Starting phenix.real_space_refine on Mon Sep 14 13:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbr_13300/09_2026/7pbr_13300_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbr_13300/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pbr_13300/09_2026/7pbr_13300_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbr_13300/09_2026/7pbr_13300_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbr_13300/09_2026/7pbr_13300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbr_13300/09_2026/7pbr_13300.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.34, per 1000 atoms: 0.17 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: 2.98 Conformation dependent library (CDL) restraints added in 910.0 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: 5.38 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: 6.96 Time building geometry restraints manager: 4.11 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 - 2.15: 55353 2.15 - 4.29: 577 4.29 - 6.44: 47 6.44 - 8.59: 17 8.59 - 10.73: 12 Bond angle restraints: 56006 Sorted by residual: angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.21 -3.21 7.00e-01 2.04e+00 2.10e+01 angle pdb=" O4' DT V 7 " pdb=" C1' DT V 7 " pdb=" N1 DT V 7 " ideal model delta sigma weight residual 108.00 111.05 -3.05 7.00e-01 2.04e+00 1.90e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" O4' DC V 6 " pdb=" C1' DC V 6 " pdb=" N1 DC V 6 " ideal model delta sigma weight residual 108.00 110.86 -2.86 7.00e-01 2.04e+00 1.67e+01 angle pdb=" N3 DT U 7 " pdb=" C4 DT U 7 " pdb=" O4 DT U 7 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 ... (remaining 56001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 13758 31.16 - 62.32: 602 62.32 - 93.48: 64 93.48 - 124.63: 0 124.63 - 155.79: 2 Dihedral angle restraints: 14426 sinusoidal: 8303 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=" C1' ADP F 600 " pdb=" C4' ADP F 600 " pdb=" O4' ADP F 600 " pdb=" C5' ADP F 600 " ideal model delta sinusoidal sigma weight residual -150.00 -93.52 -56.48 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 14423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2171 0.077 - 0.153: 246 0.153 - 0.230: 8 0.230 - 0.307: 4 0.307 - 0.383: 1 Chirality restraints: 2430 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 2.34 -2.72 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' AGS D 401 " pdb=" C2' AGS D 401 " pdb=" C4' AGS D 401 " pdb=" O3' AGS D 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2427 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: 2.970 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: 0.170 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 34.190 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.005 0.099 15865 Z= 0.280 Angle : 0.805 10.734 21613 Z= 0.463 Chirality : 0.048 0.383 2430 Planarity : 0.009 0.119 2674 Dihedral : 15.891 155.793 6212 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/Z covalent geometry : bond 0.00518 / 0.28 (15865) covalent geometry : angle 0.80471 / 0.46 (21613) hydrogen bonds : bond 0.26514 / 17.05 ( 759) hydrogen bonds : angle 8.47130 / 5.84 ( 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 : 0.701 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: 1.6403 time to fit residues: 810.2833 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 : 0.822 ------------------------------------------------------------------------------- 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: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN C 286 ASN D 146 HIS E 79 ASN E 324 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.077041 restraints weight = 69638.188| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.29 r_work: 0.2805 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15865 Z= 0.206 Angle : 0.707 6.422 21613 Z= 0.386 Chirality : 0.044 0.160 2430 Planarity : 0.006 0.057 2674 Dihedral : 15.572 148.258 2575 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.17 % Allowed : 16.15 % Favored : 81.68 % 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: 0.40 (0.19), residues: 1856 helix: 0.18 (0.16), residues: 991 sheet: 1.09 (0.30), residues: 283 loop : 0.31 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 310 TYR 0.017 0.001 TYR C 124 PHE 0.009 0.001 PHE B 25 HIS 0.005 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 (15865) covalent geometry : angle 0.70680 / 0.39 (21613) hydrogen bonds : bond 0.08910 / 5.89 ( 759) hydrogen bonds : angle 6.16944 / 4.26 ( 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: 34 poor density : 325 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8651 (mttp) cc_final: 0.8389 (mttt) REVERT: A 325 MET cc_start: 0.8332 (mmm) cc_final: 0.8015 (mmm) REVERT: B 81 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8617 (mmmm) REVERT: C 325 MET cc_start: 0.9137 (mmm) cc_final: 0.8878 (mmm) REVERT: D 169 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8160 (tpp80) REVERT: D 171 ARG cc_start: 0.6684 (mpt-90) cc_final: 0.6427 (mpt180) REVERT: E 23 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7751 (mm110) REVERT: E 99 ASN cc_start: 0.8724 (t0) cc_final: 0.8254 (t0) REVERT: E 111 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7689 (mt-10) REVERT: E 185 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: F 82 GLN cc_start: 0.8706 (mt0) cc_final: 0.8475 (mt0) REVERT: F 272 MET cc_start: 0.8377 (ttp) cc_final: 0.8140 (ttp) REVERT: F 295 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7740 (mt-10) outliers start: 34 outliers final: 9 residues processed: 335 average time/residue: 1.6337 time to fit residues: 596.2297 Evaluate side-chains 315 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 304 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 C residue 194 SER 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 250 MET Chi-restraints excluded: chain F residue 284 SER 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: 1.9990 chunk 119 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN C 286 ASN D 177 HIS 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 = 0.3402 r_free = 0.3402 target = 0.105585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.077536 restraints weight = 69612.462| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.30 r_work: 0.2817 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15865 Z= 0.149 Angle : 0.613 6.406 21613 Z= 0.323 Chirality : 0.042 0.141 2430 Planarity : 0.005 0.054 2674 Dihedral : 14.568 149.642 2571 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.17 % Allowed : 16.34 % Favored : 81.49 % 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: 0.77 (0.19), residues: 1856 helix: 0.64 (0.17), residues: 989 sheet: 1.03 (0.30), residues: 278 loop : 0.29 (0.23), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 211 TYR 0.012 0.001 TYR D 124 PHE 0.009 0.001 PHE E 307 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (15865) covalent geometry : angle 0.61348 / 0.32 (21613) hydrogen bonds : bond 0.06558 / 4.35 ( 759) hydrogen bonds : angle 5.45142 / 3.75 ( 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 348 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 314 time to evaluate : 0.819 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: A 198 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8080 (mm-30) REVERT: A 260 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.7019 (p90) REVERT: A 325 MET cc_start: 0.8303 (mmm) cc_final: 0.8093 (mmm) REVERT: B 81 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8621 (mmmm) REVERT: B 111 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: C 325 MET cc_start: 0.9122 (mmm) cc_final: 0.8785 (mmm) REVERT: D 120 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: D 129 ASP cc_start: 0.7950 (m-30) cc_final: 0.7683 (p0) REVERT: D 171 ARG cc_start: 0.6471 (mpt-90) cc_final: 0.6259 (mpt180) REVERT: D 188 GLU cc_start: 0.8178 (mp0) cc_final: 0.7973 (mp0) REVERT: E 99 ASN cc_start: 0.8753 (t0) cc_final: 0.8307 (t0) REVERT: E 111 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7884 (mt-10) REVERT: E 166 ASN cc_start: 0.8098 (t0) cc_final: 0.7897 (t0) REVERT: F 68 MET cc_start: 0.9077 (tpp) cc_final: 0.8802 (tpt) REVERT: F 234 MET cc_start: 0.8050 (tpp) cc_final: 0.6980 (tmm) REVERT: F 309 MET cc_start: 0.7929 (tpt) cc_final: 0.7492 (tpt) outliers start: 34 outliers final: 11 residues processed: 328 average time/residue: 1.6407 time to fit residues: 585.6107 Evaluate side-chains 316 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 301 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 260 TYR 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 133 ASP Chi-restraints excluded: chain D residue 120 GLU 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 23 GLN Chi-restraints excluded: chain F residue 250 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: 0.9990 chunk 115 optimal weight: 0.5980 chunk 69 optimal weight: 0.4980 chunk 168 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.077427 restraints weight = 69249.357| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.29 r_work: 0.2816 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15865 Z= 0.149 Angle : 0.606 7.764 21613 Z= 0.317 Chirality : 0.041 0.157 2430 Planarity : 0.005 0.057 2674 Dihedral : 14.186 151.719 2571 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.30 % Allowed : 17.04 % Favored : 80.66 % 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: 0.94 (0.19), residues: 1856 helix: 0.82 (0.17), residues: 992 sheet: 0.93 (0.31), residues: 277 loop : 0.38 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 291 TYR 0.007 0.001 TYR F 260 PHE 0.011 0.001 PHE D 58 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15865) covalent geometry : angle 0.60566 / 0.32 (21613) hydrogen bonds : bond 0.05742 / 3.81 ( 759) hydrogen bonds : angle 5.21848 / 3.59 ( 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 341 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 305 time to evaluate : 0.986 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: A 33 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8355 (mtmm) REVERT: A 100 ASP cc_start: 0.7955 (m-30) cc_final: 0.7711 (m-30) REVERT: B 81 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8622 (mmmm) REVERT: B 111 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: C 325 MET cc_start: 0.9119 (mmm) cc_final: 0.8868 (mmm) REVERT: D 120 GLU cc_start: 0.8196 (tt0) cc_final: 0.7848 (tt0) REVERT: D 129 ASP cc_start: 0.7961 (m-30) cc_final: 0.7700 (p0) REVERT: D 169 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8144 (tpp80) REVERT: D 171 ARG cc_start: 0.6536 (mpt-90) cc_final: 0.6267 (mpt180) REVERT: D 188 GLU cc_start: 0.8230 (mp0) cc_final: 0.7954 (mp0) REVERT: E 99 ASN cc_start: 0.8744 (t0) cc_final: 0.8304 (t0) REVERT: E 166 ASN cc_start: 0.8081 (t0) cc_final: 0.7876 (t0) REVERT: E 259 ASP cc_start: 0.7516 (t0) cc_final: 0.7274 (t0) REVERT: F 68 MET cc_start: 0.9067 (tpp) cc_final: 0.8809 (tpt) REVERT: F 93 ASP cc_start: 0.8432 (m-30) cc_final: 0.8202 (m-30) REVERT: F 297 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7873 (tmm) REVERT: F 309 MET cc_start: 0.7937 (tpt) cc_final: 0.7535 (tpt) outliers start: 36 outliers final: 16 residues processed: 323 average time/residue: 1.6252 time to fit residues: 572.4501 Evaluate side-chains 316 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 296 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 A residue 312 ARG 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 C residue 328 ASP 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 23 GLN Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 264 LYS 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: 0.9990 chunk 137 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 99 ASN C 99 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.076506 restraints weight = 69724.775| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.25 r_work: 0.2801 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15865 Z= 0.175 Angle : 0.613 8.000 21613 Z= 0.320 Chirality : 0.041 0.163 2430 Planarity : 0.005 0.044 2674 Dihedral : 14.067 156.947 2571 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.81 % Allowed : 16.85 % Favored : 80.34 % 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: 0.87 (0.19), residues: 1856 helix: 0.84 (0.17), residues: 994 sheet: 0.81 (0.30), residues: 276 loop : 0.25 (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 0.011 0.001 PHE D 58 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (15865) covalent geometry : angle 0.61261 / 0.32 (21613) hydrogen bonds : bond 0.05653 / 3.74 ( 759) hydrogen bonds : angle 5.08928 / 3.51 ( 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 343 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8376 (mtmm) REVERT: B 81 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8608 (mmmm) REVERT: B 111 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: C 325 MET cc_start: 0.9157 (mmm) cc_final: 0.8876 (mmm) REVERT: D 129 ASP cc_start: 0.7952 (m-30) cc_final: 0.7673 (p0) REVERT: D 188 GLU cc_start: 0.8320 (mp0) cc_final: 0.8006 (mp0) REVERT: E 99 ASN cc_start: 0.8752 (t0) cc_final: 0.8310 (t0) REVERT: E 232 GLN cc_start: 0.7672 (mt0) cc_final: 0.6739 (tm-30) REVERT: F 68 MET cc_start: 0.9064 (tpp) cc_final: 0.8818 (tpt) REVERT: F 234 MET cc_start: 0.8250 (tpp) cc_final: 0.7661 (tmm) REVERT: F 297 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7866 (tmm) REVERT: F 309 MET cc_start: 0.7955 (tpt) cc_final: 0.7556 (tpt) outliers start: 44 outliers final: 16 residues processed: 321 average time/residue: 1.6416 time to fit residues: 574.2965 Evaluate side-chains 315 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 295 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 133 ASP 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 F residue 23 GLN Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 264 LYS 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: 0.9980 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3387 r_free = 0.3387 target = 0.104468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.076460 restraints weight = 69583.607| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.31 r_work: 0.2796 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15865 Z= 0.167 Angle : 0.603 7.334 21613 Z= 0.315 Chirality : 0.041 0.166 2430 Planarity : 0.005 0.040 2674 Dihedral : 14.007 158.822 2571 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.49 % Allowed : 17.80 % 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: 0.85 (0.19), residues: 1856 helix: 0.87 (0.17), residues: 995 sheet: 0.77 (0.30), residues: 276 loop : 0.16 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 310 TYR 0.014 0.001 TYR D 124 PHE 0.011 0.001 PHE D 58 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (15865) covalent geometry : angle 0.60336 / 0.32 (21613) hydrogen bonds : bond 0.05416 / 3.57 ( 759) hydrogen bonds : angle 4.99177 / 3.45 ( 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 341 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 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: A 33 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: A 81 LYS cc_start: 0.8640 (mttt) cc_final: 0.8308 (mttt) REVERT: A 198 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 260 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.7020 (p90) REVERT: B 81 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8626 (mmmm) REVERT: B 111 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: C 325 MET cc_start: 0.9111 (mmm) cc_final: 0.8818 (mmm) REVERT: D 120 GLU cc_start: 0.8277 (tt0) cc_final: 0.7873 (tt0) REVERT: D 129 ASP cc_start: 0.7953 (m-30) cc_final: 0.7673 (p0) REVERT: D 188 GLU cc_start: 0.8333 (mp0) cc_final: 0.7994 (mp0) REVERT: E 81 LYS cc_start: 0.8427 (mppt) cc_final: 0.8150 (mmtp) REVERT: E 99 ASN cc_start: 0.8730 (t0) cc_final: 0.8296 (t0) REVERT: E 232 GLN cc_start: 0.7669 (mt0) cc_final: 0.6778 (tm-30) REVERT: F 68 MET cc_start: 0.9063 (tpp) cc_final: 0.8746 (tpt) REVERT: F 234 MET cc_start: 0.8269 (tpp) cc_final: 0.7733 (tmm) REVERT: F 297 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7818 (tmm) outliers start: 39 outliers final: 17 residues processed: 321 average time/residue: 1.6390 time to fit residues: 573.8773 Evaluate side-chains 313 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 291 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 260 TYR 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 133 ASP 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 E residue 261 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 83 THR 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: 0.9990 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3384 r_free = 0.3384 target = 0.104279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.076753 restraints weight = 69718.454| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.29 r_work: 0.2803 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15865 Z= 0.151 Angle : 0.601 8.687 21613 Z= 0.312 Chirality : 0.041 0.165 2430 Planarity : 0.005 0.050 2674 Dihedral : 13.932 158.759 2571 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.11 % Allowed : 19.21 % Favored : 78.69 % 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: 0.89 (0.19), residues: 1856 helix: 0.94 (0.17), residues: 994 sheet: 0.77 (0.30), residues: 276 loop : 0.12 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 310 TYR 0.011 0.001 TYR D 124 PHE 0.011 0.001 PHE D 58 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15865) covalent geometry : angle 0.60106 / 0.31 (21613) hydrogen bonds : bond 0.05136 / 3.38 ( 759) hydrogen bonds : angle 4.91377 / 3.39 ( 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 327 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.868 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 81 LYS cc_start: 0.8657 (mttt) cc_final: 0.8319 (mttt) REVERT: A 198 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8126 (mm-30) REVERT: B 81 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8615 (mmmm) REVERT: B 111 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: B 245 ASP cc_start: 0.8578 (t0) cc_final: 0.8302 (t0) REVERT: C 166 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8121 (m-40) REVERT: C 325 MET cc_start: 0.9128 (mmm) cc_final: 0.8828 (mmm) REVERT: D 120 GLU cc_start: 0.8264 (tt0) cc_final: 0.7800 (tt0) REVERT: D 129 ASP cc_start: 0.8020 (m-30) cc_final: 0.7721 (p0) REVERT: D 188 GLU cc_start: 0.8318 (mp0) cc_final: 0.7963 (mp0) REVERT: E 81 LYS cc_start: 0.8456 (mppt) cc_final: 0.8175 (mmtp) REVERT: E 99 ASN cc_start: 0.8754 (t0) cc_final: 0.8324 (t0) REVERT: E 232 GLN cc_start: 0.7636 (mt0) cc_final: 0.6769 (tm-30) REVERT: F 68 MET cc_start: 0.9048 (tpp) cc_final: 0.8758 (tpt) REVERT: F 188 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8031 (tp30) REVERT: F 234 MET cc_start: 0.8229 (tpp) cc_final: 0.7731 (tmm) REVERT: F 297 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7809 (tmm) outliers start: 33 outliers final: 15 residues processed: 311 average time/residue: 1.6226 time to fit residues: 550.4329 Evaluate side-chains 311 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 292 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 261 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 147 LEU 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: 1.9990 chunk 156 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 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 = 0.3379 r_free = 0.3379 target = 0.104066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.076524 restraints weight = 69436.722| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.27 r_work: 0.2799 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15865 Z= 0.160 Angle : 0.606 9.392 21613 Z= 0.314 Chirality : 0.041 0.170 2430 Planarity : 0.005 0.056 2674 Dihedral : 13.901 160.118 2571 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.11 % Allowed : 19.46 % Favored : 78.43 % 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: 0.92 (0.19), residues: 1856 helix: 1.00 (0.17), residues: 994 sheet: 0.75 (0.30), residues: 276 loop : 0.07 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 312 TYR 0.012 0.001 TYR D 131 PHE 0.012 0.001 PHE D 58 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (15865) covalent geometry : angle 0.60604 / 0.31 (21613) hydrogen bonds : bond 0.05105 / 3.35 ( 759) hydrogen bonds : angle 4.85152 / 3.35 ( 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 335 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 302 time to evaluate : 0.853 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: 0.8788 (OUTLIER) cc_final: 0.8384 (mtmm) REVERT: A 81 LYS cc_start: 0.8673 (mttt) cc_final: 0.8343 (mttt) REVERT: A 83 THR cc_start: 0.9478 (t) cc_final: 0.9211 (m) REVERT: A 134 ILE cc_start: 0.8265 (mm) cc_final: 0.7899 (pt) REVERT: A 198 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8153 (mm-30) REVERT: B 81 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8635 (mmmm) REVERT: B 111 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: B 245 ASP cc_start: 0.8583 (t0) cc_final: 0.8301 (t0) REVERT: C 166 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8137 (m-40) REVERT: C 325 MET cc_start: 0.9131 (mmm) cc_final: 0.8789 (mmm) REVERT: D 120 GLU cc_start: 0.8308 (tt0) cc_final: 0.7568 (tm-30) REVERT: D 129 ASP cc_start: 0.8027 (m-30) cc_final: 0.7719 (p0) REVERT: D 169 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8082 (tpp80) REVERT: D 188 GLU cc_start: 0.8348 (mp0) cc_final: 0.7988 (mp0) REVERT: D 242 LYS cc_start: 0.8310 (tttm) cc_final: 0.8085 (tmtt) REVERT: E 81 LYS cc_start: 0.8494 (mppt) cc_final: 0.8203 (mmtp) REVERT: E 99 ASN cc_start: 0.8565 (t0) cc_final: 0.8161 (t0) REVERT: E 232 GLN cc_start: 0.7632 (mt0) cc_final: 0.6811 (tm-30) REVERT: F 68 MET cc_start: 0.9054 (tpp) cc_final: 0.8775 (tpt) REVERT: F 188 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8037 (tp30) REVERT: F 234 MET cc_start: 0.8242 (tpp) cc_final: 0.7786 (tmm) REVERT: F 297 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7792 (tmm) outliers start: 33 outliers final: 16 residues processed: 319 average time/residue: 1.6417 time to fit residues: 570.5799 Evaluate side-chains 316 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 295 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 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 E residue 42 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 287 ILE 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: 0.9980 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 47 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3388 r_free = 0.3388 target = 0.104661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.077052 restraints weight = 69448.986| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.28 r_work: 0.2808 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4144 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= 0.138 Angle : 0.600 10.099 21613 Z= 0.309 Chirality : 0.040 0.169 2430 Planarity : 0.005 0.056 2674 Dihedral : 13.841 159.074 2571 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.85 % Allowed : 19.85 % Favored : 78.30 % 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: 1.03 (0.19), residues: 1856 helix: 1.09 (0.17), residues: 994 sheet: 0.76 (0.30), residues: 276 loop : 0.14 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 310 TYR 0.011 0.001 TYR D 131 PHE 0.011 0.001 PHE D 58 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15865) covalent geometry : angle 0.59966 / 0.31 (21613) hydrogen bonds : bond 0.04755 / 3.12 ( 759) hydrogen bonds : angle 4.77352 / 3.30 ( 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 334 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 305 time to evaluate : 0.887 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: 0.8748 (OUTLIER) cc_final: 0.8347 (mtmm) REVERT: A 81 LYS cc_start: 0.8674 (mttt) cc_final: 0.8371 (mttt) REVERT: A 83 THR cc_start: 0.9472 (t) cc_final: 0.9218 (m) REVERT: A 198 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8154 (mm-30) REVERT: B 81 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8648 (mmmm) REVERT: B 111 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: B 245 ASP cc_start: 0.8590 (t0) cc_final: 0.8314 (t0) REVERT: C 166 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8112 (m-40) REVERT: C 325 MET cc_start: 0.9144 (mmm) cc_final: 0.8831 (mmm) REVERT: D 79 ASN cc_start: 0.8537 (m-40) cc_final: 0.8304 (m-40) REVERT: D 120 GLU cc_start: 0.8276 (tt0) cc_final: 0.7674 (tm-30) REVERT: D 124 TYR cc_start: 0.7930 (m-10) cc_final: 0.7544 (m-10) REVERT: D 129 ASP cc_start: 0.8012 (m-30) cc_final: 0.7706 (p0) REVERT: D 188 GLU cc_start: 0.8359 (mp0) cc_final: 0.7969 (mp0) REVERT: E 81 LYS cc_start: 0.8456 (mppt) cc_final: 0.8157 (mmtp) REVERT: E 99 ASN cc_start: 0.8597 (t0) cc_final: 0.8201 (t0) REVERT: E 105 ASP cc_start: 0.8425 (m-30) cc_final: 0.7758 (m-30) REVERT: E 232 GLN cc_start: 0.7613 (mt0) cc_final: 0.6817 (tm-30) REVERT: F 68 MET cc_start: 0.9042 (tpp) cc_final: 0.8770 (tpt) REVERT: F 188 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8084 (tp30) REVERT: F 234 MET cc_start: 0.8177 (tpp) cc_final: 0.7786 (tmm) REVERT: F 291 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7754 (mtp180) REVERT: F 297 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7770 (tmm) outliers start: 29 outliers final: 16 residues processed: 322 average time/residue: 1.6125 time to fit residues: 566.6350 Evaluate side-chains 315 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 294 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 90 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 E residue 42 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 147 LEU 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: 0.4980 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.0770 chunk 184 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3398 r_free = 0.3398 target = 0.105355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.077431 restraints weight = 69354.952| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.33 r_work: 0.2814 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15865 Z= 0.129 Angle : 0.599 9.116 21613 Z= 0.308 Chirality : 0.040 0.166 2430 Planarity : 0.005 0.093 2674 Dihedral : 13.796 157.968 2571 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.72 % Allowed : 20.42 % 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: 1.12 (0.19), residues: 1856 helix: 1.18 (0.17), residues: 994 sheet: 0.71 (0.30), residues: 278 loop : 0.18 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.013 0.001 TYR E 329 PHE 0.011 0.001 PHE D 58 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15865) covalent geometry : angle 0.59926 / 0.31 (21613) hydrogen bonds : bond 0.04519 / 2.97 ( 759) hydrogen bonds : angle 4.71434 / 3.26 ( 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 325 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.844 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: 0.8728 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: A 81 LYS cc_start: 0.8687 (mttt) cc_final: 0.8389 (mttt) REVERT: A 83 THR cc_start: 0.9451 (t) cc_final: 0.9216 (m) REVERT: A 198 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8135 (mm-30) REVERT: B 81 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8655 (mmmm) REVERT: B 111 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: B 245 ASP cc_start: 0.8570 (t0) cc_final: 0.8298 (t0) REVERT: C 125 SER cc_start: 0.9007 (m) cc_final: 0.8701 (p) REVERT: C 166 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8106 (m-40) REVERT: C 325 MET cc_start: 0.9135 (mmm) cc_final: 0.8896 (mmm) REVERT: D 79 ASN cc_start: 0.8470 (m-40) cc_final: 0.8255 (m-40) REVERT: D 120 GLU cc_start: 0.8273 (tt0) cc_final: 0.7660 (tm-30) REVERT: D 124 TYR cc_start: 0.7954 (m-10) cc_final: 0.7113 (m-10) REVERT: D 129 ASP cc_start: 0.8019 (m-30) cc_final: 0.7715 (p0) REVERT: D 188 GLU cc_start: 0.8369 (mp0) cc_final: 0.8156 (mp0) REVERT: D 242 LYS cc_start: 0.8348 (tmtt) cc_final: 0.8118 (tmtt) REVERT: E 81 LYS cc_start: 0.8465 (mppt) cc_final: 0.8198 (mmtm) REVERT: E 84 SER cc_start: 0.8975 (p) cc_final: 0.8756 (t) REVERT: E 99 ASN cc_start: 0.8610 (t0) cc_final: 0.8201 (t0) REVERT: E 105 ASP cc_start: 0.8433 (m-30) cc_final: 0.7778 (m-30) REVERT: E 232 GLN cc_start: 0.7613 (mt0) cc_final: 0.6838 (tm-30) REVERT: F 68 MET cc_start: 0.9037 (tpp) cc_final: 0.8767 (tpt) REVERT: F 188 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8089 (tp30) REVERT: F 234 MET cc_start: 0.8173 (tpp) cc_final: 0.7838 (tmm) REVERT: F 291 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7819 (mtp180) REVERT: F 297 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7785 (tmm) outliers start: 27 outliers final: 12 residues processed: 314 average time/residue: 1.6240 time to fit residues: 556.0711 Evaluate side-chains 311 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 294 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 232 GLN 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 144 SER 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: 0.9990 chunk 174 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.076812 restraints weight = 69656.096| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.33 r_work: 0.2802 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15865 Z= 0.158 Angle : 0.616 9.009 21613 Z= 0.317 Chirality : 0.041 0.176 2430 Planarity : 0.005 0.092 2674 Dihedral : 13.824 159.893 2571 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.53 % Allowed : 20.68 % Favored : 77.79 % 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: 1.06 (0.19), residues: 1856 helix: 1.16 (0.17), residues: 994 sheet: 0.68 (0.30), residues: 278 loop : 0.11 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 169 TYR 0.012 0.001 TYR D 131 PHE 0.014 0.001 PHE D 58 HIS 0.008 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15865) covalent geometry : angle 0.61625 / 0.32 (21613) hydrogen bonds : bond 0.04764 / 3.13 ( 759) hydrogen bonds : angle 4.71330 / 3.27 ( 2137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12978.36 seconds wall clock time: 219 minutes 31.65 seconds (13171.65 seconds total)