Starting phenix.real_space_refine on Mon Sep 14 17:44:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbp_13298/09_2026/7pbp_13298_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbp_13298/09_2026/7pbp_13298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbp_13298/09_2026/7pbp_13298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbp_13298/09_2026/7pbp_13298.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbp_13298/09_2026/7pbp_13298_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbp_13298/09_2026/7pbp_13298_neut_trim.cif" } resolution = 3.2 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 45 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3219 1.98 5 H 15818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32077 Number of models: 1 Model: "" Number of chains: 16 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: "G" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 718 Classifications: {'peptide': 48} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 760 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 5.22, per 1000 atoms: 0.16 Number of scatterers: 32077 At special positions: 0 Unit cell: (125.35, 137.34, 106.82, 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 101 16.00 P 45 15.00 Mg 3 11.99 O 3219 8.00 N 2757 7.00 C 10134 6.00 H 15818 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: 2.89 Conformation dependent library (CDL) restraints added in 865.0 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 19 sheets defined 60.3% alpha, 10.5% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 5.24 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.554A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 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: 3.737A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 130 removed outlier: 4.054A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.740A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.645A 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 Processing helix chain 'A' and resid 290 through 298 removed outlier: 3.567A pdb=" N TYR A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.767A 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 Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.641A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.622A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.684A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.829A 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: 3.524A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 232 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.554A pdb=" N TYR B 273 " --> pdb=" O MET B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.567A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.597A 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 31 through 49 Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.700A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 100 removed outlier: 3.618A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 130 removed outlier: 4.291A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 128 " --> pdb=" O TYR C 124 " (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: 3.552A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.923A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.677A 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: 3.819A 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 removed outlier: 3.658A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 removed outlier: 3.674A pdb=" N ALA D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 71 " --> pdb=" O THR D 67 " (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: 3.726A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 122 through 130 removed outlier: 4.039A 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 160 through 164 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.598A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.773A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 234 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 removed outlier: 3.561A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.679A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 removed outlier: 3.513A pdb=" N HIS D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.705A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.648A pdb=" N PHE E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) 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: 3.772A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.678A pdb=" N MET E 115 " --> pdb=" O ILE E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.573A pdb=" N GLU E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.823A 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 Processing helix chain 'E' and resid 202 through 213 Processing helix chain 'E' and resid 216 through 234 removed outlier: 3.538A 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 279 through 287 Processing helix chain 'E' and resid 290 through 298 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: 3.755A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.506A pdb=" N ALA F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) 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 99 removed outlier: 3.791A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.599A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 234 removed outlier: 3.560A pdb=" N ASP F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 251 removed outlier: 3.680A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 273 Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.901A 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 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing helix chain 'H' and resid 159 through 170 Processing helix chain 'H' and resid 173 through 184 removed outlier: 3.836A pdb=" N ILE H 184 " --> pdb=" O MET H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 203 removed outlier: 4.008A pdb=" N ARG H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 202 " --> pdb=" O ALA H 198 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.169A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.670A 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 136 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: 6.542A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.714A 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: 6.338A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.616A 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: 6.135A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.494A 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: 6.800A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.824A 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 200 through 201 removed outlier: 7.036A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 308 through 310 Processing sheet with id=AB8, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.430A pdb=" N LYS F 81 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASP F 110 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR F 83 " --> pdb=" O ASP F 110 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'F' and resid 308 through 310 795 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.06: 15818 1.06 - 1.28: 2720 1.28 - 1.50: 6914 1.50 - 1.72: 6773 1.72 - 1.94: 199 Bond restraints: 32424 Sorted by residual: 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 2.52e+01 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 E 19 " pdb=" H1 THR E 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 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 2.51e+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 ... (remaining 32419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 58266 2.43 - 4.86: 369 4.86 - 7.29: 31 7.29 - 9.71: 18 9.71 - 12.14: 5 Bond angle restraints: 58689 Sorted by residual: angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 110.10 105.48 4.62 1.00e+00 1.00e+00 2.13e+01 angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.00 -3.00 7.00e-01 2.04e+00 1.84e+01 angle pdb=" N3 DT U 6 " pdb=" C4 DT U 6 " pdb=" O4 DT U 6 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " pdb=" O4 DT V 4 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" O1A AGS C 401 " pdb=" PA AGS C 401 " pdb=" O2A AGS C 401 " ideal model delta sigma weight residual 122.09 109.95 12.14 3.00e+00 1.11e-01 1.64e+01 ... (remaining 58684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.30: 14352 28.30 - 56.60: 624 56.60 - 84.89: 110 84.89 - 113.19: 4 113.19 - 141.49: 3 Dihedral angle restraints: 15093 sinusoidal: 8660 harmonic: 6433 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 81.49 -141.49 1 2.00e+01 2.50e-03 4.28e+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 77.02 -137.02 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C5' ADP A 600 " pdb=" O5' ADP A 600 " pdb=" PA ADP A 600 " pdb=" O2A ADP A 600 " ideal model delta sinusoidal sigma weight residual -60.00 -175.99 115.99 1 2.00e+01 2.50e-03 3.45e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2332 0.085 - 0.170: 209 0.170 - 0.255: 5 0.255 - 0.340: 1 0.340 - 0.426: 1 Chirality restraints: 2548 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 -2.76 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.28 2.00e-01 2.50e+01 2.03e+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 ... (remaining 2545 not shown) Planarity restraints: 4701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 160 " 0.386 9.50e-02 1.11e+02 1.34e-01 4.68e+01 pdb=" NE ARG F 160 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG F 160 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 160 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG F 160 " -0.077 2.00e-02 2.50e+03 pdb="HH11 ARG F 160 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 160 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG F 160 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG F 160 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 211 " -0.331 9.50e-02 1.11e+02 1.15e-01 3.60e+01 pdb=" NE ARG F 211 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 211 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG F 211 " 0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG F 211 " 0.067 2.00e-02 2.50e+03 pdb="HH11 ARG F 211 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 211 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG F 211 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG F 211 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.038 2.00e-02 2.50e+03 4.74e-02 3.37e+01 pdb=" CD GLN C 31 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.076 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.002 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.073 2.00e-02 2.50e+03 ... (remaining 4698 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 513 2.10 - 2.72: 52949 2.72 - 3.35: 86156 3.35 - 3.97: 108735 3.97 - 4.60: 176786 Nonbonded interactions: 425139 Sorted by model distance: nonbonded pdb=" HG1 THR F 311 " pdb=" O GLY F 314 " model vdw 1.473 2.450 nonbonded pdb=" HG1 THR E 311 " pdb=" O GLY E 314 " model vdw 1.478 2.450 nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.539 2.450 nonbonded pdb=" OE1 GLU A 299 " pdb="HH11 ARG A 315 " model vdw 1.581 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.590 2.450 ... (remaining 425134 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)) } ncs_group { reference = (chain 'G' and resid 158 through 203) selection = (chain 'H' and resid 158 through 203) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.230 Find NCS groups from input model: 0.810 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: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 16606 Z= 0.267 Angle : 0.795 12.142 22612 Z= 0.457 Chirality : 0.047 0.426 2548 Planarity : 0.010 0.137 2807 Dihedral : 14.951 141.489 6465 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.12 % Allowed : 1.28 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.71 (0.18), residues: 1950 helix: -1.01 (0.14), residues: 1036 sheet: 0.40 (0.29), residues: 320 loop : 0.54 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG B 310 TYR 0.023 0.004 TYR E 131 PHE 0.021 0.003 PHE D 25 HIS 0.017 0.003 HIS F 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.27 (16606) covalent geometry : angle 0.79471 / 0.46 (22612) hydrogen bonds : bond 0.26311 / 17.15 ( 825) hydrogen bonds : angle 8.27970 / 5.97 ( 2334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 0.835 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: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.9122 (mtp) cc_final: 0.8870 (mtp) REVERT: A 252 ASP cc_start: 0.8078 (t0) cc_final: 0.7837 (t0) REVERT: A 325 MET cc_start: 0.8062 (mmm) cc_final: 0.7199 (mmt) REVERT: B 178 MET cc_start: 0.9362 (mmm) cc_final: 0.8849 (mmt) REVERT: C 135 MET cc_start: 0.7184 (mmm) cc_final: 0.6937 (mmm) REVERT: C 199 MET cc_start: 0.7721 (mmt) cc_final: 0.7502 (tpt) REVERT: C 286 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8966 (t0) REVERT: D 114 ARG cc_start: 0.6665 (mtp85) cc_final: 0.6446 (mtt180) REVERT: D 232 GLN cc_start: 0.8328 (pt0) cc_final: 0.8127 (pt0) REVERT: E 65 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8631 (mtpt) REVERT: E 100 ASP cc_start: 0.7475 (t0) cc_final: 0.7143 (t0) REVERT: E 147 LEU cc_start: 0.6900 (mt) cc_final: 0.6563 (mt) REVERT: E 234 MET cc_start: 0.7845 (tpp) cc_final: 0.7606 (mmm) REVERT: F 298 TYR cc_start: 0.8033 (m-80) cc_final: 0.7730 (m-80) REVERT: F 309 MET cc_start: 0.7923 (ttt) cc_final: 0.7658 (mtp) REVERT: G 203 LEU cc_start: 0.7164 (tp) cc_final: 0.6136 (tp) REVERT: H 197 ASP cc_start: 0.7583 (m-30) cc_final: 0.7231 (m-30) REVERT: H 203 LEU cc_start: 0.8130 (tp) cc_final: 0.7924 (tt) outliers start: 2 outliers final: 0 residues processed: 422 average time/residue: 0.3683 time to fit residues: 215.2585 Evaluate side-chains 265 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 HIS B 166 ASN C 99 ASN C 166 ASN D 79 ASN E 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085359 restraints weight = 73630.714| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.35 r_work: 0.2756 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16606 Z= 0.171 Angle : 0.661 6.386 22612 Z= 0.361 Chirality : 0.043 0.164 2548 Planarity : 0.006 0.070 2807 Dihedral : 13.978 135.579 2652 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.16 % Allowed : 5.85 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.39 (0.18), residues: 1950 helix: 0.20 (0.15), residues: 1056 sheet: 1.03 (0.33), residues: 268 loop : 0.33 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 171 TYR 0.011 0.001 TYR D 131 PHE 0.008 0.001 PHE C 25 HIS 0.003 0.001 HIS E 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (16606) covalent geometry : angle 0.66081 / 0.36 (22612) hydrogen bonds : bond 0.08069 / 5.31 ( 825) hydrogen bonds : angle 5.97117 / 4.31 ( 2334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 269 time to evaluate : 0.925 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 252 ASP cc_start: 0.8634 (t0) cc_final: 0.8317 (t0) REVERT: B 100 ASP cc_start: 0.8232 (m-30) cc_final: 0.7749 (t0) REVERT: D 135 MET cc_start: 0.7358 (mtm) cc_final: 0.6870 (ptm) REVERT: E 100 ASP cc_start: 0.7942 (t0) cc_final: 0.7702 (t0) REVERT: E 234 MET cc_start: 0.8338 (tpp) cc_final: 0.8097 (mmm) REVERT: F 268 THR cc_start: 0.7197 (m) cc_final: 0.6877 (m) REVERT: F 309 MET cc_start: 0.8226 (ttt) cc_final: 0.7917 (mtp) REVERT: G 183 LYS cc_start: 0.8591 (tttt) cc_final: 0.8349 (tppt) REVERT: G 203 LEU cc_start: 0.7326 (tp) cc_final: 0.6768 (tp) REVERT: H 197 ASP cc_start: 0.7845 (m-30) cc_final: 0.7511 (m-30) REVERT: H 203 LEU cc_start: 0.7856 (tp) cc_final: 0.7613 (tt) outliers start: 19 outliers final: 11 residues processed: 276 average time/residue: 0.3265 time to fit residues: 130.9134 Evaluate side-chains 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 251 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 HIS D 79 ASN D 232 GLN E 255 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.085548 restraints weight = 73560.884| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.13 r_work: 0.2839 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 16606 Z= 0.210 Angle : 0.609 6.567 22612 Z= 0.327 Chirality : 0.042 0.141 2548 Planarity : 0.005 0.043 2807 Dihedral : 13.819 145.903 2650 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.28 % Allowed : 6.76 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.56 (0.19), residues: 1950 helix: 0.60 (0.16), residues: 1057 sheet: 0.77 (0.32), residues: 267 loop : 0.05 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 160 TYR 0.009 0.001 TYR D 24 PHE 0.009 0.001 PHE C 25 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (16606) covalent geometry : angle 0.60907 / 0.33 (22612) hydrogen bonds : bond 0.07213 / 4.77 ( 825) hydrogen bonds : angle 5.38168 / 3.88 ( 2334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8008 (mt-10) REVERT: A 252 ASP cc_start: 0.8640 (t0) cc_final: 0.8294 (t0) REVERT: A 291 ARG cc_start: 0.7999 (tpp80) cc_final: 0.7609 (ttt90) REVERT: C 199 MET cc_start: 0.8279 (tpt) cc_final: 0.8003 (tpt) REVERT: D 58 PHE cc_start: 0.8366 (m-80) cc_final: 0.8128 (m-80) REVERT: D 98 LEU cc_start: 0.8990 (mt) cc_final: 0.8732 (tp) REVERT: D 135 MET cc_start: 0.7289 (mtm) cc_final: 0.6875 (ptm) REVERT: E 100 ASP cc_start: 0.7936 (t0) cc_final: 0.7674 (t0) REVERT: F 309 MET cc_start: 0.8266 (ttt) cc_final: 0.7850 (mtp) REVERT: H 197 ASP cc_start: 0.7962 (m-30) cc_final: 0.7708 (m-30) REVERT: H 203 LEU cc_start: 0.7870 (tp) cc_final: 0.7643 (tt) outliers start: 21 outliers final: 16 residues processed: 254 average time/residue: 0.3189 time to fit residues: 118.8562 Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 134 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 ASN D 232 GLN D 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.087220 restraints weight = 73440.377| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.30 r_work: 0.2845 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16606 Z= 0.134 Angle : 0.555 6.466 22612 Z= 0.293 Chirality : 0.040 0.155 2548 Planarity : 0.004 0.043 2807 Dihedral : 13.660 147.991 2650 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.28 % Allowed : 6.76 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1950 helix: 0.92 (0.16), residues: 1057 sheet: 0.80 (0.32), residues: 265 loop : 0.05 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 48 TYR 0.009 0.001 TYR F 230 PHE 0.006 0.001 PHE C 108 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16606) covalent geometry : angle 0.55462 / 0.29 (22612) hydrogen bonds : bond 0.05450 / 3.60 ( 825) hydrogen bonds : angle 4.99257 / 3.60 ( 2334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7986 (mt-10) REVERT: A 252 ASP cc_start: 0.8657 (t0) cc_final: 0.8350 (t0) REVERT: A 291 ARG cc_start: 0.7969 (tpp80) cc_final: 0.7687 (ttt90) REVERT: B 100 ASP cc_start: 0.8268 (m-30) cc_final: 0.7792 (t0) REVERT: C 199 MET cc_start: 0.8250 (tpt) cc_final: 0.8006 (tpt) REVERT: D 98 LEU cc_start: 0.8994 (mt) cc_final: 0.8716 (tp) REVERT: D 135 MET cc_start: 0.7312 (mtm) cc_final: 0.6868 (ptm) REVERT: E 100 ASP cc_start: 0.8008 (t0) cc_final: 0.7741 (t0) REVERT: F 268 THR cc_start: 0.7231 (m) cc_final: 0.7028 (m) REVERT: F 309 MET cc_start: 0.8223 (ttt) cc_final: 0.7795 (mtp) REVERT: G 183 LYS cc_start: 0.8581 (tttt) cc_final: 0.8278 (tppt) REVERT: H 197 ASP cc_start: 0.7967 (m-30) cc_final: 0.7703 (m-30) REVERT: H 203 LEU cc_start: 0.7732 (tp) cc_final: 0.7514 (tt) outliers start: 21 outliers final: 15 residues processed: 260 average time/residue: 0.2966 time to fit residues: 114.0447 Evaluate side-chains 256 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 178 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 113 HIS D 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.086563 restraints weight = 73690.604| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.23 r_work: 0.2855 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16606 Z= 0.148 Angle : 0.542 6.548 22612 Z= 0.287 Chirality : 0.040 0.212 2548 Planarity : 0.005 0.042 2807 Dihedral : 13.605 150.714 2650 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.22 % Allowed : 7.68 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.96 (0.19), residues: 1950 helix: 1.06 (0.16), residues: 1057 sheet: 0.77 (0.32), residues: 265 loop : 0.05 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 143 TYR 0.008 0.001 TYR D 131 PHE 0.007 0.001 PHE C 108 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (16606) covalent geometry : angle 0.54248 / 0.29 (22612) hydrogen bonds : bond 0.05334 / 3.53 ( 825) hydrogen bonds : angle 4.89400 / 3.53 ( 2334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8043 (mt-10) REVERT: A 252 ASP cc_start: 0.8702 (t0) cc_final: 0.8412 (t0) REVERT: A 291 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7749 (ttt90) REVERT: B 100 ASP cc_start: 0.8293 (m-30) cc_final: 0.8055 (p0) REVERT: D 81 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7724 (mptt) REVERT: D 98 LEU cc_start: 0.8991 (mt) cc_final: 0.8711 (tp) REVERT: D 135 MET cc_start: 0.7344 (mtm) cc_final: 0.6872 (ptm) REVERT: F 268 THR cc_start: 0.7170 (m) cc_final: 0.6963 (m) REVERT: F 309 MET cc_start: 0.8173 (ttt) cc_final: 0.7725 (mtp) REVERT: G 183 LYS cc_start: 0.8593 (tttt) cc_final: 0.8334 (tppt) REVERT: H 197 ASP cc_start: 0.7988 (m-30) cc_final: 0.7727 (m-30) REVERT: H 203 LEU cc_start: 0.7684 (tp) cc_final: 0.7475 (tt) outliers start: 20 outliers final: 15 residues processed: 253 average time/residue: 0.3014 time to fit residues: 111.3249 Evaluate side-chains 258 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 8 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 142 optimal weight: 0.4980 chunk 149 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 ASN D 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087598 restraints weight = 73373.935| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.29 r_work: 0.2860 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16606 Z= 0.119 Angle : 0.520 6.587 22612 Z= 0.273 Chirality : 0.039 0.152 2548 Planarity : 0.004 0.041 2807 Dihedral : 13.510 150.932 2650 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.10 % Allowed : 8.35 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.19 (0.19), residues: 1950 helix: 1.29 (0.16), residues: 1054 sheet: 0.76 (0.32), residues: 263 loop : 0.11 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 143 TYR 0.009 0.001 TYR F 329 PHE 0.006 0.001 PHE C 108 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16606) covalent geometry : angle 0.51992 / 0.27 (22612) hydrogen bonds : bond 0.04677 / 3.10 ( 825) hydrogen bonds : angle 4.71039 / 3.40 ( 2334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8023 (mt-10) REVERT: A 252 ASP cc_start: 0.8661 (t0) cc_final: 0.8368 (t0) REVERT: B 100 ASP cc_start: 0.8278 (m-30) cc_final: 0.8067 (p0) REVERT: B 292 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8224 (mp0) REVERT: D 81 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7727 (mptt) REVERT: D 98 LEU cc_start: 0.9017 (mt) cc_final: 0.8723 (tp) REVERT: D 135 MET cc_start: 0.7265 (mtm) cc_final: 0.6794 (ptm) REVERT: D 160 ARG cc_start: 0.8529 (mtp180) cc_final: 0.8115 (mtm-85) REVERT: F 309 MET cc_start: 0.8145 (ttt) cc_final: 0.7759 (mtp) REVERT: G 183 LYS cc_start: 0.8605 (tttt) cc_final: 0.8331 (tppt) REVERT: H 197 ASP cc_start: 0.7978 (m-30) cc_final: 0.7727 (m-30) REVERT: H 203 LEU cc_start: 0.7564 (tp) cc_final: 0.7358 (tt) outliers start: 18 outliers final: 13 residues processed: 253 average time/residue: 0.3234 time to fit residues: 118.8738 Evaluate side-chains 255 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 ASN E 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.086441 restraints weight = 74185.593| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.25 r_work: 0.2845 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16606 Z= 0.165 Angle : 0.541 6.691 22612 Z= 0.286 Chirality : 0.040 0.228 2548 Planarity : 0.004 0.042 2807 Dihedral : 13.533 154.092 2650 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.10 % Allowed : 8.59 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.14 (0.19), residues: 1950 helix: 1.30 (0.16), residues: 1051 sheet: 0.72 (0.32), residues: 263 loop : 0.01 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 143 TYR 0.014 0.001 TYR C 124 PHE 0.007 0.001 PHE C 108 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (16606) covalent geometry : angle 0.54080 / 0.29 (22612) hydrogen bonds : bond 0.05006 / 3.32 ( 825) hydrogen bonds : angle 4.72458 / 3.41 ( 2334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.940 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 111 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8088 (mt-10) REVERT: A 252 ASP cc_start: 0.8730 (t0) cc_final: 0.8408 (t0) REVERT: B 100 ASP cc_start: 0.8304 (m-30) cc_final: 0.8102 (p0) REVERT: B 292 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8220 (mp0) REVERT: D 81 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7749 (mptt) REVERT: D 98 LEU cc_start: 0.9018 (mt) cc_final: 0.8790 (tp) REVERT: D 135 MET cc_start: 0.7272 (mtm) cc_final: 0.6796 (ptm) REVERT: F 309 MET cc_start: 0.8125 (ttt) cc_final: 0.7724 (mtp) REVERT: G 183 LYS cc_start: 0.8603 (tttt) cc_final: 0.8357 (tppt) REVERT: H 197 ASP cc_start: 0.7974 (m-30) cc_final: 0.7725 (m-30) outliers start: 18 outliers final: 17 residues processed: 245 average time/residue: 0.3333 time to fit residues: 118.6189 Evaluate side-chains 256 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 20 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 286 ASN D 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.086545 restraints weight = 73893.865| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.20 r_work: 0.2845 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16606 Z= 0.138 Angle : 0.528 6.518 22612 Z= 0.276 Chirality : 0.040 0.153 2548 Planarity : 0.004 0.042 2807 Dihedral : 13.522 155.143 2650 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.28 % Allowed : 8.96 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.19 (0.19), residues: 1950 helix: 1.36 (0.16), residues: 1053 sheet: 0.73 (0.32), residues: 266 loop : -0.01 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 143 TYR 0.026 0.001 TYR C 124 PHE 0.007 0.001 PHE C 108 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16606) covalent geometry : angle 0.52801 / 0.28 (22612) hydrogen bonds : bond 0.04806 / 3.19 ( 825) hydrogen bonds : angle 4.66246 / 3.36 ( 2334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.910 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 111 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8097 (mt-10) REVERT: A 252 ASP cc_start: 0.8727 (t0) cc_final: 0.8426 (t0) REVERT: B 100 ASP cc_start: 0.8300 (m-30) cc_final: 0.8098 (p0) REVERT: B 292 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8228 (mp0) REVERT: D 81 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7716 (mptt) REVERT: D 135 MET cc_start: 0.7234 (mtm) cc_final: 0.6715 (ptm) REVERT: D 160 ARG cc_start: 0.8497 (mtp180) cc_final: 0.8097 (mtm-85) REVERT: F 309 MET cc_start: 0.8133 (ttt) cc_final: 0.7732 (mtp) REVERT: G 183 LYS cc_start: 0.8616 (tttt) cc_final: 0.8371 (tppt) REVERT: H 197 ASP cc_start: 0.7977 (m-30) cc_final: 0.7732 (m-30) outliers start: 21 outliers final: 19 residues processed: 246 average time/residue: 0.3365 time to fit residues: 120.5954 Evaluate side-chains 255 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 108 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 ASN E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.086743 restraints weight = 73597.157| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.23 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16606 Z= 0.133 Angle : 0.527 6.511 22612 Z= 0.275 Chirality : 0.039 0.151 2548 Planarity : 0.004 0.041 2807 Dihedral : 13.512 155.361 2650 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.28 % Allowed : 8.96 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.26 (0.19), residues: 1950 helix: 1.43 (0.16), residues: 1053 sheet: 0.73 (0.32), residues: 266 loop : 0.01 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 143 TYR 0.022 0.001 TYR C 124 PHE 0.006 0.001 PHE C 108 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16606) covalent geometry : angle 0.52672 / 0.28 (22612) hydrogen bonds : bond 0.04660 / 3.09 ( 825) hydrogen bonds : angle 4.62857 / 3.33 ( 2334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.031 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 111 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8121 (mt-10) REVERT: A 252 ASP cc_start: 0.8731 (t0) cc_final: 0.8429 (t0) REVERT: B 100 ASP cc_start: 0.8334 (m-30) cc_final: 0.8116 (p0) REVERT: B 292 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8226 (mp0) REVERT: D 81 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7717 (mptt) REVERT: D 135 MET cc_start: 0.7263 (mtm) cc_final: 0.6771 (ptm) REVERT: D 160 ARG cc_start: 0.8515 (mtp180) cc_final: 0.8096 (mtm-85) REVERT: F 222 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7658 (mtp85) REVERT: F 309 MET cc_start: 0.8138 (ttt) cc_final: 0.7724 (mtp) REVERT: G 183 LYS cc_start: 0.8605 (tttt) cc_final: 0.8365 (tppt) REVERT: H 197 ASP cc_start: 0.7974 (m-30) cc_final: 0.7730 (m-30) outliers start: 21 outliers final: 19 residues processed: 243 average time/residue: 0.3279 time to fit residues: 117.0039 Evaluate side-chains 256 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 148 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 124 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 ASN E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.087847 restraints weight = 73439.904| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.19 r_work: 0.2866 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16606 Z= 0.118 Angle : 0.515 6.357 22612 Z= 0.269 Chirality : 0.039 0.172 2548 Planarity : 0.004 0.042 2807 Dihedral : 13.470 154.067 2650 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.16 % Allowed : 9.02 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.38 (0.19), residues: 1950 helix: 1.52 (0.16), residues: 1053 sheet: 0.75 (0.32), residues: 266 loop : 0.08 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 143 TYR 0.025 0.001 TYR C 124 PHE 0.006 0.001 PHE C 108 HIS 0.003 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16606) covalent geometry : angle 0.51536 / 0.27 (22612) hydrogen bonds : bond 0.04379 / 2.90 ( 825) hydrogen bonds : angle 4.56238 / 3.29 ( 2334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.892 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 111 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8131 (mt-10) REVERT: A 252 ASP cc_start: 0.8704 (t0) cc_final: 0.8409 (t0) REVERT: B 292 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8219 (mp0) REVERT: D 81 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7711 (mptt) REVERT: D 135 MET cc_start: 0.7128 (mtm) cc_final: 0.6756 (ptm) REVERT: D 160 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8017 (mtm-85) REVERT: F 222 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7772 (mtp85) REVERT: F 309 MET cc_start: 0.8114 (ttt) cc_final: 0.7831 (mtp) REVERT: G 183 LYS cc_start: 0.8597 (tttt) cc_final: 0.8371 (tppt) REVERT: H 197 ASP cc_start: 0.7968 (m-30) cc_final: 0.7727 (m-30) outliers start: 19 outliers final: 17 residues processed: 245 average time/residue: 0.3279 time to fit residues: 117.7301 Evaluate side-chains 250 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 191 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 ASN E 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.084737 restraints weight = 74296.324| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.25 r_work: 0.2816 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.006 0.041 16606 Z= 0.238 Angle : 0.588 6.427 22612 Z= 0.310 Chirality : 0.042 0.145 2548 Planarity : 0.005 0.050 2807 Dihedral : 13.650 161.543 2650 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.10 % Allowed : 9.32 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.97 (0.19), residues: 1950 helix: 1.27 (0.16), residues: 1056 sheet: 0.46 (0.31), residues: 268 loop : -0.22 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 114 TYR 0.025 0.001 TYR C 124 PHE 0.011 0.002 PHE C 108 HIS 0.006 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (16606) covalent geometry : angle 0.58757 / 0.31 (22612) hydrogen bonds : bond 0.05673 / 3.76 ( 825) hydrogen bonds : angle 4.73416 / 3.41 ( 2334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8302.42 seconds wall clock time: 141 minutes 10.13 seconds (8470.13 seconds total)