 0.2941 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17815 Z= 0.129 Angle : 0.543 8.793 25345 Z= 0.319 Chirality : 0.037 0.189 2863 Planarity : 0.003 0.035 2164 Dihedral : 29.671 159.218 4864 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.63 % Allowed : 22.30 % Favored : 74.07 % 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: 1.54 (0.23), residues: 1340 helix: 2.51 (0.20), residues: 675 sheet: 0.41 (0.36), residues: 214 loop : -1.04 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.008 0.001 TYR B 51 PHE 0.005 0.001 PHE F 61 TRP 0.004 0.001 TRP N 132 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (17811) covalent geometry : angle 0.54251 / 0.32 (25337) SS BOND : bond 0.00362 / 0.22 ( 4) SS BOND : angle 0.82740 / 0.40 ( 8) hydrogen bonds : bond 0.03817 / 2.51 ( 947) hydrogen bonds : angle 3.68055 / 2.72 ( 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 270 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.586 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: 0.9193 (p) cc_final: 0.8915 (p) REVERT: C 91 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8625 (tm-30) REVERT: G 91 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: H 33 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8411 (p) REVERT: N 68 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: N 95 ASP cc_start: 0.8757 (t0) cc_final: 0.8190 (t0) outliers start: 42 outliers final: 28 residues processed: 243 average time/residue: 0.8034 time to fit residues: 213.9453 Evaluate side-chains 260 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 139 THR 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 115 VAL 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: 0.8980 chunk 49 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 0.0970 chunk 89 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.088094 restraints weight = 31641.570| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.86 r_work: 0.2952 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17815 Z= 0.140 Angle : 0.511 8.116 25345 Z= 0.305 Chirality : 0.036 0.193 2863 Planarity : 0.003 0.041 2164 Dihedral : 29.627 159.240 4860 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.80 % Allowed : 22.21 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.24), residues: 1340 helix: 2.79 (0.20), residues: 675 sheet: 0.37 (0.36), residues: 220 loop : -0.94 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE H 71 TRP 0.006 0.001 TRP N 132 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (17811) covalent geometry : angle 0.51101 / 0.30 (25337) SS BOND : bond 0.00425 / 0.25 ( 4) SS BOND : angle 0.72748 / 0.35 ( 8) hydrogen bonds : bond 0.03643 / 2.40 ( 947) hydrogen bonds : angle 3.41126 / 2.53 ( 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 281 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.531 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: 0.8941 (pm20) cc_final: 0.8548 (pm20) REVERT: A 87 SER cc_start: 0.9166 (p) cc_final: 0.8914 (p) REVERT: E 59 GLU cc_start: 0.8971 (pm20) cc_final: 0.8535 (pm20) REVERT: G 91 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8493 (tm-30) REVERT: H 72 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8439 (tm-30) REVERT: H 87 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8555 (mtt90) REVERT: K 104 GLU cc_start: 0.8354 (tp30) cc_final: 0.8066 (mm-30) REVERT: N 95 ASP cc_start: 0.8716 (t0) cc_final: 0.8084 (t0) REVERT: N 237 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8262 (mp0) REVERT: N 263 GLU cc_start: 0.8245 (tp30) cc_final: 0.7983 (tm-30) outliers start: 44 outliers final: 28 residues processed: 249 average time/residue: 0.7688 time to fit residues: 209.3799 Evaluate side-chains 256 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS 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 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 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 87 ARG 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 139 THR Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 108 optimal weight: 50.0000 chunk 95 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086491 restraints weight = 31305.521| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.84 r_work: 0.2914 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17815 Z= 0.193 Angle : 0.547 8.099 25345 Z= 0.317 Chirality : 0.038 0.203 2863 Planarity : 0.003 0.041 2164 Dihedral : 29.780 160.288 4856 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.54 % Allowed : 22.90 % Favored : 73.55 % 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: 2.74 (0.20), residues: 675 sheet: 0.41 (0.36), residues: 214 loop : -1.00 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.010 0.001 TYR B 51 PHE 0.008 0.001 PHE E 104 TRP 0.007 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (17811) covalent geometry : angle 0.54652 / 0.32 (25337) SS BOND : bond 0.00488 / 0.29 ( 4) SS BOND : angle 0.68948 / 0.34 ( 8) hydrogen bonds : bond 0.04020 / 2.65 ( 947) hydrogen bonds : angle 3.45799 / 2.57 ( 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 269 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 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: 0.8964 (pm20) cc_final: 0.8553 (pm20) REVERT: A 87 SER cc_start: 0.9198 (p) cc_final: 0.8954 (p) REVERT: C 71 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8272 (ttm-80) REVERT: C 77 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8226 (ttp-110) REVERT: E 49 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8390 (ptp90) REVERT: E 59 GLU cc_start: 0.8954 (pm20) cc_final: 0.8486 (pm20) REVERT: G 91 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: H 72 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8452 (tm-30) REVERT: H 87 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8730 (mtt90) REVERT: K 23 GLU cc_start: 0.7406 (tp30) cc_final: 0.7193 (tp30) REVERT: K 93 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8628 (t) REVERT: K 112 ASP cc_start: 0.8423 (m-30) cc_final: 0.8003 (m-30) REVERT: N 95 ASP cc_start: 0.8741 (t0) cc_final: 0.8180 (t0) REVERT: N 169 MET cc_start: 0.8836 (ptp) cc_final: 0.8586 (ptm) outliers start: 41 outliers final: 30 residues processed: 245 average time/residue: 0.7482 time to fit residues: 200.7560 Evaluate side-chains 263 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 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 165 SER Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 72 optimal weight: 50.0000 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 50.0000 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.084882 restraints weight = 31601.669| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.90 r_work: 0.2902 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17815 Z= 0.195 Angle : 0.548 7.952 25345 Z= 0.318 Chirality : 0.038 0.197 2863 Planarity : 0.003 0.044 2164 Dihedral : 29.858 160.705 4856 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.98 % Allowed : 22.47 % Favored : 73.55 % 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: 1.70 (0.24), residues: 1340 helix: 2.73 (0.20), residues: 675 sheet: 0.60 (0.37), residues: 198 loop : -1.12 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 176 TYR 0.010 0.001 TYR B 51 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (17811) covalent geometry : angle 0.54842 / 0.32 (25337) SS BOND : bond 0.00483 / 0.29 ( 4) SS BOND : angle 0.66771 / 0.32 ( 8) hydrogen bonds : bond 0.03959 / 2.61 ( 947) hydrogen bonds : angle 3.43943 / 2.56 ( 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 281 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8861 (pm20) cc_final: 0.8493 (pm20) REVERT: A 87 SER cc_start: 0.9133 (p) cc_final: 0.8886 (p) REVERT: C 71 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8156 (ttm-80) REVERT: C 77 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8058 (ttp-110) REVERT: E 49 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8232 (ptp90) REVERT: E 59 GLU cc_start: 0.8854 (pm20) cc_final: 0.8354 (pm20) REVERT: G 91 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: H 72 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8196 (tm-30) REVERT: K 93 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8575 (t) REVERT: N 95 ASP cc_start: 0.8696 (t0) cc_final: 0.8103 (t0) REVERT: N 169 MET cc_start: 0.8782 (ptp) cc_final: 0.8551 (ptm) REVERT: N 237 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8282 (mp0) REVERT: N 263 GLU cc_start: 0.8194 (tp30) cc_final: 0.7966 (tm-30) outliers start: 46 outliers final: 32 residues processed: 252 average time/residue: 0.7821 time to fit residues: 215.5902 Evaluate side-chains 272 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 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 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 108 optimal weight: 50.0000 chunk 140 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 116 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083272 restraints weight = 31401.313| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.89 r_work: 0.2845 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17815 Z= 0.245 Angle : 0.589 7.758 25345 Z= 0.334 Chirality : 0.040 0.205 2863 Planarity : 0.004 0.040 2164 Dihedral : 29.967 161.054 4856 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.06 % Allowed : 23.08 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.23), residues: 1340 helix: 2.61 (0.20), residues: 675 sheet: 0.53 (0.37), residues: 198 loop : -1.17 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.011 0.001 TYR C 57 PHE 0.009 0.001 PHE F 100 TRP 0.007 0.001 TRP N 132 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.25 (17811) covalent geometry : angle 0.58848 / 0.33 (25337) SS BOND : bond 0.00579 / 0.34 ( 4) SS BOND : angle 0.72656 / 0.36 ( 8) hydrogen bonds : bond 0.04407 / 2.91 ( 947) hydrogen bonds : angle 3.52669 / 2.63 ( 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 281 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 0.561 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: 0.8983 (pm20) cc_final: 0.8544 (pm20) REVERT: A 87 SER cc_start: 0.9210 (p) cc_final: 0.8966 (p) REVERT: C 77 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8204 (ttp-110) REVERT: E 49 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8332 (ptp90) REVERT: E 59 GLU cc_start: 0.8909 (pm20) cc_final: 0.8368 (pm20) REVERT: F 92 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8199 (ttp80) REVERT: G 91 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: H 72 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8446 (tm-30) REVERT: K 93 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8539 (t) REVERT: N 95 ASP cc_start: 0.8665 (t0) cc_final: 0.8064 (t0) REVERT: N 103 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.7063 (tpt) REVERT: N 263 GLU cc_start: 0.8266 (tp30) cc_final: 0.8033 (tm-30) outliers start: 47 outliers final: 34 residues processed: 252 average time/residue: 0.8266 time to fit residues: 227.5688 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 : 0.555 ------------------------------------------------------------------------------- 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 C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 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 G residue 95 LYS Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 73 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.083874 restraints weight = 31306.140| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.88 r_work: 0.2837 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17815 Z= 0.184 Angle : 0.571 8.003 25345 Z= 0.327 Chirality : 0.038 0.202 2863 Planarity : 0.004 0.042 2164 Dihedral : 29.971 160.997 4856 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.80 % Allowed : 23.51 % Favored : 72.69 % 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: 1.59 (0.23), residues: 1340 helix: 2.64 (0.20), residues: 675 sheet: 0.50 (0.37), residues: 198 loop : -1.15 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.011 0.001 TYR D 41 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (17811) covalent geometry : angle 0.57103 / 0.33 (25337) SS BOND : bond 0.00562 / 0.33 ( 4) SS BOND : angle 0.78942 / 0.38 ( 8) hydrogen bonds : bond 0.04138 / 2.73 ( 947) hydrogen bonds : angle 3.51197 / 2.62 ( 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 279 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.570 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: 0.9002 (pm20) cc_final: 0.8631 (pm20) REVERT: A 87 SER cc_start: 0.9227 (p) cc_final: 0.8989 (p) REVERT: C 77 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8232 (ttp-110) REVERT: E 49 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8373 (ptp90) REVERT: E 59 GLU cc_start: 0.8933 (pm20) cc_final: 0.8399 (pm20) REVERT: F 92 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8236 (ttp80) REVERT: G 91 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: H 72 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8461 (tm-30) REVERT: K 93 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8580 (t) REVERT: N 95 ASP cc_start: 0.8686 (t0) cc_final: 0.8076 (t0) REVERT: N 103 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.7068 (tpt) REVERT: N 263 GLU cc_start: 0.8264 (tp30) cc_final: 0.8035 (tm-30) outliers start: 44 outliers final: 33 residues processed: 251 average time/residue: 0.8138 time to fit residues: 223.3673 Evaluate side-chains 271 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 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 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 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 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 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 165 SER Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 123 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 0.0000 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 108 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.085213 restraints weight = 31259.307| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.89 r_work: 0.2869 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.002 0.047 17815 Z= 0.118 Angle : 0.540 8.095 25345 Z= 0.314 Chirality : 0.037 0.203 2863 Planarity : 0.003 0.036 2164 Dihedral : 29.920 160.776 4856 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.77 % Allowed : 24.72 % Favored : 72.52 % 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: 1.74 (0.24), residues: 1340 helix: 2.80 (0.20), residues: 671 sheet: 0.49 (0.37), residues: 198 loop : -1.09 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.011 0.001 TYR B 51 PHE 0.007 0.001 PHE A 67 TRP 0.005 0.001 TRP N 58 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.12 (17811) covalent geometry : angle 0.54016 / 0.31 (25337) SS BOND : bond 0.00433 / 0.26 ( 4) SS BOND : angle 1.00777 / 0.51 ( 8) hydrogen bonds : bond 0.03634 / 2.39 ( 947) hydrogen bonds : angle 3.45683 / 2.58 ( 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 269 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.664 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: 0.8991 (pm20) cc_final: 0.8567 (pm20) REVERT: A 87 SER cc_start: 0.9203 (p) cc_final: 0.8966 (p) REVERT: C 77 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8213 (ttp-110) REVERT: C 91 GLU cc_start: 0.9255 (tp30) cc_final: 0.8551 (tp30) REVERT: E 49 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8358 (ptp90) REVERT: E 59 GLU cc_start: 0.8934 (pm20) cc_final: 0.8413 (pm20) REVERT: F 92 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8284 (ttp80) REVERT: G 91 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8443 (tm-30) REVERT: H 72 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8445 (tm-30) REVERT: N 95 ASP cc_start: 0.8651 (t0) cc_final: 0.8060 (t0) REVERT: N 263 GLU cc_start: 0.8235 (tp30) cc_final: 0.8016 (tm-30) outliers start: 32 outliers final: 23 residues processed: 246 average time/residue: 0.8266 time to fit residues: 222.4057 Evaluate side-chains 264 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 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 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU 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 40 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 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 0.0270 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.141146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085138 restraints weight = 31253.852| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.89 r_work: 0.2878 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1440 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= 0.139 Angle : 0.535 7.766 25345 Z= 0.312 Chirality : 0.036 0.201 2863 Planarity : 0.003 0.036 2164 Dihedral : 29.864 160.695 4856 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.42 % Allowed : 24.89 % Favored : 72.69 % 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: 2.90 (0.20), residues: 671 sheet: 0.55 (0.37), residues: 198 loop : -1.08 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 83 TYR 0.009 0.001 TYR 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/Z covalent geometry : bond 0.00265 / 0.14 (17811) covalent geometry : angle 0.53519 / 0.31 (25337) SS BOND : bond 0.00442 / 0.26 ( 4) SS BOND : angle 0.76204 / 0.38 ( 8) hydrogen bonds : bond 0.03615 / 2.38 ( 947) hydrogen bonds : angle 3.40124 / 2.54 ( 2470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9197.29 seconds wall clock time: 156 minutes 39.94 seconds (9399.94 seconds total)