Starting phenix.real_space_refine on Sat Dec 28 09:42:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwc_27752/12_2024/8dwc_27752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwc_27752/12_2024/8dwc_27752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwc_27752/12_2024/8dwc_27752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwc_27752/12_2024/8dwc_27752.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwc_27752/12_2024/8dwc_27752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwc_27752/12_2024/8dwc_27752.cif" } resolution = 2.87 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= 0.001 sd= 0.022 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 56 5.16 5 C 5318 2.51 5 N 1413 2.21 5 O 1511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8298 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 109 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2480 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1925 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 5.36, per 1000 atoms: 0.65 Number of scatterers: 8298 At special positions: 0 Unit cell: (104.72, 115.28, 118.8, 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 56 16.00 O 1511 8.00 N 1413 7.00 C 5318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.667A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.559A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.503A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.565A pdb=" N GLY R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 removed outlier: 3.686A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.991A pdb=" N ILE R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Proline residue: R 100 - end of helix removed outlier: 4.759A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE R 107 " --> pdb=" O MET R 103 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 161 Processing helix chain 'R' and resid 170 through 204 removed outlier: 3.807A pdb=" N GLN R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER R 176 " --> pdb=" O TRP R 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 227 Processing helix chain 'R' and resid 230 through 239 removed outlier: 3.607A pdb=" N ILE R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 253 Processing helix chain 'R' and resid 253 through 273 Proline residue: R 269 - end of helix Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.191A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.518A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.997A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.622A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.965A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.779A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.133A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.620A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.533A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.729A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.180A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.896A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.011A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.657A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.647A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.538A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.648A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.515A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.663A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS E 96 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY E 114 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR E 94 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR E 116 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA E 92 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.556A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.597A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1176 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: 2.39 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2603 1.33 - 1.45: 1529 1.45 - 1.57: 4274 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8482 Sorted by residual: bond pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.29e-02 6.01e+03 6.29e+00 bond pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.19e+00 bond pdb=" N THR B 221 " pdb=" CA THR B 221 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.37e-02 5.33e+03 4.69e+00 bond pdb=" N ALA B 218 " pdb=" CA ALA B 218 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.33e-02 5.65e+03 3.86e+00 bond pdb=" CG1 ILE B 49 " pdb=" CD1 ILE B 49 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.46e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11113 1.47 - 2.95: 362 2.95 - 4.42: 54 4.42 - 5.90: 12 5.90 - 7.37: 4 Bond angle restraints: 11545 Sorted by residual: angle pdb=" N THR B 221 " pdb=" CA THR B 221 " pdb=" C THR B 221 " ideal model delta sigma weight residual 113.72 109.31 4.41 1.30e+00 5.92e-01 1.15e+01 angle pdb=" N ALA B 218 " pdb=" CA ALA B 218 " pdb=" C ALA B 218 " ideal model delta sigma weight residual 113.23 109.46 3.77 1.24e+00 6.50e-01 9.26e+00 angle pdb=" N VAL B 219 " pdb=" CA VAL B 219 " pdb=" C VAL B 219 " ideal model delta sigma weight residual 112.80 109.75 3.05 1.15e+00 7.56e-01 7.03e+00 angle pdb=" CA ASP B 220 " pdb=" C ASP B 220 " pdb=" O ASP B 220 " ideal model delta sigma weight residual 120.92 118.34 2.58 1.14e+00 7.69e-01 5.13e+00 angle pdb=" C ASP B 42 " pdb=" N ASN B 43 " pdb=" CA ASN B 43 " ideal model delta sigma weight residual 124.82 128.66 -3.84 1.78e+00 3.16e-01 4.66e+00 ... (remaining 11540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4465 15.94 - 31.87: 379 31.87 - 47.81: 78 47.81 - 63.74: 10 63.74 - 79.68: 3 Dihedral angle restraints: 4935 sinusoidal: 1742 harmonic: 3193 Sorted by residual: dihedral pdb=" CA MET E 128 " pdb=" C MET E 128 " pdb=" N THR E 129 " pdb=" CA THR E 129 " ideal model delta harmonic sigma weight residual 180.00 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP C 258 " pdb=" C ASP C 258 " pdb=" N GLN C 259 " pdb=" CA GLN C 259 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 125.65 -32.65 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 872 0.042 - 0.084: 349 0.084 - 0.126: 109 0.126 - 0.168: 9 0.168 - 0.210: 3 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CB VAL B 109 " pdb=" CA VAL B 109 " pdb=" CG1 VAL B 109 " pdb=" CG2 VAL B 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU B 143 " pdb=" CB LEU B 143 " pdb=" CD1 LEU B 143 " pdb=" CD2 LEU B 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA VAL B 219 " pdb=" N VAL B 219 " pdb=" C VAL B 219 " pdb=" CB VAL B 219 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1339 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 217 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C CYS B 217 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS B 217 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 218 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO C 194 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 209 " 0.012 2.00e-02 2.50e+03 1.37e-02 2.82e+00 pdb=" CG HIS B 209 " -0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS B 209 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 209 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 209 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 209 " 0.004 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 111 2.66 - 3.22: 7580 3.22 - 3.78: 12389 3.78 - 4.34: 17741 4.34 - 4.90: 29887 Nonbonded interactions: 67708 Sorted by model distance: nonbonded pdb=" OH TYR R 130 " pdb=" OH TYR B 243 " model vdw 2.095 3.040 nonbonded pdb=" NH2 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.123 3.120 nonbonded pdb=" O SER B 44 " pdb=" ND2 ASN B 144 " model vdw 2.149 3.120 nonbonded pdb=" OD2 ASP R 177 " pdb=" NE1 TRP R 241 " model vdw 2.229 3.120 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.232 3.040 ... (remaining 67703 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.008 0.073 8482 Z= 0.503 Angle : 0.645 7.370 11545 Z= 0.354 Chirality : 0.047 0.210 1342 Planarity : 0.004 0.044 1448 Dihedral : 12.543 79.679 2867 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.14 (0.24), residues: 1082 helix: -1.16 (0.24), residues: 365 sheet: 0.11 (0.31), residues: 282 loop : -0.78 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 63 HIS 0.016 0.002 HIS B 82 PHE 0.020 0.003 PHE B 215 TYR 0.026 0.002 TYR C 59 ARG 0.013 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.951 Fit side-chains REVERT: C 163 ASP cc_start: 0.7475 (p0) cc_final: 0.7192 (p0) REVERT: C 188 MET cc_start: 0.7933 (mmp) cc_final: 0.7514 (mmp) REVERT: B 25 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 114 ASP cc_start: 0.7198 (t70) cc_final: 0.6969 (t70) REVERT: B 229 ASN cc_start: 0.8236 (m-40) cc_final: 0.7986 (m-40) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 1.1366 time to fit residues: 245.5620 Evaluate side-chains 188 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 88 ASN C 132 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8482 Z= 0.250 Angle : 0.574 8.645 11545 Z= 0.304 Chirality : 0.043 0.169 1342 Planarity : 0.005 0.039 1448 Dihedral : 4.558 17.377 1181 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.94 % Allowed : 10.39 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.18 (0.25), residues: 1082 helix: 1.02 (0.26), residues: 348 sheet: 0.39 (0.31), residues: 283 loop : -0.70 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.009 0.001 HIS B 82 PHE 0.017 0.002 PHE C 199 TYR 0.016 0.002 TYR E 178 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 0.858 Fit side-chains REVERT: C 59 TYR cc_start: 0.7643 (m-80) cc_final: 0.6955 (m-80) REVERT: C 75 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7702 (mm-40) REVERT: C 259 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: R 85 LEU cc_start: 0.7071 (mt) cc_final: 0.6843 (mm) REVERT: R 211 LEU cc_start: 0.7988 (mp) cc_final: 0.7730 (tp) REVERT: E 69 THR cc_start: 0.8407 (p) cc_final: 0.8168 (t) REVERT: E 192 SER cc_start: 0.8179 (t) cc_final: 0.7958 (t) REVERT: B 9 ASP cc_start: 0.7037 (m-30) cc_final: 0.6685 (m-30) REVERT: B 25 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6793 (tm-30) REVERT: B 229 ASN cc_start: 0.8180 (m-40) cc_final: 0.7924 (m-40) outliers start: 8 outliers final: 3 residues processed: 192 average time/residue: 1.0678 time to fit residues: 219.5180 Evaluate side-chains 185 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 176 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS B 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8482 Z= 0.235 Angle : 0.541 7.716 11545 Z= 0.285 Chirality : 0.042 0.144 1342 Planarity : 0.004 0.037 1448 Dihedral : 4.314 16.415 1181 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.18 % Allowed : 14.17 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.62 (0.26), residues: 1082 helix: 1.77 (0.27), residues: 349 sheet: 0.46 (0.30), residues: 294 loop : -0.70 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.008 0.001 HIS B 82 PHE 0.016 0.002 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.008 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 1.010 Fit side-chains REVERT: C 223 THR cc_start: 0.7904 (p) cc_final: 0.7673 (t) REVERT: C 249 THR cc_start: 0.8528 (p) cc_final: 0.8280 (t) REVERT: C 307 VAL cc_start: 0.8592 (t) cc_final: 0.8318 (p) REVERT: R 144 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8152 (t) REVERT: R 211 LEU cc_start: 0.7973 (mp) cc_final: 0.7701 (tp) REVERT: E 69 THR cc_start: 0.8385 (p) cc_final: 0.8084 (t) REVERT: E 192 SER cc_start: 0.8190 (t) cc_final: 0.7983 (t) REVERT: B 25 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 29 LYS cc_start: 0.7837 (mttt) cc_final: 0.7576 (mtmt) REVERT: B 196 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7226 (mm-30) REVERT: B 229 ASN cc_start: 0.8160 (m-40) cc_final: 0.7891 (m-40) outliers start: 10 outliers final: 2 residues processed: 198 average time/residue: 1.0711 time to fit residues: 227.1960 Evaluate side-chains 187 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.0060 chunk 87 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN C 176 GLN B 22 ASN B 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8482 Z= 0.218 Angle : 0.522 7.468 11545 Z= 0.275 Chirality : 0.042 0.144 1342 Planarity : 0.004 0.040 1448 Dihedral : 4.200 15.918 1181 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.42 % Allowed : 16.29 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.86 (0.26), residues: 1082 helix: 2.18 (0.27), residues: 349 sheet: 0.54 (0.30), residues: 293 loop : -0.72 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.006 0.001 HIS B 82 PHE 0.016 0.001 PHE C 199 TYR 0.014 0.001 TYR E 178 ARG 0.008 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 1.049 Fit side-chains REVERT: C 59 TYR cc_start: 0.7712 (m-80) cc_final: 0.7210 (m-80) REVERT: C 75 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7979 (mm110) REVERT: C 188 MET cc_start: 0.7973 (mmm) cc_final: 0.7273 (mmm) REVERT: C 223 THR cc_start: 0.7927 (p) cc_final: 0.7681 (t) REVERT: C 249 THR cc_start: 0.8517 (p) cc_final: 0.8280 (t) REVERT: C 307 VAL cc_start: 0.8588 (t) cc_final: 0.8332 (p) REVERT: R 144 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8164 (t) REVERT: R 211 LEU cc_start: 0.7955 (mp) cc_final: 0.7702 (tp) REVERT: E 69 THR cc_start: 0.8371 (p) cc_final: 0.8057 (t) REVERT: E 192 SER cc_start: 0.8171 (t) cc_final: 0.7962 (t) REVERT: B 20 ASP cc_start: 0.7239 (m-30) cc_final: 0.7033 (m-30) REVERT: B 25 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6723 (tm-30) REVERT: B 29 LYS cc_start: 0.7809 (mttt) cc_final: 0.7519 (mtmt) REVERT: B 195 LYS cc_start: 0.7605 (ttpp) cc_final: 0.7370 (ttpp) REVERT: B 196 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 229 ASN cc_start: 0.8190 (m-40) cc_final: 0.7945 (m-40) outliers start: 12 outliers final: 6 residues processed: 193 average time/residue: 1.1686 time to fit residues: 241.1150 Evaluate side-chains 194 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.2980 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN R 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8482 Z= 0.373 Angle : 0.578 9.105 11545 Z= 0.303 Chirality : 0.045 0.141 1342 Planarity : 0.004 0.043 1448 Dihedral : 4.387 16.680 1181 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.60 % Allowed : 16.41 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.74 (0.26), residues: 1082 helix: 1.99 (0.27), residues: 350 sheet: 0.51 (0.30), residues: 294 loop : -0.73 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 211 HIS 0.007 0.001 HIS B 82 PHE 0.019 0.002 PHE C 199 TYR 0.015 0.002 TYR E 59 ARG 0.010 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.907 Fit side-chains REVERT: C 17 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: C 59 TYR cc_start: 0.7770 (m-80) cc_final: 0.7281 (m-80) REVERT: C 75 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7852 (mm-40) REVERT: C 150 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7967 (mmt180) REVERT: C 188 MET cc_start: 0.7846 (mmm) cc_final: 0.7233 (mmm) REVERT: C 223 THR cc_start: 0.7979 (p) cc_final: 0.7752 (t) REVERT: C 251 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7795 (mtt90) REVERT: C 259 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: R 144 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8173 (t) REVERT: R 211 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7780 (tp) REVERT: E 69 THR cc_start: 0.8390 (p) cc_final: 0.8046 (t) REVERT: E 192 SER cc_start: 0.8167 (t) cc_final: 0.7956 (t) REVERT: B 20 ASP cc_start: 0.7233 (m-30) cc_final: 0.7015 (m-30) REVERT: B 25 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6668 (tm-30) REVERT: B 29 LYS cc_start: 0.7875 (mttt) cc_final: 0.7506 (mtmt) REVERT: B 196 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7216 (mm-30) REVERT: B 229 ASN cc_start: 0.8213 (m-40) cc_final: 0.7954 (m-40) outliers start: 22 outliers final: 10 residues processed: 205 average time/residue: 1.0635 time to fit residues: 233.4999 Evaluate side-chains 213 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.0270 chunk 101 optimal weight: 0.0050 overall best weight: 0.2850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8482 Z= 0.153 Angle : 0.489 7.539 11545 Z= 0.258 Chirality : 0.041 0.141 1342 Planarity : 0.004 0.044 1448 Dihedral : 4.053 15.846 1181 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.13 % Allowed : 17.36 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.11 (0.26), residues: 1082 helix: 2.50 (0.28), residues: 350 sheet: 0.61 (0.31), residues: 279 loop : -0.59 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.005 0.001 HIS B 82 PHE 0.013 0.001 PHE C 199 TYR 0.016 0.001 TYR E 178 ARG 0.011 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 1.036 Fit side-chains REVERT: C 59 TYR cc_start: 0.7734 (m-80) cc_final: 0.7282 (m-80) REVERT: C 75 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7887 (mm-40) REVERT: C 188 MET cc_start: 0.7807 (mmm) cc_final: 0.7239 (mmm) REVERT: C 251 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8013 (mtt90) REVERT: C 258 ASP cc_start: 0.6738 (t70) cc_final: 0.6499 (t0) REVERT: C 259 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: R 144 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8132 (t) REVERT: E 69 THR cc_start: 0.8371 (p) cc_final: 0.8158 (m) REVERT: E 192 SER cc_start: 0.8192 (t) cc_final: 0.7986 (t) REVERT: B 20 ASP cc_start: 0.7234 (m-30) cc_final: 0.6998 (m-30) REVERT: B 25 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6773 (tm-30) REVERT: B 29 LYS cc_start: 0.7795 (mttt) cc_final: 0.7402 (mtmt) REVERT: B 195 LYS cc_start: 0.7604 (ttpp) cc_final: 0.7366 (ttpp) REVERT: B 196 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 229 ASN cc_start: 0.8200 (m-40) cc_final: 0.7953 (m-40) outliers start: 18 outliers final: 5 residues processed: 212 average time/residue: 1.0818 time to fit residues: 246.2349 Evaluate side-chains 204 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8482 Z= 0.271 Angle : 0.527 8.124 11545 Z= 0.279 Chirality : 0.043 0.139 1342 Planarity : 0.004 0.039 1448 Dihedral : 4.157 16.191 1181 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.01 % Allowed : 17.83 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.08 (0.26), residues: 1082 helix: 2.53 (0.27), residues: 347 sheet: 0.53 (0.30), residues: 294 loop : -0.62 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 82 PHE 0.018 0.002 PHE C 199 TYR 0.013 0.002 TYR E 178 ARG 0.009 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 1.063 Fit side-chains REVERT: C 59 TYR cc_start: 0.7753 (m-80) cc_final: 0.7256 (m-80) REVERT: C 75 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7997 (mm110) REVERT: C 188 MET cc_start: 0.7714 (mmm) cc_final: 0.7288 (mmm) REVERT: C 259 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: R 144 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8180 (t) REVERT: E 69 THR cc_start: 0.8371 (p) cc_final: 0.8162 (m) REVERT: E 192 SER cc_start: 0.8156 (t) cc_final: 0.7938 (t) REVERT: B 20 ASP cc_start: 0.7242 (m-30) cc_final: 0.7020 (m-30) REVERT: B 25 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6741 (tm-30) REVERT: B 29 LYS cc_start: 0.7827 (mttt) cc_final: 0.7429 (mtmt) REVERT: B 195 LYS cc_start: 0.7535 (ttpp) cc_final: 0.7314 (ttpp) REVERT: B 196 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 229 ASN cc_start: 0.8200 (m-40) cc_final: 0.7954 (m-40) outliers start: 17 outliers final: 9 residues processed: 206 average time/residue: 1.0563 time to fit residues: 233.5175 Evaluate side-chains 215 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 161 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.0770 chunk 20 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8482 Z= 0.192 Angle : 0.508 8.625 11545 Z= 0.266 Chirality : 0.041 0.140 1342 Planarity : 0.004 0.034 1448 Dihedral : 4.081 15.860 1181 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.53 % Allowed : 18.42 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.19 (0.26), residues: 1082 helix: 2.65 (0.27), residues: 348 sheet: 0.54 (0.31), residues: 281 loop : -0.53 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.005 0.001 HIS B 82 PHE 0.018 0.001 PHE E 68 TYR 0.015 0.001 TYR E 178 ARG 0.008 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.934 Fit side-chains REVERT: C 59 TYR cc_start: 0.7741 (m-80) cc_final: 0.7296 (m-80) REVERT: C 75 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7914 (mm-40) REVERT: C 188 MET cc_start: 0.7708 (mmm) cc_final: 0.7286 (mmm) REVERT: C 259 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: R 144 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8175 (t) REVERT: E 166 LEU cc_start: 0.8516 (tt) cc_final: 0.8245 (tm) REVERT: E 192 SER cc_start: 0.8149 (t) cc_final: 0.7927 (t) REVERT: B 20 ASP cc_start: 0.7220 (m-30) cc_final: 0.6993 (m-30) REVERT: B 25 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6756 (tm-30) REVERT: B 29 LYS cc_start: 0.7801 (mttt) cc_final: 0.7405 (mtmt) REVERT: B 195 LYS cc_start: 0.7584 (ttpp) cc_final: 0.7362 (ttpp) REVERT: B 196 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 229 ASN cc_start: 0.8197 (m-40) cc_final: 0.7942 (m-40) outliers start: 13 outliers final: 7 residues processed: 208 average time/residue: 1.0687 time to fit residues: 238.2509 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.0040 chunk 63 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8482 Z= 0.203 Angle : 0.508 8.421 11545 Z= 0.267 Chirality : 0.042 0.139 1342 Planarity : 0.004 0.034 1448 Dihedral : 4.040 15.799 1181 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.77 % Allowed : 18.77 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.21 (0.26), residues: 1082 helix: 2.69 (0.27), residues: 348 sheet: 0.53 (0.31), residues: 281 loop : -0.51 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.016 0.001 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.007 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 1.018 Fit side-chains REVERT: C 59 TYR cc_start: 0.7724 (m-80) cc_final: 0.7284 (m-80) REVERT: C 75 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7923 (mm-40) REVERT: C 150 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7904 (mmt180) REVERT: C 188 MET cc_start: 0.7688 (mmm) cc_final: 0.7273 (mmm) REVERT: C 259 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: R 144 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8177 (t) REVERT: E 166 LEU cc_start: 0.8495 (tt) cc_final: 0.8222 (tm) REVERT: E 192 SER cc_start: 0.8151 (t) cc_final: 0.7927 (t) REVERT: B 20 ASP cc_start: 0.7219 (m-30) cc_final: 0.6994 (m-30) REVERT: B 25 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6758 (tm-30) REVERT: B 29 LYS cc_start: 0.7814 (mttt) cc_final: 0.7420 (mtmt) REVERT: B 195 LYS cc_start: 0.7580 (ttpp) cc_final: 0.7372 (ttpp) REVERT: B 196 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 229 ASN cc_start: 0.8194 (m-40) cc_final: 0.7950 (m-40) outliers start: 15 outliers final: 8 residues processed: 206 average time/residue: 1.0461 time to fit residues: 231.2260 Evaluate side-chains 213 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0980 chunk 71 optimal weight: 0.0170 chunk 108 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8482 Z= 0.161 Angle : 0.491 8.594 11545 Z= 0.258 Chirality : 0.041 0.141 1342 Planarity : 0.003 0.032 1448 Dihedral : 3.920 15.455 1181 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.42 % Allowed : 18.77 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.29 (0.26), residues: 1082 helix: 2.74 (0.28), residues: 351 sheet: 0.57 (0.31), residues: 281 loop : -0.47 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.004 0.001 HIS B 82 PHE 0.014 0.001 PHE C 199 TYR 0.016 0.001 TYR E 178 ARG 0.007 0.000 ARG B 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.923 Fit side-chains REVERT: C 59 TYR cc_start: 0.7711 (m-80) cc_final: 0.7278 (m-80) REVERT: C 75 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7894 (mm-40) REVERT: C 150 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7992 (mmt180) REVERT: C 259 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: R 144 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8146 (t) REVERT: E 68 PHE cc_start: 0.7731 (m-10) cc_final: 0.7323 (m-80) REVERT: E 166 LEU cc_start: 0.8476 (tt) cc_final: 0.8207 (tm) REVERT: E 192 SER cc_start: 0.8143 (t) cc_final: 0.7912 (t) REVERT: B 20 ASP cc_start: 0.7218 (m-30) cc_final: 0.6996 (m-30) REVERT: B 25 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6809 (tm-30) REVERT: B 29 LYS cc_start: 0.7786 (mttt) cc_final: 0.7387 (mtmt) REVERT: B 195 LYS cc_start: 0.7595 (ttpp) cc_final: 0.7372 (ttpp) REVERT: B 229 ASN cc_start: 0.8191 (m-40) cc_final: 0.7945 (m-40) outliers start: 12 outliers final: 7 residues processed: 209 average time/residue: 1.0483 time to fit residues: 234.8204 Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101622 restraints weight = 11802.711| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.77 r_work: 0.3144 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8482 Z= 0.195 Angle : 0.514 8.570 11545 Z= 0.269 Chirality : 0.042 0.139 1342 Planarity : 0.004 0.066 1448 Dihedral : 3.951 15.486 1181 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.53 % Allowed : 19.13 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.30 (0.26), residues: 1082 helix: 2.82 (0.27), residues: 349 sheet: 0.55 (0.31), residues: 275 loop : -0.47 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.017 0.001 PHE E 68 TYR 0.015 0.001 TYR E 178 ARG 0.016 0.001 ARG B 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4093.99 seconds wall clock time: 73 minutes 50.97 seconds (4430.97 seconds total)