Starting phenix.real_space_refine on Fri Mar 6 11:49:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbr_13300/03_2026/7pbr_13300_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbr_13300/03_2026/7pbr_13300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbr_13300/03_2026/7pbr_13300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbr_13300/03_2026/7pbr_13300.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbr_13300/03_2026/7pbr_13300_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbr_13300/03_2026/7pbr_13300_neut_trim.cif" } resolution = 3.0 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= 0.002 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: 7 Type Number sf(0) Gaussians P 46 5.49 5 Mg 4 5.21 5 S 100 5.16 5 C 9682 2.51 5 N 2619 2.21 5 O 3076 1.98 5 H 15077 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30604 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.86, per 1000 atoms: 0.19 Number of scatterers: 30604 At special positions: 0 Unit cell: (124.26, 138.43, 103.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 46 15.00 Mg 4 11.99 O 3076 8.00 N 2619 7.00 C 9682 6.00 H 15077 1.00 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: 2.83 Conformation dependent library (CDL) restraints added in 768.3 milliseconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 18 sheets defined 59.6% alpha, 11.2% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.617A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.656A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.514A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 removed outlier: 3.506A pdb=" N MET A 115 " --> pdb=" O ILE A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.571A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.528A pdb=" N MET A 163 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.751A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.531A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.738A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.530A pdb=" N VAL A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.574A pdb=" N GLU A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.670A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.505A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.705A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.415A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.558A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 234 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.673A pdb=" N ILE B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.560A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 31 through 49 Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.638A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 90 through 100 removed outlier: 3.749A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 removed outlier: 3.511A pdb=" N MET C 115 " --> pdb=" O ILE C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 115' Processing helix chain 'C' and resid 116 through 129 removed outlier: 4.160A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.523A pdb=" N GLU C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.920A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 235 Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.879A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.669A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 64 through 77 removed outlier: 3.674A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.853A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 130 removed outlier: 4.086A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.935A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.706A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 232 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.655A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.509A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.652A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.556A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.662A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 213 removed outlier: 3.617A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 235 removed outlier: 4.122A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 290 through 297 Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.604A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 through 100 removed outlier: 3.696A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.626A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.561A pdb=" N GLU F 188 " --> pdb=" O PRO F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 removed outlier: 3.638A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 272 Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.528A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 removed outlier: 3.531A pdb=" N TYR F 322 " --> pdb=" O THR F 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.505A pdb=" N LYS A 81 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASP A 110 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR A 83 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 56 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.519A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 56 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.416A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 56 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 84 removed outlier: 3.695A pdb=" N ASP D 110 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB3, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB4, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.597A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB7, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.585A pdb=" N LYS F 81 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASP F 110 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR F 83 " --> pdb=" O ASP F 110 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 56 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AB9, first strand: chain 'F' and resid 308 through 310 730 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 15077 1.05 - 1.28: 2588 1.28 - 1.50: 6574 1.50 - 1.72: 6507 1.72 - 1.95: 196 Bond restraints: 30942 Sorted by residual: bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 30937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 55338 2.04 - 4.07: 614 4.07 - 6.11: 47 6.11 - 8.15: 4 8.15 - 10.18: 3 Bond angle restraints: 56006 Sorted by residual: angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.82 10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 117.02 -9.02 3.00e+00 1.11e-01 9.03e+00 angle pdb=" N MET D 250 " pdb=" CA MET D 250 " pdb=" C MET D 250 " ideal model delta sigma weight residual 111.14 107.89 3.25 1.08e+00 8.57e-01 9.03e+00 angle pdb=" N GLU A 140 " pdb=" CA GLU A 140 " pdb=" C GLU A 140 " ideal model delta sigma weight residual 111.40 107.87 3.53 1.22e+00 6.72e-01 8.39e+00 angle pdb=" C2' ADP F 600 " pdb=" C3' ADP F 600 " pdb=" C4' ADP F 600 " ideal model delta sigma weight residual 111.00 102.57 8.43 3.00e+00 1.11e-01 7.90e+00 ... (remaining 56001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 13730 31.16 - 62.32: 591 62.32 - 93.48: 27 93.48 - 124.63: 0 124.63 - 155.79: 6 Dihedral angle restraints: 14354 sinusoidal: 8231 harmonic: 6123 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 95.79 -155.79 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 89.63 -149.63 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 62.78 -130.51 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 14351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2178 0.075 - 0.149: 258 0.149 - 0.224: 1 0.224 - 0.298: 0 0.298 - 0.373: 1 Chirality restraints: 2438 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.72 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA PRO D 300 " pdb=" N PRO D 300 " pdb=" C PRO D 300 " pdb=" CB PRO D 300 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA PRO C 300 " pdb=" N PRO C 300 " pdb=" C PRO C 300 " pdb=" CB PRO C 300 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2435 not shown) Planarity restraints: 4476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 218 " 0.069 9.50e-02 1.11e+02 6.18e-02 7.46e+01 pdb=" NE ARG E 218 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG E 218 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG E 218 " 0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG E 218 " -0.111 2.00e-02 2.50e+03 pdb="HH11 ARG E 218 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 218 " -0.036 2.00e-02 2.50e+03 pdb="HH21 ARG E 218 " -0.008 2.00e-02 2.50e+03 pdb="HH22 ARG E 218 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 211 " -0.364 9.50e-02 1.11e+02 1.30e-01 6.43e+01 pdb=" NE ARG E 211 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 211 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG E 211 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG E 211 " 0.091 2.00e-02 2.50e+03 pdb="HH11 ARG E 211 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 211 " 0.045 2.00e-02 2.50e+03 pdb="HH21 ARG E 211 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG E 211 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.173 9.50e-02 1.11e+02 7.71e-02 6.25e+01 pdb=" NE ARG C 192 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.093 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.059 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.095 2.00e-02 2.50e+03 ... (remaining 4473 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 651 2.12 - 2.74: 53318 2.74 - 3.36: 81034 3.36 - 3.98: 104027 3.98 - 4.60: 168257 Nonbonded interactions: 407287 Sorted by model distance: nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.505 2.450 nonbonded pdb=" OE2 GLU D 120 " pdb=" HG SER D 165 " model vdw 1.556 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.559 2.450 nonbonded pdb=" OE2 GLU A 299 " pdb="HH21 ARG A 310 " model vdw 1.574 2.450 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.579 2.450 ... (remaining 407282 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 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } 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: 3.570 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: 0.160 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.790 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.004 0.038 15865 Z= 0.179 Angle : 0.715 10.184 21613 Z= 0.413 Chirality : 0.045 0.373 2438 Planarity : 0.009 0.119 2674 Dihedral : 15.019 155.793 6140 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.13 % Allowed : 1.15 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 1856 helix: -1.03 (0.15), residues: 970 sheet: 0.70 (0.29), residues: 322 loop : 0.42 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG E 211 TYR 0.022 0.005 TYR D 124 PHE 0.024 0.003 PHE A 25 HIS 0.010 0.003 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00411 (15865) covalent geometry : angle 0.71501 (21613) hydrogen bonds : bond 0.26514 ( 759) hydrogen bonds : angle 8.47130 ( 2137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 454 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8032 (mttp) cc_final: 0.7828 (mttt) REVERT: A 287 ILE cc_start: 0.8447 (pt) cc_final: 0.8135 (pt) REVERT: A 325 MET cc_start: 0.8599 (mmm) cc_final: 0.8265 (mmm) REVERT: C 325 MET cc_start: 0.9002 (mmm) cc_final: 0.8747 (mmm) REVERT: D 232 GLN cc_start: 0.8699 (pt0) cc_final: 0.8464 (pt0) REVERT: E 23 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7404 (mm110) REVERT: E 230 TYR cc_start: 0.7457 (t80) cc_final: 0.7236 (t80) REVERT: E 260 TYR cc_start: 0.7616 (t80) cc_final: 0.7394 (t80) REVERT: E 310 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7206 (ptp-110) REVERT: F 37 GLN cc_start: 0.8640 (mt0) cc_final: 0.8438 (mt0) REVERT: F 225 LYS cc_start: 0.8747 (mttt) cc_final: 0.8540 (mtmm) REVERT: F 297 MET cc_start: 0.8282 (tpp) cc_final: 0.7786 (tmm) outliers start: 2 outliers final: 2 residues processed: 455 average time/residue: 1.8761 time to fit residues: 916.4942 Evaluate side-chains 311 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain C residue 79 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 286 ASN E 79 ASN E 324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.076927 restraints weight = 69743.874| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.29 r_work: 0.2801 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15865 Z= 0.195 Angle : 0.666 6.683 21613 Z= 0.359 Chirality : 0.042 0.138 2438 Planarity : 0.006 0.057 2674 Dihedral : 15.108 149.280 2503 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.30 % Allowed : 15.63 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1856 helix: 0.25 (0.16), residues: 989 sheet: 1.06 (0.31), residues: 280 loop : 0.37 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 211 TYR 0.012 0.001 TYR C 124 PHE 0.009 0.001 PHE B 25 HIS 0.005 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00434 (15865) covalent geometry : angle 0.66626 (21613) hydrogen bonds : bond 0.08079 ( 759) hydrogen bonds : angle 5.93535 ( 2137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 323 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8679 (mttp) cc_final: 0.8413 (mttt) REVERT: A 143 ARG cc_start: 0.8091 (ptp90) cc_final: 0.7681 (pmm150) REVERT: B 81 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8618 (mmmm) REVERT: C 325 MET cc_start: 0.9133 (mmm) cc_final: 0.8865 (mmm) REVERT: D 169 ARG cc_start: 0.8512 (tpp80) cc_final: 0.8123 (tpp80) REVERT: D 188 GLU cc_start: 0.8248 (mp0) cc_final: 0.7909 (mp0) REVERT: E 23 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7754 (mm110) REVERT: E 99 ASN cc_start: 0.8727 (t0) cc_final: 0.8267 (t0) REVERT: E 111 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7721 (mt-10) REVERT: E 185 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: F 234 MET cc_start: 0.7998 (tpp) cc_final: 0.6921 (tmm) REVERT: F 272 MET cc_start: 0.8341 (ttp) cc_final: 0.8072 (ttp) outliers start: 36 outliers final: 9 residues processed: 336 average time/residue: 1.8097 time to fit residues: 655.5282 Evaluate side-chains 312 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 301 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 250 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 5 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 184 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 324 HIS C 286 ASN D 82 GLN D 177 HIS D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.077480 restraints weight = 69862.933| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.29 r_work: 0.2817 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15865 Z= 0.152 Angle : 0.582 6.094 21613 Z= 0.310 Chirality : 0.041 0.140 2438 Planarity : 0.005 0.045 2674 Dihedral : 15.012 152.161 2499 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.85 % Allowed : 17.36 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1856 helix: 0.78 (0.17), residues: 992 sheet: 1.03 (0.30), residues: 281 loop : 0.33 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 211 TYR 0.012 0.001 TYR D 124 PHE 0.008 0.001 PHE E 307 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00338 (15865) covalent geometry : angle 0.58190 (21613) hydrogen bonds : bond 0.05900 ( 759) hydrogen bonds : angle 5.25549 ( 2137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 309 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8673 (mttp) cc_final: 0.8464 (mttt) REVERT: A 198 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8117 (mm-30) REVERT: B 81 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8617 (mmmm) REVERT: B 111 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: C 325 MET cc_start: 0.9117 (mmm) cc_final: 0.8868 (mmm) REVERT: D 120 GLU cc_start: 0.8111 (tt0) cc_final: 0.7824 (tt0) REVERT: D 124 TYR cc_start: 0.8020 (m-10) cc_final: 0.7817 (m-10) REVERT: D 129 ASP cc_start: 0.7965 (m-30) cc_final: 0.7671 (p0) REVERT: D 188 GLU cc_start: 0.8288 (mp0) cc_final: 0.7890 (mp0) REVERT: E 23 GLN cc_start: 0.8241 (mm-40) cc_final: 0.8040 (mt0) REVERT: E 99 ASN cc_start: 0.8753 (t0) cc_final: 0.8307 (t0) REVERT: F 68 MET cc_start: 0.9080 (tpp) cc_final: 0.8808 (tpt) REVERT: F 234 MET cc_start: 0.8095 (tpp) cc_final: 0.7032 (tmm) REVERT: F 297 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7883 (tmm) REVERT: F 309 MET cc_start: 0.7920 (tpt) cc_final: 0.7529 (tpt) outliers start: 29 outliers final: 7 residues processed: 321 average time/residue: 1.7853 time to fit residues: 619.2899 Evaluate side-chains 306 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 296 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 260 TYR Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 133 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 324 HIS C 99 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.076649 restraints weight = 69797.398| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.32 r_work: 0.2797 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15865 Z= 0.177 Angle : 0.595 6.368 21613 Z= 0.313 Chirality : 0.041 0.149 2438 Planarity : 0.005 0.058 2674 Dihedral : 15.029 158.541 2499 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.43 % Allowed : 17.36 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1856 helix: 0.87 (0.17), residues: 994 sheet: 0.90 (0.31), residues: 277 loop : 0.24 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 291 TYR 0.010 0.001 TYR D 124 PHE 0.008 0.001 PHE A 172 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00413 (15865) covalent geometry : angle 0.59518 (21613) hydrogen bonds : bond 0.05595 ( 759) hydrogen bonds : angle 5.07797 ( 2137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8399 (mtmm) REVERT: A 81 LYS cc_start: 0.8640 (mttp) cc_final: 0.8404 (mttt) REVERT: B 81 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8611 (mmmm) REVERT: B 111 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: B 245 ASP cc_start: 0.8581 (t0) cc_final: 0.8308 (t0) REVERT: C 325 MET cc_start: 0.9141 (mmm) cc_final: 0.8855 (mmm) REVERT: D 120 GLU cc_start: 0.8134 (tt0) cc_final: 0.7898 (tt0) REVERT: D 129 ASP cc_start: 0.7994 (m-30) cc_final: 0.7685 (p0) REVERT: E 81 LYS cc_start: 0.8395 (mppt) cc_final: 0.8131 (mmtp) REVERT: E 99 ASN cc_start: 0.8753 (t0) cc_final: 0.8309 (t0) REVERT: E 232 GLN cc_start: 0.7642 (mt0) cc_final: 0.6709 (tm-30) REVERT: F 68 MET cc_start: 0.9068 (tpp) cc_final: 0.8827 (tpt) REVERT: F 234 MET cc_start: 0.8269 (tpp) cc_final: 0.7665 (tmm) REVERT: F 295 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 297 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7850 (tmm) REVERT: F 309 MET cc_start: 0.7945 (tpt) cc_final: 0.7589 (tpt) outliers start: 38 outliers final: 12 residues processed: 315 average time/residue: 1.7773 time to fit residues: 604.1387 Evaluate side-chains 311 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 295 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 106 optimal weight: 2.9990 chunk 171 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 99 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.076687 restraints weight = 70143.352| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.33 r_work: 0.2800 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15865 Z= 0.157 Angle : 0.578 7.413 21613 Z= 0.303 Chirality : 0.041 0.129 2438 Planarity : 0.005 0.048 2674 Dihedral : 14.999 158.995 2499 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.55 % Allowed : 17.74 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 1856 helix: 0.98 (0.17), residues: 994 sheet: 0.77 (0.30), residues: 276 loop : 0.17 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 312 TYR 0.011 0.001 TYR E 329 PHE 0.007 0.001 PHE C 108 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00362 (15865) covalent geometry : angle 0.57830 (21613) hydrogen bonds : bond 0.05165 ( 759) hydrogen bonds : angle 4.91972 ( 2137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 302 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8362 (mtmm) REVERT: A 81 LYS cc_start: 0.8679 (mttp) cc_final: 0.8463 (mttt) REVERT: A 83 THR cc_start: 0.9471 (t) cc_final: 0.9186 (m) REVERT: A 198 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8139 (mm-30) REVERT: B 81 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8624 (mmmm) REVERT: B 111 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: C 166 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8144 (m-40) REVERT: C 325 MET cc_start: 0.9107 (mmm) cc_final: 0.8812 (mmm) REVERT: D 129 ASP cc_start: 0.7962 (m-30) cc_final: 0.7693 (p0) REVERT: E 81 LYS cc_start: 0.8460 (mppt) cc_final: 0.8195 (mmtp) REVERT: E 99 ASN cc_start: 0.8549 (t0) cc_final: 0.8149 (t0) REVERT: E 232 GLN cc_start: 0.7619 (mt0) cc_final: 0.6746 (tm-30) REVERT: F 68 MET cc_start: 0.9052 (tpp) cc_final: 0.8738 (tpt) REVERT: F 234 MET cc_start: 0.8251 (tpp) cc_final: 0.7734 (tmm) REVERT: F 252 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7981 (t0) REVERT: F 297 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7834 (tmm) outliers start: 40 outliers final: 14 residues processed: 323 average time/residue: 1.7949 time to fit residues: 624.9112 Evaluate side-chains 318 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 298 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 260 TYR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 139 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 286 ASN D 177 HIS ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.077318 restraints weight = 70000.277| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.32 r_work: 0.2813 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15865 Z= 0.133 Angle : 0.575 8.276 21613 Z= 0.298 Chirality : 0.040 0.137 2438 Planarity : 0.005 0.057 2674 Dihedral : 14.929 157.742 2499 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.17 % Allowed : 18.76 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1856 helix: 1.12 (0.17), residues: 996 sheet: 0.79 (0.30), residues: 274 loop : 0.20 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.020 0.001 TYR D 124 PHE 0.005 0.001 PHE A 172 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00307 (15865) covalent geometry : angle 0.57454 (21613) hydrogen bonds : bond 0.04617 ( 759) hydrogen bonds : angle 4.78340 ( 2137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8322 (mtmm) REVERT: A 83 THR cc_start: 0.9494 (t) cc_final: 0.9216 (m) REVERT: A 198 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8151 (mm-30) REVERT: A 292 GLU cc_start: 0.7425 (tp30) cc_final: 0.7175 (tp30) REVERT: A 296 ASP cc_start: 0.8371 (m-30) cc_final: 0.8119 (m-30) REVERT: B 81 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8631 (mmmm) REVERT: B 111 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: B 245 ASP cc_start: 0.8541 (t0) cc_final: 0.8268 (t0) REVERT: C 166 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8139 (m-40) REVERT: C 325 MET cc_start: 0.9121 (mmm) cc_final: 0.8809 (mmm) REVERT: D 120 GLU cc_start: 0.8352 (pt0) cc_final: 0.8148 (pt0) REVERT: D 124 TYR cc_start: 0.8085 (m-10) cc_final: 0.7798 (m-80) REVERT: D 129 ASP cc_start: 0.7962 (m-30) cc_final: 0.7721 (p0) REVERT: E 81 LYS cc_start: 0.8491 (mppt) cc_final: 0.8111 (mmtp) REVERT: E 99 ASN cc_start: 0.8596 (t0) cc_final: 0.8204 (t0) REVERT: E 232 GLN cc_start: 0.7561 (mt0) cc_final: 0.6754 (tm-30) REVERT: F 68 MET cc_start: 0.9037 (tpp) cc_final: 0.8739 (tpt) REVERT: F 234 MET cc_start: 0.8232 (tpp) cc_final: 0.7781 (tmm) REVERT: F 297 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7816 (tmm) REVERT: F 309 MET cc_start: 0.7939 (tpt) cc_final: 0.7598 (tpt) outliers start: 34 outliers final: 13 residues processed: 331 average time/residue: 1.7739 time to fit residues: 634.1319 Evaluate side-chains 315 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 154 optimal weight: 0.4980 chunk 163 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 99 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.077396 restraints weight = 70051.252| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.34 r_work: 0.2813 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15865 Z= 0.131 Angle : 0.573 8.506 21613 Z= 0.296 Chirality : 0.040 0.146 2438 Planarity : 0.005 0.091 2674 Dihedral : 14.868 156.929 2499 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.04 % Allowed : 19.97 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 1856 helix: 1.25 (0.17), residues: 996 sheet: 0.76 (0.30), residues: 276 loop : 0.22 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 169 TYR 0.013 0.001 TYR D 124 PHE 0.005 0.001 PHE B 25 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00302 (15865) covalent geometry : angle 0.57327 (21613) hydrogen bonds : bond 0.04395 ( 759) hydrogen bonds : angle 4.68240 ( 2137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 305 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8307 (mtmm) REVERT: A 83 THR cc_start: 0.9495 (t) cc_final: 0.9233 (m) REVERT: A 198 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8144 (mm-30) REVERT: A 292 GLU cc_start: 0.7529 (tp30) cc_final: 0.7208 (tp30) REVERT: A 296 ASP cc_start: 0.8328 (m-30) cc_final: 0.8100 (m-30) REVERT: B 81 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8654 (mmmm) REVERT: B 111 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: B 245 ASP cc_start: 0.8559 (t0) cc_final: 0.8281 (t0) REVERT: C 125 SER cc_start: 0.9009 (m) cc_final: 0.8706 (p) REVERT: C 166 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8146 (m-40) REVERT: D 124 TYR cc_start: 0.8031 (m-10) cc_final: 0.7753 (m-80) REVERT: D 129 ASP cc_start: 0.7997 (m-30) cc_final: 0.7728 (p0) REVERT: E 81 LYS cc_start: 0.8502 (mppt) cc_final: 0.8129 (mmtp) REVERT: E 99 ASN cc_start: 0.8605 (t0) cc_final: 0.8212 (t0) REVERT: E 201 ILE cc_start: 0.8731 (tt) cc_final: 0.8462 (pp) REVERT: E 232 GLN cc_start: 0.7592 (mt0) cc_final: 0.6818 (tm-30) REVERT: E 292 GLU cc_start: 0.7860 (mp0) cc_final: 0.7658 (mp0) REVERT: E 310 ARG cc_start: 0.7328 (ptp-170) cc_final: 0.7007 (ptp-170) REVERT: E 312 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6955 (mtt90) REVERT: F 68 MET cc_start: 0.9042 (tpp) cc_final: 0.8754 (tpt) REVERT: F 234 MET cc_start: 0.8187 (tpp) cc_final: 0.7796 (tmm) REVERT: F 297 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7795 (tmm) outliers start: 32 outliers final: 13 residues processed: 326 average time/residue: 1.8468 time to fit residues: 650.4111 Evaluate side-chains 321 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 135 optimal weight: 4.9990 chunk 118 optimal weight: 0.0670 chunk 156 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 0.0370 chunk 162 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 115 optimal weight: 0.3980 chunk 183 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.078075 restraints weight = 69813.877| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.35 r_work: 0.2825 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15865 Z= 0.118 Angle : 0.569 7.603 21613 Z= 0.292 Chirality : 0.039 0.144 2438 Planarity : 0.005 0.090 2674 Dihedral : 14.801 154.252 2499 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.91 % Allowed : 20.23 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1856 helix: 1.33 (0.17), residues: 996 sheet: 0.73 (0.30), residues: 280 loop : 0.30 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 169 TYR 0.012 0.001 TYR D 124 PHE 0.005 0.001 PHE B 25 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00272 (15865) covalent geometry : angle 0.56906 (21613) hydrogen bonds : bond 0.04071 ( 759) hydrogen bonds : angle 4.59385 ( 2137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8282 (mtmm) REVERT: A 83 THR cc_start: 0.9491 (t) cc_final: 0.9246 (m) REVERT: A 198 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8150 (mm-30) REVERT: B 81 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8670 (mmmm) REVERT: B 245 ASP cc_start: 0.8521 (t0) cc_final: 0.8252 (t0) REVERT: C 125 SER cc_start: 0.9000 (m) cc_final: 0.8663 (p) REVERT: C 166 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8130 (m-40) REVERT: D 79 ASN cc_start: 0.8444 (m-40) cc_final: 0.8223 (m-40) REVERT: D 129 ASP cc_start: 0.8002 (m-30) cc_final: 0.7728 (p0) REVERT: D 252 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7786 (t0) REVERT: E 99 ASN cc_start: 0.8577 (t0) cc_final: 0.8181 (t0) REVERT: E 105 ASP cc_start: 0.8445 (m-30) cc_final: 0.7806 (m-30) REVERT: E 201 ILE cc_start: 0.8679 (tt) cc_final: 0.8310 (mp) REVERT: E 292 GLU cc_start: 0.7888 (mp0) cc_final: 0.7687 (mp0) REVERT: E 305 LYS cc_start: 0.8302 (mppt) cc_final: 0.8001 (mmtm) REVERT: F 68 MET cc_start: 0.9025 (tpp) cc_final: 0.8755 (tpt) REVERT: F 234 MET cc_start: 0.8195 (tpp) cc_final: 0.7891 (tmm) REVERT: F 297 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7835 (tmm) REVERT: F 309 MET cc_start: 0.8023 (tpt) cc_final: 0.7715 (tpt) outliers start: 30 outliers final: 14 residues processed: 328 average time/residue: 1.8123 time to fit residues: 642.0188 Evaluate side-chains 316 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 297 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 137 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 154 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 99 ASN C 99 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.077645 restraints weight = 69833.923| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.23 r_work: 0.2823 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15865 Z= 0.136 Angle : 0.582 8.824 21613 Z= 0.298 Chirality : 0.040 0.148 2438 Planarity : 0.005 0.093 2674 Dihedral : 14.789 155.006 2499 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.91 % Allowed : 20.23 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1856 helix: 1.36 (0.17), residues: 995 sheet: 0.75 (0.30), residues: 281 loop : 0.26 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 169 TYR 0.014 0.001 TYR D 124 PHE 0.005 0.001 PHE B 25 HIS 0.012 0.001 HIS F 255 Details of bonding type rmsd covalent geometry : bond 0.00318 (15865) covalent geometry : angle 0.58154 (21613) hydrogen bonds : bond 0.04261 ( 759) hydrogen bonds : angle 4.59292 ( 2137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: A 83 THR cc_start: 0.9472 (t) cc_final: 0.9235 (m) REVERT: A 198 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8121 (mm-30) REVERT: B 81 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8655 (mmmm) REVERT: B 111 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: B 245 ASP cc_start: 0.8552 (t0) cc_final: 0.8289 (t0) REVERT: C 125 SER cc_start: 0.9017 (m) cc_final: 0.8705 (p) REVERT: C 166 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8150 (m-40) REVERT: D 79 ASN cc_start: 0.8468 (m-40) cc_final: 0.8252 (m-40) REVERT: D 252 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7704 (t0) REVERT: E 99 ASN cc_start: 0.8605 (t0) cc_final: 0.8183 (t0) REVERT: E 201 ILE cc_start: 0.8696 (tt) cc_final: 0.8326 (mp) REVERT: E 305 LYS cc_start: 0.8319 (mppt) cc_final: 0.8041 (mmtm) REVERT: F 68 MET cc_start: 0.9023 (tpp) cc_final: 0.8757 (tpt) REVERT: F 234 MET cc_start: 0.8266 (tpp) cc_final: 0.7909 (tmm) REVERT: F 297 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7806 (tmm) outliers start: 30 outliers final: 12 residues processed: 320 average time/residue: 1.8672 time to fit residues: 643.9524 Evaluate side-chains 315 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.077359 restraints weight = 69867.792| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.30 r_work: 0.2809 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15865 Z= 0.154 Angle : 0.604 10.483 21613 Z= 0.310 Chirality : 0.040 0.141 2438 Planarity : 0.005 0.092 2674 Dihedral : 14.821 157.647 2499 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.47 % Allowed : 21.00 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1856 helix: 1.32 (0.17), residues: 995 sheet: 0.71 (0.31), residues: 281 loop : 0.18 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 169 TYR 0.029 0.001 TYR D 124 PHE 0.009 0.001 PHE D 58 HIS 0.013 0.001 HIS F 255 Details of bonding type rmsd covalent geometry : bond 0.00362 (15865) covalent geometry : angle 0.60385 (21613) hydrogen bonds : bond 0.04499 ( 759) hydrogen bonds : angle 4.60664 ( 2137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8312 (mtmm) REVERT: A 83 THR cc_start: 0.9461 (t) cc_final: 0.9235 (m) REVERT: A 198 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 81 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8863 (mmmm) REVERT: B 111 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: B 245 ASP cc_start: 0.8544 (t0) cc_final: 0.8276 (t0) REVERT: C 125 SER cc_start: 0.9046 (m) cc_final: 0.8734 (p) REVERT: C 166 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8236 (m-40) REVERT: D 79 ASN cc_start: 0.8508 (m-40) cc_final: 0.8299 (m-40) REVERT: D 129 ASP cc_start: 0.8055 (m-30) cc_final: 0.7768 (p0) REVERT: D 252 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7549 (t0) REVERT: E 99 ASN cc_start: 0.8604 (t0) cc_final: 0.8182 (t0) REVERT: E 201 ILE cc_start: 0.8727 (tt) cc_final: 0.8355 (mp) REVERT: E 292 GLU cc_start: 0.8024 (mp0) cc_final: 0.7783 (mp0) REVERT: E 305 LYS cc_start: 0.8290 (mppt) cc_final: 0.8006 (mmtm) REVERT: F 68 MET cc_start: 0.9039 (tpp) cc_final: 0.8776 (tpt) REVERT: F 234 MET cc_start: 0.8305 (tpp) cc_final: 0.7947 (tmm) REVERT: F 297 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7835 (tmm) outliers start: 23 outliers final: 10 residues processed: 313 average time/residue: 1.8403 time to fit residues: 620.7614 Evaluate side-chains 312 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 296 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 56 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.077015 restraints weight = 70125.194| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.32 r_work: 0.2801 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15865 Z= 0.156 Angle : 0.601 9.070 21613 Z= 0.310 Chirality : 0.040 0.140 2438 Planarity : 0.005 0.079 2674 Dihedral : 14.841 159.259 2499 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.60 % Allowed : 21.12 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1856 helix: 1.31 (0.17), residues: 993 sheet: 0.67 (0.31), residues: 279 loop : 0.15 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 310 TYR 0.028 0.001 TYR D 124 PHE 0.010 0.001 PHE D 58 HIS 0.014 0.001 HIS F 255 Details of bonding type rmsd covalent geometry : bond 0.00367 (15865) covalent geometry : angle 0.60078 (21613) hydrogen bonds : bond 0.04588 ( 759) hydrogen bonds : angle 4.60693 ( 2137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13786.99 seconds wall clock time: 232 minutes 55.05 seconds (13975.05 seconds total)