Starting phenix.real_space_refine on Wed Sep 17 18:45:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r21_53519/09_2025/9r21_53519.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r21_53519/09_2025/9r21_53519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r21_53519/09_2025/9r21_53519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r21_53519/09_2025/9r21_53519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r21_53519/09_2025/9r21_53519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r21_53519/09_2025/9r21_53519.map" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7009 2.51 5 N 1475 2.21 5 O 1687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10231 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1846 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1846 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1846 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1846 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1846 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 198 Unusual residues: {'LFA': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 162 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 189 Unusual residues: {'LFA': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 151 Chain: "C" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 191 Unusual residues: {'LFA': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 149 Chain: "D" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 170 Unusual residues: {'LFA': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 130 Chain: "E" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 156 Unusual residues: {'LFA': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 124 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 2.39, per 1000 atoms: 0.23 Number of scatterers: 10231 At special positions: 0 Unit cell: (101.156, 99.484, 77.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1687 8.00 N 1475 7.00 C 7009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 364.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 69 Processing helix chain 'A' and resid 75 through 97 removed outlier: 4.176A pdb=" N ASP A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 125 removed outlier: 4.225A pdb=" N PHE A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 151 removed outlier: 3.601A pdb=" N ILE A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 162 through 178 Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.504A pdb=" N GLY A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 213 through 237 removed outlier: 3.721A pdb=" N LYS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 69 Processing helix chain 'B' and resid 75 through 97 removed outlier: 4.175A pdb=" N ASP B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 125 removed outlier: 4.225A pdb=" N PHE B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 151 removed outlier: 3.592A pdb=" N ILE B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 213 through 237 removed outlier: 3.753A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 32 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 69 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 75 through 97 removed outlier: 4.179A pdb=" N ASP C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 91 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 125 removed outlier: 4.224A pdb=" N PHE C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 120 " --> pdb=" O MET C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 151 removed outlier: 3.604A pdb=" N ILE C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 162 through 178 Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.504A pdb=" N GLY C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 209 Processing helix chain 'C' and resid 213 through 237 removed outlier: 3.744A pdb=" N LYS C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 32 Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 97 removed outlier: 4.174A pdb=" N ASP D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE D 91 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 125 removed outlier: 4.225A pdb=" N PHE D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP D 107 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D 120 " --> pdb=" O MET D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 removed outlier: 3.602A pdb=" N ILE D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.505A pdb=" N GLY D 193 " --> pdb=" O ILE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 213 through 237 removed outlier: 3.728A pdb=" N LYS D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 32 Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 69 Processing helix chain 'E' and resid 75 through 97 removed outlier: 4.172A pdb=" N ASP E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 125 removed outlier: 4.223A pdb=" N PHE E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU E 120 " --> pdb=" O MET E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 removed outlier: 3.603A pdb=" N ILE E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 159 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.507A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 209 Processing helix chain 'E' and resid 213 through 237 removed outlier: 3.743A pdb=" N LYS E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2033 1.33 - 1.45: 2732 1.45 - 1.57: 5386 1.57 - 1.69: 7 1.69 - 1.82: 115 Bond restraints: 10273 Sorted by residual: bond pdb=" CA SER E 54 " pdb=" CB SER E 54 " ideal model delta sigma weight residual 1.528 1.444 0.085 1.56e-02 4.11e+03 2.96e+01 bond pdb=" CA SER B 54 " pdb=" CB SER B 54 " ideal model delta sigma weight residual 1.528 1.447 0.082 1.56e-02 4.11e+03 2.73e+01 bond pdb=" CA SER A 54 " pdb=" CB SER A 54 " ideal model delta sigma weight residual 1.528 1.449 0.080 1.56e-02 4.11e+03 2.60e+01 bond pdb=" CA SER D 54 " pdb=" CB SER D 54 " ideal model delta sigma weight residual 1.528 1.449 0.079 1.56e-02 4.11e+03 2.59e+01 bond pdb=" CA SER C 54 " pdb=" CB SER C 54 " ideal model delta sigma weight residual 1.528 1.450 0.079 1.56e-02 4.11e+03 2.55e+01 ... (remaining 10268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 12547 3.65 - 7.30: 914 7.30 - 10.94: 127 10.94 - 14.59: 12 14.59 - 18.24: 2 Bond angle restraints: 13602 Sorted by residual: angle pdb=" NE ARG E 76 " pdb=" CZ ARG E 76 " pdb=" NH2 ARG E 76 " ideal model delta sigma weight residual 119.20 110.55 8.65 9.00e-01 1.23e+00 9.23e+01 angle pdb=" NE ARG D 76 " pdb=" CZ ARG D 76 " pdb=" NH2 ARG D 76 " ideal model delta sigma weight residual 119.20 110.61 8.59 9.00e-01 1.23e+00 9.11e+01 angle pdb=" CA ARG E 231 " pdb=" CB ARG E 231 " pdb=" CG ARG E 231 " ideal model delta sigma weight residual 114.10 131.24 -17.14 2.00e+00 2.50e-01 7.35e+01 angle pdb=" CG MET C 20 " pdb=" SD MET C 20 " pdb=" CE MET C 20 " ideal model delta sigma weight residual 100.90 119.14 -18.24 2.20e+00 2.07e-01 6.87e+01 angle pdb=" CA PHE D 218 " pdb=" CB PHE D 218 " pdb=" CG PHE D 218 " ideal model delta sigma weight residual 113.80 105.66 8.14 1.00e+00 1.00e+00 6.63e+01 ... (remaining 13597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5147 17.95 - 35.91: 662 35.91 - 53.86: 145 53.86 - 71.81: 36 71.81 - 89.77: 6 Dihedral angle restraints: 5996 sinusoidal: 2641 harmonic: 3355 Sorted by residual: dihedral pdb=" CD ARG D 33 " pdb=" NE ARG D 33 " pdb=" CZ ARG D 33 " pdb=" NH1 ARG D 33 " ideal model delta sinusoidal sigma weight residual 0.00 84.32 -84.32 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" C GLU D 120 " pdb=" N GLU D 120 " pdb=" CA GLU D 120 " pdb=" CB GLU D 120 " ideal model delta harmonic sigma weight residual -122.60 -141.24 18.64 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" C GLU A 120 " pdb=" N GLU A 120 " pdb=" CA GLU A 120 " pdb=" CB GLU A 120 " ideal model delta harmonic sigma weight residual -122.60 -136.71 14.11 0 2.50e+00 1.60e-01 3.19e+01 ... (remaining 5993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1267 0.125 - 0.250: 212 0.250 - 0.376: 19 0.376 - 0.501: 6 0.501 - 0.626: 1 Chirality restraints: 1505 Sorted by residual: chirality pdb=" CA GLU D 120 " pdb=" N GLU D 120 " pdb=" C GLU D 120 " pdb=" CB GLU D 120 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.79e+00 chirality pdb=" CB VAL C 89 " pdb=" CA VAL C 89 " pdb=" CG1 VAL C 89 " pdb=" CG2 VAL C 89 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CB VAL B 89 " pdb=" CA VAL B 89 " pdb=" CG1 VAL B 89 " pdb=" CG2 VAL B 89 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 1502 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 33 " -0.763 9.50e-02 1.11e+02 3.48e-01 1.20e+02 pdb=" NE ARG D 33 " 0.092 2.00e-02 2.50e+03 pdb=" CZ ARG D 33 " -0.111 2.00e-02 2.50e+03 pdb=" NH1 ARG D 33 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG D 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 173 " -0.541 9.50e-02 1.11e+02 2.44e-01 4.66e+01 pdb=" NE ARG B 173 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 173 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG B 173 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 173 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 35 " -0.547 9.50e-02 1.11e+02 2.46e-01 4.08e+01 pdb=" NE ARG C 35 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG C 35 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG C 35 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 35 " -0.030 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 84 2.55 - 3.14: 8371 3.14 - 3.73: 15948 3.73 - 4.31: 26972 4.31 - 4.90: 41354 Nonbonded interactions: 92729 Sorted by model distance: nonbonded pdb=" OH TYR D 58 " pdb=" OD2 ASP D 209 " model vdw 1.968 3.040 nonbonded pdb=" OH TYR E 58 " pdb=" OD2 ASP E 209 " model vdw 1.973 3.040 nonbonded pdb=" OH TYR C 58 " pdb=" OD2 ASP C 209 " model vdw 1.975 3.040 nonbonded pdb=" OH TYR B 58 " pdb=" OD2 ASP B 209 " model vdw 1.980 3.040 nonbonded pdb=" OH TYR A 58 " pdb=" OD2 ASP A 209 " model vdw 1.980 3.040 ... (remaining 92724 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' and (resid 2 through 301 or (resid 302 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C2 or name C3 or name C4 or name C5 or na \ me C6 or name C7 or name C8 or name C9 )) or (resid 305 and (name C8 or name C9 \ )) or resid 309 or (resid 313 through 314 and (name C1 or name C2 or name C3 or \ name C4 or name C5 or name C6 or name C7 )))) selection = (chain 'B' and (resid 2 through 237 or (resid 301 through 302 and (name C1 or na \ me C10 or name C11 or name C12 or name C13 or name C2 or name C3 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 305 and (name C8 \ or name C9 )) or (resid 309 and (name C1 or name C2 or name C3 or name C4 or na \ me C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 313 through 314 a \ nd (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) \ )) selection = (chain 'C' and (resid 2 through 237 or (resid 301 through 302 and (name C1 or na \ me C10 or name C11 or name C12 or name C13 or name C2 or name C3 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 305 and (name C8 \ or name C9 )) or resid 309 or (resid 313 and (name C11 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18)) or resid 314)) selection = (chain 'D' and (resid 2 through 237 or (resid 301 through 302 and (name C1 or na \ me C10 or name C11 or name C12 or name C13 or name C2 or name C3 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 305 and (name C8 \ or name C9 )) or resid 309 or (resid 313 through 314 and (name C1 or name C2 or \ name C3 or name C4 or name C5 or name C6 or name C7 )))) selection = (chain 'E' and (resid 2 through 237 or (resid 301 through 302 and (name C1 or na \ me C10 or name C11 or name C12 or name C13 or name C2 or name C3 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 305 and (name C8 \ or name C9 )) or resid 309 or (resid 313 and (name C1 or name C2 or name C3 or \ name C4 or name C5 or name C6 or name C7 )) or resid 314)) } 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: 5.800 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.620 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 0.085 10273 Z= 0.797 Angle : 2.085 18.241 13602 Z= 1.284 Chirality : 0.096 0.626 1505 Planarity : 0.024 0.348 1555 Dihedral : 16.728 89.766 3876 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.58 % Allowed : 9.90 % Favored : 85.52 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.09 (0.19), residues: 1170 helix: -2.88 (0.11), residues: 950 sheet: None (None), residues: 0 loop : -0.39 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.120 0.009 ARG D 33 TYR 0.046 0.012 TYR B 77 PHE 0.046 0.012 PHE A 210 TRP 0.051 0.016 TRP C 180 HIS 0.013 0.005 HIS E 41 Details of bonding type rmsd covalent geometry : bond 0.01230 (10273) covalent geometry : angle 2.08529 (13602) hydrogen bonds : bond 0.19295 ( 766) hydrogen bonds : angle 8.28711 ( 2298) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.394 Fit side-chains REVERT: A 35 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7224 (mmp-170) REVERT: A 70 LYS cc_start: 0.8324 (mttt) cc_final: 0.7968 (mtmm) REVERT: A 120 GLU cc_start: 0.8711 (tt0) cc_final: 0.7915 (mt-10) REVERT: B 51 MET cc_start: 0.8980 (mmp) cc_final: 0.8594 (mmp) REVERT: B 70 LYS cc_start: 0.8206 (mttt) cc_final: 0.7814 (mtmm) REVERT: B 120 GLU cc_start: 0.8717 (tt0) cc_final: 0.8084 (mt-10) REVERT: C 51 MET cc_start: 0.8968 (mmp) cc_final: 0.8728 (mmp) REVERT: C 70 LYS cc_start: 0.8296 (mttt) cc_final: 0.8009 (mtmm) REVERT: C 150 MET cc_start: 0.8759 (mtp) cc_final: 0.8487 (mtp) REVERT: C 167 MET cc_start: 0.8393 (mtp) cc_final: 0.7864 (mtm) REVERT: D 51 MET cc_start: 0.8989 (mmp) cc_final: 0.8627 (mmp) REVERT: D 70 LYS cc_start: 0.8230 (mtpt) cc_final: 0.8014 (mtmm) REVERT: D 120 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: E 70 LYS cc_start: 0.8246 (mmtp) cc_final: 0.7921 (mtmm) REVERT: E 90 MET cc_start: 0.8794 (tpp) cc_final: 0.8510 (tpt) REVERT: E 150 MET cc_start: 0.8739 (mtp) cc_final: 0.8494 (mtp) outliers start: 44 outliers final: 27 residues processed: 155 average time/residue: 0.5734 time to fit residues: 96.0280 Evaluate side-chains 139 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 87 GLN A 166 HIS B 34 ASN B 87 GLN B 166 HIS C 87 GLN C 166 HIS D 34 ASN D 87 GLN D 166 HIS E 34 ASN E 87 GLN E 166 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113056 restraints weight = 10150.422| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.01 r_work: 0.3230 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10273 Z= 0.151 Angle : 0.550 5.930 13602 Z= 0.299 Chirality : 0.039 0.129 1505 Planarity : 0.004 0.049 1555 Dihedral : 12.273 59.572 1985 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.60 % Allowed : 11.67 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.24), residues: 1170 helix: 0.80 (0.16), residues: 965 sheet: None (None), residues: 0 loop : 0.42 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 33 TYR 0.012 0.002 TYR D 77 PHE 0.017 0.002 PHE D 216 TRP 0.010 0.002 TRP C 107 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00335 (10273) covalent geometry : angle 0.55009 (13602) hydrogen bonds : bond 0.05087 ( 766) hydrogen bonds : angle 4.57700 ( 2298) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.387 Fit side-chains REVERT: A 44 MET cc_start: 0.8523 (mmm) cc_final: 0.8287 (mmp) REVERT: A 116 MET cc_start: 0.8865 (ttt) cc_final: 0.8530 (ttp) REVERT: A 120 GLU cc_start: 0.8365 (tt0) cc_final: 0.7799 (mt-10) REVERT: A 167 MET cc_start: 0.8236 (mtp) cc_final: 0.7740 (mtm) REVERT: B 70 LYS cc_start: 0.8360 (mttt) cc_final: 0.8099 (mtmm) REVERT: B 103 SER cc_start: 0.8099 (p) cc_final: 0.7804 (m) REVERT: C 51 MET cc_start: 0.8942 (mmp) cc_final: 0.8720 (mmp) REVERT: C 70 LYS cc_start: 0.8410 (mttt) cc_final: 0.8197 (mtmm) REVERT: C 155 ARG cc_start: 0.7356 (ttm110) cc_final: 0.7139 (ttp-170) REVERT: C 167 MET cc_start: 0.8289 (mtp) cc_final: 0.7499 (mtm) REVERT: D 35 ARG cc_start: 0.7797 (mmm160) cc_final: 0.7502 (mmm160) REVERT: D 120 GLU cc_start: 0.8260 (pt0) cc_final: 0.7460 (mt-10) REVERT: E 35 ARG cc_start: 0.7778 (mmm160) cc_final: 0.7493 (mmm-85) REVERT: E 70 LYS cc_start: 0.8319 (mmtp) cc_final: 0.8059 (mtmm) outliers start: 25 outliers final: 16 residues processed: 173 average time/residue: 0.5991 time to fit residues: 111.4452 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 162 ASN C 162 ASN D 162 ASN E 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119465 restraints weight = 10328.327| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.97 r_work: 0.3324 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10273 Z= 0.148 Angle : 0.520 5.883 13602 Z= 0.277 Chirality : 0.039 0.139 1505 Planarity : 0.003 0.026 1555 Dihedral : 10.974 58.849 1959 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 3.02 % Allowed : 13.44 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.25), residues: 1170 helix: 1.82 (0.17), residues: 970 sheet: None (None), residues: 0 loop : 0.83 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.013 0.002 TYR D 58 PHE 0.014 0.002 PHE A 216 TRP 0.010 0.001 TRP C 107 HIS 0.001 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00330 (10273) covalent geometry : angle 0.51952 (13602) hydrogen bonds : bond 0.04733 ( 766) hydrogen bonds : angle 4.31450 ( 2298) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.324 Fit side-chains REVERT: A 44 MET cc_start: 0.8558 (mmm) cc_final: 0.8319 (mmp) REVERT: A 70 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7292 (tptp) REVERT: A 116 MET cc_start: 0.8908 (ttt) cc_final: 0.8543 (ttp) REVERT: A 120 GLU cc_start: 0.8321 (tt0) cc_final: 0.7776 (mt-10) REVERT: B 70 LYS cc_start: 0.8370 (mttt) cc_final: 0.8131 (mtmm) REVERT: B 103 SER cc_start: 0.8122 (p) cc_final: 0.7810 (m) REVERT: C 155 ARG cc_start: 0.7395 (ttm110) cc_final: 0.7092 (ttp-170) REVERT: C 167 MET cc_start: 0.8344 (mtp) cc_final: 0.7638 (mtm) REVERT: D 35 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7633 (mmm160) REVERT: D 120 GLU cc_start: 0.8373 (pt0) cc_final: 0.7678 (mt-10) REVERT: E 35 ARG cc_start: 0.7792 (mmm160) cc_final: 0.7456 (mmm-85) REVERT: E 70 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8153 (mtmm) outliers start: 29 outliers final: 18 residues processed: 161 average time/residue: 0.5491 time to fit residues: 95.1550 Evaluate side-chains 154 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN E 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110178 restraints weight = 9941.872| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 0.96 r_work: 0.3170 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10273 Z= 0.136 Angle : 0.487 5.596 13602 Z= 0.259 Chirality : 0.038 0.137 1505 Planarity : 0.003 0.021 1555 Dihedral : 10.286 57.361 1955 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.60 % Allowed : 14.58 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.25), residues: 1170 helix: 2.11 (0.17), residues: 970 sheet: None (None), residues: 0 loop : 0.82 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 76 TYR 0.012 0.001 TYR D 58 PHE 0.014 0.002 PHE A 216 TRP 0.010 0.001 TRP C 107 HIS 0.001 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00300 (10273) covalent geometry : angle 0.48660 (13602) hydrogen bonds : bond 0.04428 ( 766) hydrogen bonds : angle 4.21371 ( 2298) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.403 Fit side-chains REVERT: A 44 MET cc_start: 0.8492 (mmm) cc_final: 0.8224 (mmp) REVERT: A 70 LYS cc_start: 0.8410 (mtmm) cc_final: 0.7218 (tptp) REVERT: A 116 MET cc_start: 0.8854 (ttt) cc_final: 0.8473 (ttp) REVERT: A 120 GLU cc_start: 0.8299 (tt0) cc_final: 0.7736 (mt-10) REVERT: B 70 LYS cc_start: 0.8344 (mttt) cc_final: 0.7992 (mtmm) REVERT: C 155 ARG cc_start: 0.7328 (ttm110) cc_final: 0.7044 (ttp-170) REVERT: C 167 MET cc_start: 0.8278 (mtp) cc_final: 0.7524 (mtm) REVERT: D 35 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7671 (mmm160) REVERT: D 120 GLU cc_start: 0.8260 (pt0) cc_final: 0.7511 (mt-10) REVERT: E 35 ARG cc_start: 0.7792 (mmm160) cc_final: 0.7405 (mmm-85) REVERT: E 70 LYS cc_start: 0.8396 (mmtp) cc_final: 0.8067 (mtmm) outliers start: 25 outliers final: 18 residues processed: 159 average time/residue: 0.6123 time to fit residues: 104.3864 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 7 optimal weight: 0.0470 chunk 109 optimal weight: 0.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111786 restraints weight = 9843.749| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 0.96 r_work: 0.3195 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10273 Z= 0.119 Angle : 0.459 5.582 13602 Z= 0.246 Chirality : 0.037 0.130 1505 Planarity : 0.003 0.020 1555 Dihedral : 9.707 59.517 1955 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.98 % Allowed : 16.15 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.00 (0.25), residues: 1170 helix: 2.22 (0.17), residues: 975 sheet: None (None), residues: 0 loop : 0.92 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 76 TYR 0.012 0.001 TYR D 58 PHE 0.014 0.002 PHE A 216 TRP 0.009 0.001 TRP D 107 HIS 0.002 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00254 (10273) covalent geometry : angle 0.45885 (13602) hydrogen bonds : bond 0.04168 ( 766) hydrogen bonds : angle 4.12677 ( 2298) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.368 Fit side-chains REVERT: A 44 MET cc_start: 0.8439 (mmm) cc_final: 0.8169 (mmp) REVERT: A 70 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7144 (tptp) REVERT: A 116 MET cc_start: 0.8806 (ttt) cc_final: 0.8450 (ttp) REVERT: A 120 GLU cc_start: 0.8279 (tt0) cc_final: 0.7725 (mt-10) REVERT: B 70 LYS cc_start: 0.8274 (mttt) cc_final: 0.7906 (mtmm) REVERT: C 155 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6972 (ttp-170) REVERT: D 35 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7685 (mmm160) REVERT: D 120 GLU cc_start: 0.8200 (pt0) cc_final: 0.7438 (mt-10) REVERT: E 35 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7359 (mmm-85) REVERT: E 70 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7957 (mtmm) outliers start: 19 outliers final: 15 residues processed: 152 average time/residue: 0.6475 time to fit residues: 105.2643 Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110199 restraints weight = 9951.594| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 0.97 r_work: 0.3172 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10273 Z= 0.138 Angle : 0.486 5.587 13602 Z= 0.258 Chirality : 0.038 0.132 1505 Planarity : 0.003 0.029 1555 Dihedral : 9.870 59.631 1953 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.29 % Allowed : 16.25 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.25), residues: 1170 helix: 2.22 (0.17), residues: 970 sheet: None (None), residues: 0 loop : 0.64 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 155 TYR 0.013 0.001 TYR D 58 PHE 0.014 0.002 PHE D 216 TRP 0.009 0.001 TRP D 107 HIS 0.002 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00307 (10273) covalent geometry : angle 0.48585 (13602) hydrogen bonds : bond 0.04426 ( 766) hydrogen bonds : angle 4.20034 ( 2298) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.393 Fit side-chains REVERT: A 44 MET cc_start: 0.8501 (mmm) cc_final: 0.8232 (mmp) REVERT: A 116 MET cc_start: 0.8858 (ttt) cc_final: 0.8468 (ttp) REVERT: A 120 GLU cc_start: 0.8279 (tt0) cc_final: 0.7650 (mt-10) REVERT: B 70 LYS cc_start: 0.8299 (mttt) cc_final: 0.7936 (mtmm) REVERT: C 155 ARG cc_start: 0.7276 (ttm110) cc_final: 0.6960 (ttp-170) REVERT: C 167 MET cc_start: 0.8203 (mtp) cc_final: 0.7439 (mtm) REVERT: D 35 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7678 (mmm160) REVERT: D 120 GLU cc_start: 0.8237 (pt0) cc_final: 0.7447 (mt-10) REVERT: E 35 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7331 (mmm-85) REVERT: E 70 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7943 (mtmm) outliers start: 22 outliers final: 19 residues processed: 151 average time/residue: 0.6225 time to fit residues: 100.7755 Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 154 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 0.0010 chunk 43 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110488 restraints weight = 9814.188| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 0.96 r_work: 0.3180 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10273 Z= 0.136 Angle : 0.483 5.570 13602 Z= 0.256 Chirality : 0.037 0.133 1505 Planarity : 0.003 0.027 1555 Dihedral : 9.751 58.950 1953 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.19 % Allowed : 16.25 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.25), residues: 1170 helix: 2.19 (0.17), residues: 975 sheet: None (None), residues: 0 loop : 0.79 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 155 TYR 0.013 0.001 TYR D 58 PHE 0.014 0.002 PHE A 216 TRP 0.009 0.001 TRP A 107 HIS 0.002 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00301 (10273) covalent geometry : angle 0.48276 (13602) hydrogen bonds : bond 0.04367 ( 766) hydrogen bonds : angle 4.18027 ( 2298) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.300 Fit side-chains REVERT: A 44 MET cc_start: 0.8517 (mmm) cc_final: 0.8241 (mmp) REVERT: A 116 MET cc_start: 0.8859 (ttt) cc_final: 0.8473 (ttp) REVERT: A 120 GLU cc_start: 0.8278 (tt0) cc_final: 0.7677 (mt-10) REVERT: B 70 LYS cc_start: 0.8300 (mttt) cc_final: 0.7947 (mtmm) REVERT: C 155 ARG cc_start: 0.7303 (ttm110) cc_final: 0.6995 (ttp-170) REVERT: C 167 MET cc_start: 0.8196 (mtp) cc_final: 0.7425 (mtm) REVERT: D 120 GLU cc_start: 0.8236 (pt0) cc_final: 0.7438 (mt-10) REVERT: E 35 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7328 (mmm-85) REVERT: E 70 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7951 (mtmm) outliers start: 21 outliers final: 18 residues processed: 149 average time/residue: 0.6420 time to fit residues: 102.3454 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110554 restraints weight = 9773.916| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 0.96 r_work: 0.3180 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10273 Z= 0.136 Angle : 0.482 5.567 13602 Z= 0.256 Chirality : 0.037 0.130 1505 Planarity : 0.003 0.024 1555 Dihedral : 9.712 59.841 1952 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.98 % Allowed : 16.35 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.25), residues: 1170 helix: 2.19 (0.17), residues: 975 sheet: None (None), residues: 0 loop : 0.74 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.013 0.001 TYR D 58 PHE 0.014 0.002 PHE D 216 TRP 0.009 0.001 TRP C 107 HIS 0.002 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00301 (10273) covalent geometry : angle 0.48209 (13602) hydrogen bonds : bond 0.04372 ( 766) hydrogen bonds : angle 4.17377 ( 2298) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.365 Fit side-chains REVERT: A 44 MET cc_start: 0.8518 (mmm) cc_final: 0.8243 (mmp) REVERT: A 116 MET cc_start: 0.8859 (ttt) cc_final: 0.8473 (ttp) REVERT: A 120 GLU cc_start: 0.8272 (tt0) cc_final: 0.7676 (mt-10) REVERT: B 70 LYS cc_start: 0.8296 (mttt) cc_final: 0.7945 (mtmm) REVERT: C 150 MET cc_start: 0.8281 (mtm) cc_final: 0.7999 (mpp) REVERT: C 155 ARG cc_start: 0.7238 (ttm110) cc_final: 0.6923 (ttp-170) REVERT: C 167 MET cc_start: 0.8188 (mtp) cc_final: 0.7419 (mtm) REVERT: D 120 GLU cc_start: 0.8233 (pt0) cc_final: 0.7409 (mt-10) REVERT: E 35 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7321 (mmm-85) REVERT: E 70 LYS cc_start: 0.8287 (mmtp) cc_final: 0.7955 (mtmm) outliers start: 19 outliers final: 19 residues processed: 148 average time/residue: 0.6614 time to fit residues: 104.7174 Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 154 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111150 restraints weight = 9851.214| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 0.97 r_work: 0.3187 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10273 Z= 0.128 Angle : 0.470 5.546 13602 Z= 0.250 Chirality : 0.037 0.122 1505 Planarity : 0.003 0.023 1555 Dihedral : 9.496 58.868 1952 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.77 % Allowed : 16.56 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.97 (0.25), residues: 1170 helix: 2.23 (0.17), residues: 975 sheet: None (None), residues: 0 loop : 0.70 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.013 0.001 TYR D 58 PHE 0.014 0.002 PHE A 216 TRP 0.008 0.001 TRP C 107 HIS 0.002 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00281 (10273) covalent geometry : angle 0.46989 (13602) hydrogen bonds : bond 0.04255 ( 766) hydrogen bonds : angle 4.12627 ( 2298) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.378 Fit side-chains REVERT: A 44 MET cc_start: 0.8495 (mmm) cc_final: 0.8216 (mmp) REVERT: A 116 MET cc_start: 0.8830 (ttt) cc_final: 0.8456 (ttp) REVERT: A 120 GLU cc_start: 0.8257 (tt0) cc_final: 0.7670 (mt-10) REVERT: B 70 LYS cc_start: 0.8275 (mttt) cc_final: 0.7915 (mtmm) REVERT: C 150 MET cc_start: 0.8222 (mtm) cc_final: 0.7940 (mpp) REVERT: C 155 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6924 (ttp-170) REVERT: C 167 MET cc_start: 0.8156 (mtp) cc_final: 0.7375 (mtm) REVERT: D 120 GLU cc_start: 0.8195 (pt0) cc_final: 0.7387 (mt-10) REVERT: E 35 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7301 (mmm-85) REVERT: E 70 LYS cc_start: 0.8244 (mmtp) cc_final: 0.7910 (mtmm) outliers start: 17 outliers final: 16 residues processed: 147 average time/residue: 0.6271 time to fit residues: 98.6976 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109841 restraints weight = 9773.428| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 0.96 r_work: 0.3172 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10273 Z= 0.150 Angle : 0.502 5.747 13602 Z= 0.265 Chirality : 0.038 0.136 1505 Planarity : 0.003 0.023 1555 Dihedral : 9.869 59.382 1950 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.67 % Allowed : 16.67 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.25), residues: 1170 helix: 2.18 (0.17), residues: 970 sheet: None (None), residues: 0 loop : 0.50 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 155 TYR 0.014 0.002 TYR D 58 PHE 0.014 0.002 PHE A 216 TRP 0.010 0.001 TRP D 107 HIS 0.002 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00340 (10273) covalent geometry : angle 0.50182 (13602) hydrogen bonds : bond 0.04551 ( 766) hydrogen bonds : angle 4.21618 ( 2298) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.380 Fit side-chains REVERT: A 44 MET cc_start: 0.8542 (mmm) cc_final: 0.8267 (mmp) REVERT: A 120 GLU cc_start: 0.8278 (tt0) cc_final: 0.7661 (mt-10) REVERT: B 70 LYS cc_start: 0.8281 (mttt) cc_final: 0.7930 (mtmm) REVERT: C 150 MET cc_start: 0.8317 (mtm) cc_final: 0.8001 (mpp) REVERT: C 155 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6917 (ttp-170) REVERT: C 167 MET cc_start: 0.8192 (mtp) cc_final: 0.7431 (mtm) REVERT: D 120 GLU cc_start: 0.8262 (pt0) cc_final: 0.7455 (mt-10) REVERT: E 35 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7309 (mmm-85) REVERT: E 70 LYS cc_start: 0.8281 (mmtp) cc_final: 0.7955 (mtmm) outliers start: 16 outliers final: 16 residues processed: 144 average time/residue: 0.6340 time to fit residues: 97.6282 Evaluate side-chains 148 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 99 optimal weight: 0.0270 chunk 94 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112350 restraints weight = 9888.495| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 0.97 r_work: 0.3202 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10273 Z= 0.114 Angle : 0.451 5.826 13602 Z= 0.241 Chirality : 0.036 0.120 1505 Planarity : 0.003 0.023 1555 Dihedral : 9.130 59.671 1950 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.67 % Allowed : 16.56 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.08 (0.25), residues: 1170 helix: 2.32 (0.17), residues: 975 sheet: None (None), residues: 0 loop : 0.67 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.012 0.001 TYR D 58 PHE 0.015 0.001 PHE D 216 TRP 0.008 0.001 TRP D 107 HIS 0.002 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00239 (10273) covalent geometry : angle 0.45108 (13602) hydrogen bonds : bond 0.04034 ( 766) hydrogen bonds : angle 4.04427 ( 2298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.01 seconds wall clock time: 60 minutes 21.07 seconds (3621.07 seconds total)