Starting phenix.real_space_refine on Sun Jun 15 20:52:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0i_26260/06_2025/7u0i_26260.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0i_26260/06_2025/7u0i_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_26260/06_2025/7u0i_26260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0i_26260/06_2025/7u0i_26260.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0i_26260/06_2025/7u0i_26260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0i_26260/06_2025/7u0i_26260.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.139 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.91, per 1000 atoms: 0.55 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: 4.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 7.13 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: 7.10 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1225 1.03 - 1.23: 240 1.23 - 1.43: 7975 1.43 - 1.62: 9532 1.62 - 1.82: 59 Bond restraints: 19031 Sorted by residual: bond pdb=" C LYS B 59 " pdb=" O LYS B 59 " ideal model delta sigma weight residual 1.237 1.008 0.228 1.19e-02 7.06e+03 3.68e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.237 1.019 0.218 1.16e-02 7.43e+03 3.53e+02 bond pdb=" C MET G 51 " pdb=" O MET G 51 " ideal model delta sigma weight residual 1.237 1.013 0.223 1.19e-02 7.06e+03 3.52e+02 bond pdb=" C ARG D 93 " pdb=" O ARG D 93 " ideal model delta sigma weight residual 1.236 1.013 0.223 1.22e-02 6.72e+03 3.35e+02 bond pdb=" C ARG E 63 " pdb=" O ARG E 63 " ideal model delta sigma weight residual 1.234 1.031 0.203 1.27e-02 6.20e+03 2.55e+02 ... (remaining 19026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 27993 4.70 - 9.40: 110 9.40 - 14.10: 10 14.10 - 18.80: 4 18.80 - 23.51: 4 Bond angle restraints: 28121 Sorted by residual: angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 110.80 132.35 -21.55 2.13e+00 2.20e-01 1.02e+02 angle pdb=" CG ARG F 95 " pdb=" CD ARG F 95 " pdb=" NE ARG F 95 " ideal model delta sigma weight residual 112.00 90.95 21.05 2.20e+00 2.07e-01 9.16e+01 angle pdb=" CG MET C 51 " pdb=" SD MET C 51 " pdb=" CE MET C 51 " ideal model delta sigma weight residual 100.90 82.71 18.19 2.20e+00 2.07e-01 6.84e+01 angle pdb=" C MET C 51 " pdb=" CA MET C 51 " pdb=" CB MET C 51 " ideal model delta sigma weight residual 110.90 97.89 13.01 1.58e+00 4.01e-01 6.79e+01 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 89.19 23.51 3.00e+00 1.11e-01 6.14e+01 ... (remaining 28116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.20: 8540 32.20 - 64.40: 1808 64.40 - 96.60: 52 96.60 - 128.80: 1 128.80 - 161.00: 3 Dihedral angle restraints: 10404 sinusoidal: 6374 harmonic: 4030 Sorted by residual: dihedral pdb=" C MET C 51 " pdb=" N MET C 51 " pdb=" CA MET C 51 " pdb=" CB MET C 51 " ideal model delta harmonic sigma weight residual -122.60 -106.48 -16.12 0 2.50e+00 1.60e-01 4.16e+01 dihedral pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CA LYS C 13 " pdb=" CB LYS C 13 " ideal model delta harmonic sigma weight residual 122.80 136.47 -13.67 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" C LYS C 13 " pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" CB LYS C 13 " ideal model delta harmonic sigma weight residual -122.60 -136.23 13.63 0 2.50e+00 1.60e-01 2.97e+01 ... (remaining 10401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2842 0.145 - 0.290: 6 0.290 - 0.435: 9 0.435 - 0.580: 5 0.580 - 0.725: 1 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CA LYS C 13 " pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CB LYS C 13 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ARG B 92 " pdb=" N ARG B 92 " pdb=" C ARG B 92 " pdb=" CB ARG B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA MET G 51 " pdb=" N MET G 51 " pdb=" C MET G 51 " pdb=" CB MET G 51 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.81e+00 ... (remaining 2860 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET G 51 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" C MET G 51 " -0.099 2.00e-02 2.50e+03 pdb=" O MET G 51 " 0.038 2.00e-02 2.50e+03 pdb=" N ALA G 52 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " -0.027 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C GLU C 92 " 0.097 2.00e-02 2.50e+03 pdb=" O GLU C 92 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU C 93 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 51 " -0.025 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C MET C 51 " 0.084 2.00e-02 2.50e+03 pdb=" O MET C 51 " -0.032 2.00e-02 2.50e+03 pdb=" N ALA C 52 " -0.028 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 198 2.23 - 2.82: 9538 2.82 - 3.42: 22300 3.42 - 4.01: 44297 4.01 - 4.60: 61307 Nonbonded interactions: 137640 Sorted by model distance: nonbonded pdb=" HG LEU L 200 " pdb="HD12 LEU L 204 " model vdw 1.641 2.440 nonbonded pdb=" O ASP M 166 " pdb=" HG1 THR M 170 " model vdw 1.802 2.450 nonbonded pdb=" O GLN L 155 " pdb=" HG1 THR L 159 " model vdw 1.802 2.450 nonbonded pdb=" HE ARG L 157 " pdb=" OE2 GLU L 188 " model vdw 1.802 2.450 nonbonded pdb=" OP1 DT J 93 " pdb="HH12 ARG L 157 " model vdw 1.810 2.450 ... (remaining 137635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and ((resid 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) selection = (chain 'F' and ((resid 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 125) selection = (chain 'H' and (resid 31 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 125)) } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 23 through 264 or (resid 265 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.360 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.690 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 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:14.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.228 17815 Z= 0.748 Angle : 0.863 23.505 25345 Z= 0.487 Chirality : 0.049 0.725 2863 Planarity : 0.006 0.073 2164 Dihedral : 26.815 160.996 7468 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (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 TRP 0.015 0.001 TRP K 199 HIS 0.016 0.002 HIS A 39 PHE 0.010 0.001 PHE E 84 TYR 0.017 0.002 TYR A 41 ARG 0.029 0.001 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.12132 ( 947) hydrogen bonds : angle 5.23287 ( 2470) SS BOND : bond 0.00443 ( 4) SS BOND : angle 0.99945 ( 8) covalent geometry : bond 0.01164 (17811) covalent geometry : angle 0.86269 (25337) *********************** 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 : 1.465 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: 1.8573 time to fit residues: 541.7177 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 : 1.741 ------------------------------------------------------------------------------- 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 133 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.0570 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 123 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 overall best weight: 1.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 94 ASN C 104 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN H 96 GLN N 164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086986 restraints weight = 31722.580| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.91 r_work: 0.2926 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17815 Z= 0.204 Angle : 0.521 8.054 25345 Z= 0.310 Chirality : 0.033 0.120 2863 Planarity : 0.004 0.050 2164 Dihedral : 29.524 156.031 4876 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.20 % Allowed : 21.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1340 helix: 2.18 (0.20), residues: 674 sheet: 0.43 (0.35), residues: 238 loop : -1.10 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 132 HIS 0.005 0.001 HIS F 75 PHE 0.012 0.001 PHE D 71 TYR 0.010 0.001 TYR C 57 ARG 0.004 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 947) hydrogen bonds : angle 3.68123 ( 2470) SS BOND : bond 0.00519 ( 4) SS BOND : angle 0.75902 ( 8) covalent geometry : bond 0.00457 (17811) covalent geometry : angle 0.52082 (25337) *********************** 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 269 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9242 (p) cc_final: 0.8961 (p) REVERT: C 91 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8698 (tm-30) REVERT: G 91 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: H 72 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8475 (tm-30) REVERT: N 95 ASP cc_start: 0.8819 (t0) cc_final: 0.8286 (t0) outliers start: 37 outliers final: 24 residues processed: 241 average time/residue: 2.0578 time to fit residues: 544.8337 Evaluate side-chains 255 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain 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 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 23 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 104 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN H 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087891 restraints weight = 31612.741| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.87 r_work: 0.2945 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17815 Z= 0.147 Angle : 0.496 8.393 25345 Z= 0.296 Chirality : 0.032 0.122 2863 Planarity : 0.003 0.042 2164 Dihedral : 29.541 157.611 4858 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.77 % Allowed : 22.47 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1340 helix: 2.55 (0.20), residues: 675 sheet: 0.48 (0.35), residues: 238 loop : -1.02 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 132 HIS 0.003 0.001 HIS H 50 PHE 0.005 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.002 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 947) hydrogen bonds : angle 3.54091 ( 2470) SS BOND : bond 0.00381 ( 4) SS BOND : angle 0.68604 ( 8) covalent geometry : bond 0.00322 (17811) covalent geometry : angle 0.49558 (25337) *********************** 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 269 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9198 (p) cc_final: 0.8917 (p) REVERT: C 91 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8653 (tm-30) REVERT: G 91 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8585 (tm-30) REVERT: H 72 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8454 (tm-30) REVERT: K 112 ASP cc_start: 0.8596 (m-30) cc_final: 0.8395 (m-30) REVERT: N 68 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: N 95 ASP cc_start: 0.8750 (t0) cc_final: 0.8184 (t0) REVERT: N 237 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8293 (mp0) REVERT: N 263 GLU cc_start: 0.8206 (tp30) cc_final: 0.7919 (tm-30) outliers start: 32 outliers final: 23 residues processed: 244 average time/residue: 2.1720 time to fit residues: 579.4999 Evaluate side-chains 252 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 61 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.140377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085343 restraints weight = 31723.538| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.90 r_work: 0.2883 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 17815 Z= 0.268 Angle : 0.540 8.796 25345 Z= 0.319 Chirality : 0.035 0.126 2863 Planarity : 0.004 0.042 2164 Dihedral : 29.729 159.983 4856 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.15 % Allowed : 21.61 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1340 helix: 2.52 (0.20), residues: 675 sheet: 0.64 (0.36), residues: 222 loop : -1.12 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.003 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 947) hydrogen bonds : angle 3.54363 ( 2470) SS BOND : bond 0.00501 ( 4) SS BOND : angle 0.69368 ( 8) covalent geometry : bond 0.00607 (17811) covalent geometry : angle 0.53983 (25337) *********************** 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 274 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 1.432 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: 0.8885 (pm20) cc_final: 0.8503 (pm20) REVERT: A 87 SER cc_start: 0.9148 (p) cc_final: 0.8902 (p) REVERT: C 91 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8349 (tp30) REVERT: E 49 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8359 (ptp90) REVERT: G 91 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: H 72 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8199 (tm-30) REVERT: N 95 ASP cc_start: 0.8713 (t0) cc_final: 0.8137 (t0) REVERT: N 169 MET cc_start: 0.8782 (ptp) cc_final: 0.8439 (ptm) outliers start: 48 outliers final: 32 residues processed: 243 average time/residue: 1.6673 time to fit residues: 442.8915 Evaluate side-chains 264 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 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 40 VAL Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 120 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 108 optimal weight: 50.0000 chunk 87 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** 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 = 0.3935 r_free = 0.3935 target = 0.141580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086733 restraints weight = 31548.490| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.85 r_work: 0.2918 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17815 Z= 0.149 Angle : 0.505 8.937 25345 Z= 0.302 Chirality : 0.032 0.120 2863 Planarity : 0.003 0.039 2164 Dihedral : 29.734 159.761 4856 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.46 % Allowed : 22.64 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1340 helix: 2.64 (0.20), residues: 675 sheet: 0.66 (0.36), residues: 222 loop : -1.08 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 58 HIS 0.004 0.001 HIS K 170 PHE 0.005 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.002 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 947) hydrogen bonds : angle 3.46408 ( 2470) SS BOND : bond 0.00485 ( 4) SS BOND : angle 0.77561 ( 8) covalent geometry : bond 0.00326 (17811) covalent geometry : angle 0.50506 (25337) *********************** 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 272 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8988 (pm20) cc_final: 0.8588 (pm20) REVERT: A 87 SER cc_start: 0.9202 (p) cc_final: 0.8963 (p) REVERT: A 90 MET cc_start: 0.8752 (mmp) cc_final: 0.8530 (mmp) REVERT: C 77 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8248 (ttp-110) REVERT: C 91 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8490 (tp30) REVERT: E 49 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8398 (ptp90) REVERT: G 91 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8523 (tm-30) REVERT: H 72 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8451 (tm-30) REVERT: N 95 ASP cc_start: 0.8691 (t0) cc_final: 0.8079 (t0) REVERT: N 169 MET cc_start: 0.8824 (ptp) cc_final: 0.8580 (ptm) outliers start: 40 outliers final: 28 residues processed: 244 average time/residue: 1.7289 time to fit residues: 461.3505 Evaluate side-chains 259 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain 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 139 THR Chi-restraints excluded: chain K residue 176 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.141271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.086385 restraints weight = 31620.042| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.86 r_work: 0.2908 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17815 Z= 0.204 Angle : 0.504 8.204 25345 Z= 0.301 Chirality : 0.033 0.121 2863 Planarity : 0.003 0.040 2164 Dihedral : 29.603 158.382 4856 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.72 % Allowed : 22.39 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1340 helix: 2.81 (0.20), residues: 671 sheet: 0.60 (0.37), residues: 198 loop : -1.09 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE E 104 TYR 0.010 0.001 TYR B 51 ARG 0.002 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 947) hydrogen bonds : angle 3.37623 ( 2470) SS BOND : bond 0.00480 ( 4) SS BOND : angle 0.71290 ( 8) covalent geometry : bond 0.00458 (17811) covalent geometry : angle 0.50418 (25337) *********************** 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 277 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 1.520 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: 0.8989 (pm20) cc_final: 0.8579 (pm20) REVERT: A 87 SER cc_start: 0.9203 (p) cc_final: 0.8962 (p) REVERT: C 77 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8223 (ttp-110) REVERT: C 91 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8497 (tp30) REVERT: E 49 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8477 (ptp90) REVERT: E 59 GLU cc_start: 0.8914 (pm20) cc_final: 0.8549 (pm20) REVERT: G 91 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: H 72 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8465 (tm-30) REVERT: H 87 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8730 (mtt90) REVERT: K 93 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8628 (t) REVERT: K 112 ASP cc_start: 0.8520 (m-30) cc_final: 0.8186 (m-30) REVERT: K 237 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: N 95 ASP cc_start: 0.8653 (t0) cc_final: 0.8055 (t0) REVERT: N 237 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8230 (mp0) REVERT: N 263 GLU cc_start: 0.8278 (tp30) cc_final: 0.8066 (tm-30) outliers start: 43 outliers final: 30 residues processed: 245 average time/residue: 1.6405 time to fit residues: 439.1590 Evaluate side-chains 263 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain 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 38 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 108 optimal weight: 50.0000 chunk 148 optimal weight: 0.3980 chunk 31 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.142335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087651 restraints weight = 31457.581| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.85 r_work: 0.2939 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17815 Z= 0.130 Angle : 0.493 8.417 25345 Z= 0.295 Chirality : 0.031 0.121 2863 Planarity : 0.003 0.039 2164 Dihedral : 29.608 158.427 4856 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.46 % Allowed : 23.42 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1340 helix: 2.90 (0.20), residues: 671 sheet: 0.61 (0.37), residues: 198 loop : -1.08 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 207 HIS 0.003 0.001 HIS K 170 PHE 0.005 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.002 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 947) hydrogen bonds : angle 3.34111 ( 2470) SS BOND : bond 0.00418 ( 4) SS BOND : angle 0.90107 ( 8) covalent geometry : bond 0.00282 (17811) covalent geometry : angle 0.49266 (25337) *********************** 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 270 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 1.591 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: 0.8985 (pm20) cc_final: 0.8564 (pm20) REVERT: A 87 SER cc_start: 0.9182 (p) cc_final: 0.8937 (p) REVERT: C 51 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8528 (tpt) REVERT: C 77 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8251 (ttp-110) REVERT: E 49 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8421 (ptp90) REVERT: E 59 GLU cc_start: 0.8906 (pm20) cc_final: 0.8502 (pm20) REVERT: G 91 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: H 72 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8444 (tm-30) REVERT: K 93 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8524 (p) REVERT: N 95 ASP cc_start: 0.8627 (t0) cc_final: 0.8041 (t0) outliers start: 40 outliers final: 26 residues processed: 241 average time/residue: 1.6822 time to fit residues: 443.5101 Evaluate side-chains 266 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 88 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.085005 restraints weight = 31441.923| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.89 r_work: 0.2882 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 17815 Z= 0.276 Angle : 0.543 8.357 25345 Z= 0.321 Chirality : 0.035 0.125 2863 Planarity : 0.004 0.042 2164 Dihedral : 29.740 160.258 4856 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.80 % Allowed : 23.16 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1340 helix: 2.68 (0.20), residues: 675 sheet: 0.36 (0.37), residues: 204 loop : -1.11 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE E 104 TYR 0.011 0.001 TYR B 51 ARG 0.003 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 947) hydrogen bonds : angle 3.46197 ( 2470) SS BOND : bond 0.00558 ( 4) SS BOND : angle 0.70034 ( 8) covalent geometry : bond 0.00628 (17811) covalent geometry : angle 0.54328 (25337) *********************** 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 280 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 1.470 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: A 59 GLU cc_start: 0.9022 (pm20) cc_final: 0.8651 (pm20) REVERT: A 87 SER cc_start: 0.9232 (p) cc_final: 0.8991 (p) REVERT: C 51 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8525 (tpt) REVERT: C 77 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8217 (ttp-110) REVERT: E 49 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8468 (ptp90) REVERT: E 59 GLU cc_start: 0.8900 (pm20) cc_final: 0.8467 (pm20) REVERT: F 92 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8222 (ttp80) REVERT: G 91 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: H 72 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8472 (tm-30) REVERT: K 93 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8493 (p) REVERT: K 112 ASP cc_start: 0.8466 (m-30) cc_final: 0.8160 (m-30) REVERT: N 95 ASP cc_start: 0.8697 (t0) cc_final: 0.8146 (t0) REVERT: N 103 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.7065 (tpt) REVERT: N 263 GLU cc_start: 0.8327 (tp30) cc_final: 0.8069 (tm-30) outliers start: 44 outliers final: 30 residues processed: 250 average time/residue: 1.7756 time to fit residues: 485.5362 Evaluate side-chains 264 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 137 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.140632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.085738 restraints weight = 31561.688| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.87 r_work: 0.2891 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17815 Z= 0.228 Angle : 0.533 8.575 25345 Z= 0.316 Chirality : 0.034 0.126 2863 Planarity : 0.003 0.040 2164 Dihedral : 29.754 160.281 4856 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.06 % Allowed : 23.34 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1340 helix: 2.71 (0.20), residues: 671 sheet: 0.32 (0.37), residues: 204 loop : -1.11 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.002 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 947) hydrogen bonds : angle 3.44620 ( 2470) SS BOND : bond 0.00511 ( 4) SS BOND : angle 0.76665 ( 8) covalent geometry : bond 0.00516 (17811) covalent geometry : angle 0.53315 (25337) *********************** 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 273 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 1.465 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: A 59 GLU cc_start: 0.9009 (pm20) cc_final: 0.8633 (pm20) REVERT: A 87 SER cc_start: 0.9229 (p) cc_final: 0.8987 (p) REVERT: A 90 MET cc_start: 0.8790 (mmp) cc_final: 0.8568 (mmp) REVERT: C 51 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8483 (tpt) REVERT: C 77 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8207 (ttp-110) REVERT: E 49 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8464 (ptp90) REVERT: E 59 GLU cc_start: 0.8904 (pm20) cc_final: 0.8462 (pm20) REVERT: F 92 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8309 (ttp80) REVERT: G 91 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: H 72 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8469 (tm-30) REVERT: K 93 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8499 (p) REVERT: N 95 ASP cc_start: 0.8680 (t0) cc_final: 0.8119 (t0) REVERT: N 103 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.7071 (tpt) outliers start: 47 outliers final: 34 residues processed: 243 average time/residue: 1.6739 time to fit residues: 444.8914 Evaluate side-chains 274 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain 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 95 ASP 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 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 149 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.140641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085600 restraints weight = 31537.651| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.88 r_work: 0.2894 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17815 Z= 0.228 Angle : 0.533 8.374 25345 Z= 0.315 Chirality : 0.034 0.125 2863 Planarity : 0.003 0.036 2164 Dihedral : 29.747 160.273 4856 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.54 % Allowed : 23.68 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1340 helix: 2.72 (0.20), residues: 671 sheet: 0.32 (0.37), residues: 204 loop : -1.12 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 132 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 104 TYR 0.011 0.001 TYR B 51 ARG 0.002 0.000 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 947) hydrogen bonds : angle 3.43815 ( 2470) SS BOND : bond 0.00524 ( 4) SS BOND : angle 0.77573 ( 8) covalent geometry : bond 0.00517 (17811) covalent geometry : angle 0.53313 (25337) ********************** 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 274 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 1.758 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: A 59 GLU cc_start: 0.9024 (pm20) cc_final: 0.8600 (pm20) REVERT: A 87 SER cc_start: 0.9251 (p) cc_final: 0.9017 (p) REVERT: A 90 MET cc_start: 0.8833 (mmp) cc_final: 0.8614 (mmp) REVERT: C 51 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8508 (tpt) REVERT: C 77 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8240 (ttp-110) REVERT: E 49 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8524 (ptp90) REVERT: E 59 GLU cc_start: 0.8941 (pm20) cc_final: 0.8511 (pm20) REVERT: F 92 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8302 (ttp80) REVERT: G 91 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8565 (tm-30) REVERT: H 72 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8485 (tm-30) REVERT: K 93 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8538 (p) REVERT: N 95 ASP cc_start: 0.8709 (t0) cc_final: 0.8150 (t0) REVERT: N 103 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.7095 (tpt) REVERT: N 263 GLU cc_start: 0.8329 (tp30) cc_final: 0.8073 (tm-30) outliers start: 41 outliers final: 32 residues processed: 246 average time/residue: 2.2216 time to fit residues: 600.7007 Evaluate side-chains 265 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain 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 247 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.141446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086590 restraints weight = 31521.492| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.85 r_work: 0.2909 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17815 Z= 0.150 Angle : 0.513 8.797 25345 Z= 0.306 Chirality : 0.032 0.127 2863 Planarity : 0.003 0.035 2164 Dihedral : 29.759 160.215 4856 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.46 % Allowed : 23.77 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1340 helix: 2.80 (0.20), residues: 671 sheet: 0.31 (0.37), residues: 204 loop : -1.07 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 58 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.002 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 947) hydrogen bonds : angle 3.40937 ( 2470) SS BOND : bond 0.00482 ( 4) SS BOND : angle 0.95058 ( 8) covalent geometry : bond 0.00333 (17811) covalent geometry : angle 0.51323 (25337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20084.58 seconds wall clock time: 350 minutes 18.80 seconds (21018.80 seconds total)