Starting phenix.real_space_refine on Fri Sep 19 03:38:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6acf_9590/09_2025/6acf_9590.cif Found real_map, /net/cci-nas-00/data/ceres_data/6acf_9590/09_2025/6acf_9590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6acf_9590/09_2025/6acf_9590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6acf_9590/09_2025/6acf_9590.map" model { file = "/net/cci-nas-00/data/ceres_data/6acf_9590/09_2025/6acf_9590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6acf_9590/09_2025/6acf_9590.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 14512 2.51 5 N 4152 2.21 5 O 4344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23144 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 3.33, per 1000 atoms: 0.14 Number of scatterers: 23144 At special positions: 0 Unit cell: (126.896, 126.896, 119.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 4344 8.00 N 4152 7.00 C 14512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 1.4 microseconds 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5408 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 12 sheets defined 51.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL A 209 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.725A pdb=" N GLN A 250 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 297 through 300 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 72 removed outlier: 4.187A pdb=" N ALA B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA B 149 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.724A pdb=" N GLN B 250 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 300 Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 350 " --> pdb=" O MET B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR C 10 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 removed outlier: 4.046A pdb=" N PHE C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA C 149 " --> pdb=" O ASN C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL C 209 " --> pdb=" O ASN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.724A pdb=" N GLN C 250 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 297 through 300 Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 312 through 328 Processing helix chain 'C' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR D 10 " --> pdb=" O TYR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA D 149 " --> pdb=" O ASN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL D 209 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.725A pdb=" N GLN D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 297 through 300 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 312 through 328 Processing helix chain 'D' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 350 " --> pdb=" O MET D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR E 10 " --> pdb=" O TYR E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL E 209 " --> pdb=" O ASN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.723A pdb=" N GLN E 250 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY E 270 " --> pdb=" O GLU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE E 286 " --> pdb=" O PRO E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 297 through 300 Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 312 through 328 Processing helix chain 'E' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG E 350 " --> pdb=" O MET E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA F 54 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL F 209 " --> pdb=" O ASN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.723A pdb=" N GLN F 250 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY F 270 " --> pdb=" O GLU F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE F 286 " --> pdb=" O PRO F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 297 through 300 Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 312 through 328 Processing helix chain 'F' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP F 336 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG F 350 " --> pdb=" O MET F 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR G 10 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA G 54 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 145 through 167 removed outlier: 4.020A pdb=" N ALA G 149 " --> pdb=" O ASN G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 196 Processing helix chain 'G' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL G 209 " --> pdb=" O ASN G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 251 removed outlier: 3.724A pdb=" N GLN G 250 " --> pdb=" O THR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE G 286 " --> pdb=" O PRO G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 297 through 300 Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 312 through 328 Processing helix chain 'G' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP G 336 " --> pdb=" O TYR G 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG G 350 " --> pdb=" O MET G 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR H 10 " --> pdb=" O TYR H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA H 54 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE H 96 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 Processing helix chain 'H' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA H 149 " --> pdb=" O ASN H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 196 Processing helix chain 'H' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL H 209 " --> pdb=" O ASN H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 251 removed outlier: 3.726A pdb=" N GLN H 250 " --> pdb=" O THR H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 277 removed outlier: 3.722A pdb=" N GLY H 270 " --> pdb=" O GLU H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE H 286 " --> pdb=" O PRO H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 297 through 300 Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 312 through 328 Processing helix chain 'H' and resid 330 through 350 removed outlier: 3.775A pdb=" N ASP H 336 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG H 350 " --> pdb=" O MET H 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 114 removed outlier: 6.086A pdb=" N ALA A 39 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA A 113 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY A 41 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 40 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR A 81 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY A 42 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE A 83 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG A 44 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 78 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS A 26 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS B 26 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY B 78 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU B 40 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR B 81 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY B 42 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE B 83 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA B 39 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA B 113 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 41 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 6.404A pdb=" N VAL A 175 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA A 235 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 177 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.404A pdb=" N VAL B 175 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA B 235 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 177 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 110 through 114 removed outlier: 6.086A pdb=" N ALA C 39 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA C 113 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY C 41 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU C 40 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR C 81 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY C 42 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE C 83 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG C 44 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY C 78 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS C 26 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS D 26 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY D 78 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU D 40 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR D 81 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY D 42 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE D 83 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG D 44 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA D 39 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA D 113 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY D 41 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 198 through 202 removed outlier: 6.404A pdb=" N VAL C 175 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA C 235 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA C 177 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 202 removed outlier: 6.404A pdb=" N VAL D 175 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA D 235 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA D 177 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 110 through 114 removed outlier: 6.086A pdb=" N ALA E 39 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA E 113 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY E 41 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU E 40 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR E 81 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY E 42 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE E 83 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG E 44 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY E 78 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS E 26 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS F 26 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY F 78 " --> pdb=" O HIS F 32 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU F 40 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR F 81 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY F 42 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE F 83 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG F 44 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA F 39 " --> pdb=" O ILE F 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA F 113 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY F 41 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 198 through 202 removed outlier: 6.403A pdb=" N VAL E 175 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA E 235 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA E 177 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 198 through 202 removed outlier: 6.403A pdb=" N VAL F 175 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA F 235 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA F 177 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 110 through 114 removed outlier: 6.086A pdb=" N ALA G 39 " --> pdb=" O ILE G 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA G 113 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY G 41 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU G 40 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR G 81 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY G 42 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE G 83 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG G 44 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY G 78 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS G 26 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS H 26 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY H 78 " --> pdb=" O HIS H 32 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU H 40 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR H 81 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY H 42 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE H 83 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG H 44 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA H 39 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA H 113 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY H 41 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 198 through 202 removed outlier: 6.403A pdb=" N VAL G 175 " --> pdb=" O ILE G 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA G 235 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA G 177 " --> pdb=" O ALA G 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 198 through 202 removed outlier: 6.403A pdb=" N VAL H 175 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA H 235 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA H 177 " --> pdb=" O ALA H 235 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7242 1.34 - 1.45: 3517 1.45 - 1.57: 12585 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 23584 Sorted by residual: bond pdb=" C MET F 123 " pdb=" N ASP F 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 bond pdb=" C MET E 123 " pdb=" N ASP E 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 bond pdb=" C MET G 123 " pdb=" N ASP G 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 bond pdb=" C MET C 123 " pdb=" N ASP C 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 bond pdb=" C MET D 123 " pdb=" N ASP D 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 ... (remaining 23579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 30157 1.84 - 3.69: 1368 3.69 - 5.53: 211 5.53 - 7.38: 72 7.38 - 9.22: 32 Bond angle restraints: 31840 Sorted by residual: angle pdb=" N ASP B 124 " pdb=" CA ASP B 124 " pdb=" C ASP B 124 " ideal model delta sigma weight residual 114.62 110.15 4.47 1.14e+00 7.69e-01 1.54e+01 angle pdb=" N ASP F 124 " pdb=" CA ASP F 124 " pdb=" C ASP F 124 " ideal model delta sigma weight residual 114.62 110.18 4.44 1.14e+00 7.69e-01 1.52e+01 angle pdb=" N ASP D 124 " pdb=" CA ASP D 124 " pdb=" C ASP D 124 " ideal model delta sigma weight residual 114.62 110.18 4.44 1.14e+00 7.69e-01 1.52e+01 angle pdb=" N ASP E 124 " pdb=" CA ASP E 124 " pdb=" C ASP E 124 " ideal model delta sigma weight residual 114.62 110.18 4.44 1.14e+00 7.69e-01 1.52e+01 angle pdb=" N ASP H 124 " pdb=" CA ASP H 124 " pdb=" C ASP H 124 " ideal model delta sigma weight residual 114.62 110.18 4.44 1.14e+00 7.69e-01 1.52e+01 ... (remaining 31835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.38: 12988 11.38 - 22.76: 1019 22.76 - 34.14: 265 34.14 - 45.53: 80 45.53 - 56.91: 56 Dihedral angle restraints: 14408 sinusoidal: 5832 harmonic: 8576 Sorted by residual: dihedral pdb=" CA VAL F 120 " pdb=" C VAL F 120 " pdb=" N ALA F 121 " pdb=" CA ALA F 121 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL D 120 " pdb=" C VAL D 120 " pdb=" N ALA D 121 " pdb=" CA ALA D 121 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL E 120 " pdb=" C VAL E 120 " pdb=" N ALA E 121 " pdb=" CA ALA E 121 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 14405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1757 0.037 - 0.074: 996 0.074 - 0.111: 492 0.111 - 0.148: 138 0.148 - 0.185: 33 Chirality restraints: 3416 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CG LEU D 25 " pdb=" CB LEU D 25 " pdb=" CD1 LEU D 25 " pdb=" CD2 LEU D 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 3413 not shown) Planarity restraints: 4240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 102 " -0.014 2.00e-02 2.50e+03 1.76e-02 5.41e+00 pdb=" CG PHE B 102 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 102 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 102 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 102 " -0.014 2.00e-02 2.50e+03 1.76e-02 5.41e+00 pdb=" CG PHE G 102 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE G 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE G 102 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE G 102 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE G 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 102 " -0.014 2.00e-02 2.50e+03 1.76e-02 5.41e+00 pdb=" CG PHE A 102 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 102 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 102 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 102 " -0.001 2.00e-02 2.50e+03 ... (remaining 4237 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6114 2.80 - 3.33: 19843 3.33 - 3.85: 38006 3.85 - 4.38: 45219 4.38 - 4.90: 79681 Nonbonded interactions: 188863 Sorted by model distance: nonbonded pdb=" OH TYR A 48 " pdb=" OD2 ASP A 57 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR B 48 " pdb=" OD2 ASP B 57 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR D 48 " pdb=" OD2 ASP D 57 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR G 48 " pdb=" OD2 ASP G 57 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR E 48 " pdb=" OD2 ASP E 57 " model vdw 2.281 3.040 ... (remaining 188858 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=0.98 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.650 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 23584 Z= 0.323 Angle : 0.955 9.222 31840 Z= 0.521 Chirality : 0.057 0.185 3416 Planarity : 0.007 0.056 4240 Dihedral : 10.115 56.906 9000 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.68 % Allowed : 3.34 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.31 (0.12), residues: 2968 helix: -2.16 (0.10), residues: 1408 sheet: -1.33 (0.23), residues: 464 loop : -2.38 (0.15), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 364 TYR 0.021 0.004 TYR G 299 PHE 0.040 0.005 PHE B 102 TRP 0.005 0.001 TRP D 46 HIS 0.010 0.002 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00778 (23584) covalent geometry : angle 0.95470 (31840) hydrogen bonds : bond 0.14216 ( 1152) hydrogen bonds : angle 7.23719 ( 3336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 0.797 Fit side-chains REVERT: A 46 TRP cc_start: 0.7813 (t-100) cc_final: 0.7450 (t-100) REVERT: A 263 GLN cc_start: 0.8858 (mt0) cc_final: 0.8628 (mt0) REVERT: A 303 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7389 (mmt180) REVERT: B 46 TRP cc_start: 0.7817 (t-100) cc_final: 0.7453 (t-100) REVERT: B 263 GLN cc_start: 0.8859 (mt0) cc_final: 0.8629 (mt0) REVERT: B 303 ARG cc_start: 0.7891 (tpt170) cc_final: 0.7386 (mmt180) REVERT: C 46 TRP cc_start: 0.7815 (t-100) cc_final: 0.7449 (t-100) REVERT: C 263 GLN cc_start: 0.8861 (mt0) cc_final: 0.8630 (mt0) REVERT: C 303 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7386 (mmt180) REVERT: D 46 TRP cc_start: 0.7814 (t-100) cc_final: 0.7452 (t-100) REVERT: D 263 GLN cc_start: 0.8859 (mt0) cc_final: 0.8628 (mt0) REVERT: D 303 ARG cc_start: 0.7891 (tpt170) cc_final: 0.7387 (mmt180) REVERT: E 46 TRP cc_start: 0.7814 (t-100) cc_final: 0.7448 (t-100) REVERT: E 263 GLN cc_start: 0.8859 (mt0) cc_final: 0.8626 (mt0) REVERT: E 303 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7384 (mmt180) REVERT: F 46 TRP cc_start: 0.7813 (t-100) cc_final: 0.7450 (t-100) REVERT: F 263 GLN cc_start: 0.8859 (mt0) cc_final: 0.8626 (mt0) REVERT: F 303 ARG cc_start: 0.7895 (tpt170) cc_final: 0.7389 (mmt180) REVERT: G 46 TRP cc_start: 0.7817 (t-100) cc_final: 0.7449 (t-100) REVERT: G 263 GLN cc_start: 0.8860 (mt0) cc_final: 0.8627 (mt0) REVERT: G 303 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7389 (mmt180) REVERT: H 46 TRP cc_start: 0.7815 (t-100) cc_final: 0.7452 (t-100) REVERT: H 263 GLN cc_start: 0.8857 (mt0) cc_final: 0.8652 (mt0) REVERT: H 303 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7392 (mmt180) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.5978 time to fit residues: 406.5654 Evaluate side-chains 376 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 261 ASN A 293 ASN A 316 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 224 ASN B 261 ASN B 293 ASN B 316 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN C 261 ASN C 293 ASN C 316 ASN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 261 ASN D 293 ASN D 316 ASN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 261 ASN E 293 ASN E 316 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 261 ASN F 293 ASN F 316 ASN ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 261 ASN G 293 ASN G 316 ASN ** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN H 261 ASN H 293 ASN H 316 ASN ** H 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.188884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122089 restraints weight = 116277.138| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 5.23 r_work: 0.2871 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23584 Z= 0.122 Angle : 0.566 5.603 31840 Z= 0.306 Chirality : 0.043 0.138 3416 Planarity : 0.004 0.039 4240 Dihedral : 5.127 28.488 3392 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.03 % Allowed : 11.53 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.14), residues: 2968 helix: -0.09 (0.12), residues: 1456 sheet: -0.86 (0.23), residues: 456 loop : -2.02 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 364 TYR 0.016 0.002 TYR G 314 PHE 0.014 0.002 PHE C 102 TRP 0.001 0.000 TRP B 46 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00264 (23584) covalent geometry : angle 0.56553 (31840) hydrogen bonds : bond 0.04265 ( 1152) hydrogen bonds : angle 5.35077 ( 3336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 483 time to evaluate : 0.723 Fit side-chains REVERT: A 14 GLN cc_start: 0.9131 (mt0) cc_final: 0.8907 (mt0) REVERT: A 46 TRP cc_start: 0.8514 (t-100) cc_final: 0.8091 (t-100) REVERT: A 47 MET cc_start: 0.8583 (tpt) cc_final: 0.8363 (tpp) REVERT: A 115 ASP cc_start: 0.8770 (t70) cc_final: 0.8053 (t0) REVERT: A 262 ASN cc_start: 0.7648 (m-40) cc_final: 0.7304 (m-40) REVERT: A 303 ARG cc_start: 0.6976 (tpt170) cc_final: 0.5778 (mmt180) REVERT: A 305 ARG cc_start: 0.7186 (ttp-110) cc_final: 0.6780 (ttp-110) REVERT: A 311 GLU cc_start: 0.7167 (tt0) cc_final: 0.6867 (mt-10) REVERT: A 355 GLN cc_start: 0.9153 (pt0) cc_final: 0.8845 (pt0) REVERT: B 14 GLN cc_start: 0.9131 (mt0) cc_final: 0.8905 (mt0) REVERT: B 46 TRP cc_start: 0.8502 (t-100) cc_final: 0.7978 (t-100) REVERT: B 47 MET cc_start: 0.8589 (tpt) cc_final: 0.8266 (tpp) REVERT: B 115 ASP cc_start: 0.8761 (t70) cc_final: 0.8040 (t0) REVERT: B 262 ASN cc_start: 0.7658 (m-40) cc_final: 0.7317 (m-40) REVERT: B 303 ARG cc_start: 0.6988 (tpt170) cc_final: 0.5782 (mmt180) REVERT: B 305 ARG cc_start: 0.7194 (ttp-110) cc_final: 0.6789 (ttp-110) REVERT: B 311 GLU cc_start: 0.7188 (tt0) cc_final: 0.6887 (mt-10) REVERT: B 355 GLN cc_start: 0.9153 (pt0) cc_final: 0.8834 (pt0) REVERT: C 14 GLN cc_start: 0.9132 (mt0) cc_final: 0.8904 (mt0) REVERT: C 46 TRP cc_start: 0.8503 (t-100) cc_final: 0.8086 (t-100) REVERT: C 47 MET cc_start: 0.8572 (tpt) cc_final: 0.8356 (tpp) REVERT: C 115 ASP cc_start: 0.8761 (t70) cc_final: 0.8040 (t0) REVERT: C 262 ASN cc_start: 0.7638 (m-40) cc_final: 0.7296 (m-40) REVERT: C 303 ARG cc_start: 0.6985 (tpt170) cc_final: 0.5784 (mmt180) REVERT: C 305 ARG cc_start: 0.7197 (ttp-110) cc_final: 0.6788 (ttp-110) REVERT: C 311 GLU cc_start: 0.7177 (tt0) cc_final: 0.6879 (mt-10) REVERT: C 355 GLN cc_start: 0.9156 (pt0) cc_final: 0.8842 (pt0) REVERT: D 14 GLN cc_start: 0.9128 (mt0) cc_final: 0.8903 (mt0) REVERT: D 46 TRP cc_start: 0.8513 (t-100) cc_final: 0.8091 (t-100) REVERT: D 47 MET cc_start: 0.8592 (tpt) cc_final: 0.8373 (tpp) REVERT: D 115 ASP cc_start: 0.8761 (t70) cc_final: 0.8034 (t0) REVERT: D 262 ASN cc_start: 0.7653 (m-40) cc_final: 0.7308 (m-40) REVERT: D 303 ARG cc_start: 0.6979 (tpt170) cc_final: 0.5767 (mmt180) REVERT: D 305 ARG cc_start: 0.7185 (ttp-110) cc_final: 0.6777 (ttp-110) REVERT: D 311 GLU cc_start: 0.7179 (tt0) cc_final: 0.6880 (mt-10) REVERT: D 355 GLN cc_start: 0.9158 (pt0) cc_final: 0.8852 (pt0) REVERT: E 14 GLN cc_start: 0.9130 (mt0) cc_final: 0.8902 (mt0) REVERT: E 46 TRP cc_start: 0.8509 (t-100) cc_final: 0.8089 (t-100) REVERT: E 47 MET cc_start: 0.8591 (tpt) cc_final: 0.8372 (tpp) REVERT: E 115 ASP cc_start: 0.8759 (t70) cc_final: 0.8031 (t0) REVERT: E 262 ASN cc_start: 0.7644 (m-40) cc_final: 0.7302 (m-40) REVERT: E 303 ARG cc_start: 0.6984 (tpt170) cc_final: 0.5775 (mmt180) REVERT: E 305 ARG cc_start: 0.7178 (ttp-110) cc_final: 0.6777 (ttp-110) REVERT: E 311 GLU cc_start: 0.7184 (tt0) cc_final: 0.6883 (mt-10) REVERT: E 355 GLN cc_start: 0.9151 (pt0) cc_final: 0.8846 (pt0) REVERT: F 14 GLN cc_start: 0.9131 (mt0) cc_final: 0.8904 (mt0) REVERT: F 46 TRP cc_start: 0.8503 (t-100) cc_final: 0.8083 (t-100) REVERT: F 47 MET cc_start: 0.8575 (tpt) cc_final: 0.8357 (tpp) REVERT: F 115 ASP cc_start: 0.8771 (t70) cc_final: 0.8046 (t0) REVERT: F 262 ASN cc_start: 0.7644 (m-40) cc_final: 0.7300 (m-40) REVERT: F 303 ARG cc_start: 0.6972 (tpt170) cc_final: 0.5757 (mmt180) REVERT: F 305 ARG cc_start: 0.7166 (ttp-110) cc_final: 0.6762 (ttp-110) REVERT: F 311 GLU cc_start: 0.7174 (tt0) cc_final: 0.6873 (mt-10) REVERT: F 355 GLN cc_start: 0.9154 (pt0) cc_final: 0.8845 (pt0) REVERT: G 14 GLN cc_start: 0.9133 (mt0) cc_final: 0.8905 (mt0) REVERT: G 46 TRP cc_start: 0.8506 (t-100) cc_final: 0.8087 (t-100) REVERT: G 47 MET cc_start: 0.8594 (tpt) cc_final: 0.8376 (tpp) REVERT: G 115 ASP cc_start: 0.8756 (t70) cc_final: 0.8030 (t0) REVERT: G 262 ASN cc_start: 0.7656 (m-40) cc_final: 0.7309 (m-40) REVERT: G 303 ARG cc_start: 0.6971 (tpt170) cc_final: 0.5774 (mmt180) REVERT: G 305 ARG cc_start: 0.7176 (ttp-110) cc_final: 0.6774 (ttp-110) REVERT: G 311 GLU cc_start: 0.7186 (tt0) cc_final: 0.6887 (mt-10) REVERT: G 355 GLN cc_start: 0.9151 (pt0) cc_final: 0.8845 (pt0) REVERT: H 14 GLN cc_start: 0.9132 (mt0) cc_final: 0.8906 (mt0) REVERT: H 46 TRP cc_start: 0.8499 (t-100) cc_final: 0.8081 (t-100) REVERT: H 47 MET cc_start: 0.8585 (tpt) cc_final: 0.8369 (tpp) REVERT: H 115 ASP cc_start: 0.8775 (t70) cc_final: 0.8051 (t0) REVERT: H 262 ASN cc_start: 0.7644 (m-40) cc_final: 0.7311 (m-40) REVERT: H 303 ARG cc_start: 0.6977 (tpt170) cc_final: 0.5772 (mmt180) REVERT: H 305 ARG cc_start: 0.7191 (ttp-110) cc_final: 0.6784 (ttp-110) REVERT: H 311 GLU cc_start: 0.7183 (tt0) cc_final: 0.6881 (mt-10) REVERT: H 355 GLN cc_start: 0.9160 (pt0) cc_final: 0.8838 (pt0) outliers start: 32 outliers final: 6 residues processed: 491 average time/residue: 0.6764 time to fit residues: 372.0047 Evaluate side-chains 427 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 421 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain H residue 302 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 0.0020 chunk 168 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 179 GLN A 224 ASN A 352 GLN A 359 HIS B 107 ASN B 179 GLN B 352 GLN B 359 HIS C 107 ASN C 179 GLN C 224 ASN C 352 GLN C 359 HIS D 104 GLN D 107 ASN D 179 GLN D 224 ASN D 352 GLN D 359 HIS E 107 ASN E 179 GLN E 224 ASN E 352 GLN E 359 HIS F 104 GLN F 107 ASN F 179 GLN F 224 ASN F 352 GLN F 359 HIS G 104 GLN G 107 ASN G 179 GLN G 224 ASN G 352 GLN G 359 HIS H 107 ASN H 179 GLN H 352 GLN H 359 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.187581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125795 restraints weight = 113936.523| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.82 r_work: 0.2793 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23584 Z= 0.172 Angle : 0.577 5.557 31840 Z= 0.310 Chirality : 0.045 0.144 3416 Planarity : 0.005 0.040 4240 Dihedral : 4.915 25.220 3392 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.66 % Allowed : 11.82 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.15), residues: 2968 helix: 0.77 (0.13), residues: 1448 sheet: -0.61 (0.23), residues: 456 loop : -1.95 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 109 TYR 0.015 0.002 TYR G 314 PHE 0.013 0.002 PHE H 99 TRP 0.000 0.000 TRP B 46 HIS 0.003 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00402 (23584) covalent geometry : angle 0.57719 (31840) hydrogen bonds : bond 0.04624 ( 1152) hydrogen bonds : angle 4.97540 ( 3336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 449 time to evaluate : 0.886 Fit side-chains REVERT: A 14 GLN cc_start: 0.9168 (mt0) cc_final: 0.8891 (mt0) REVERT: A 46 TRP cc_start: 0.8540 (t-100) cc_final: 0.8074 (t-100) REVERT: A 47 MET cc_start: 0.8630 (tpt) cc_final: 0.8305 (tpp) REVERT: A 115 ASP cc_start: 0.8846 (t70) cc_final: 0.8542 (t0) REVERT: A 186 TYR cc_start: 0.7268 (t80) cc_final: 0.7040 (t80) REVERT: A 254 LYS cc_start: 0.6930 (ptpt) cc_final: 0.6358 (ttpp) REVERT: A 262 ASN cc_start: 0.7578 (m-40) cc_final: 0.7235 (m-40) REVERT: A 303 ARG cc_start: 0.6844 (tpt170) cc_final: 0.5798 (mmt180) REVERT: A 311 GLU cc_start: 0.7233 (tt0) cc_final: 0.6905 (mt-10) REVERT: A 355 GLN cc_start: 0.9286 (pt0) cc_final: 0.9083 (pt0) REVERT: B 14 GLN cc_start: 0.9154 (mt0) cc_final: 0.8877 (mt0) REVERT: B 46 TRP cc_start: 0.8553 (t-100) cc_final: 0.8086 (t-100) REVERT: B 47 MET cc_start: 0.8649 (tpt) cc_final: 0.8323 (tpp) REVERT: B 115 ASP cc_start: 0.8855 (t70) cc_final: 0.8548 (t0) REVERT: B 224 ASN cc_start: 0.7061 (t160) cc_final: 0.6526 (t0) REVERT: B 254 LYS cc_start: 0.6951 (ptpt) cc_final: 0.6368 (ttpp) REVERT: B 262 ASN cc_start: 0.7584 (m-40) cc_final: 0.7245 (m-40) REVERT: B 303 ARG cc_start: 0.6844 (tpt170) cc_final: 0.5794 (mmt180) REVERT: B 311 GLU cc_start: 0.7226 (tt0) cc_final: 0.6896 (mt-10) REVERT: B 355 GLN cc_start: 0.9284 (pt0) cc_final: 0.9081 (pt0) REVERT: C 14 GLN cc_start: 0.9148 (mt0) cc_final: 0.8871 (mt0) REVERT: C 46 TRP cc_start: 0.8555 (t-100) cc_final: 0.8088 (t-100) REVERT: C 47 MET cc_start: 0.8642 (tpt) cc_final: 0.8318 (tpp) REVERT: C 115 ASP cc_start: 0.8851 (t70) cc_final: 0.8549 (t0) REVERT: C 254 LYS cc_start: 0.6930 (ptpt) cc_final: 0.6363 (ttpp) REVERT: C 262 ASN cc_start: 0.7583 (m-40) cc_final: 0.7237 (m-40) REVERT: C 303 ARG cc_start: 0.6886 (tpt170) cc_final: 0.5839 (mmt180) REVERT: C 355 GLN cc_start: 0.9282 (pt0) cc_final: 0.9076 (pt0) REVERT: D 14 GLN cc_start: 0.9155 (mt0) cc_final: 0.8875 (mt0) REVERT: D 46 TRP cc_start: 0.8561 (t-100) cc_final: 0.8087 (t-100) REVERT: D 47 MET cc_start: 0.8650 (tpt) cc_final: 0.8323 (tpp) REVERT: D 115 ASP cc_start: 0.8850 (t70) cc_final: 0.8547 (t0) REVERT: D 186 TYR cc_start: 0.7259 (t80) cc_final: 0.7038 (t80) REVERT: D 254 LYS cc_start: 0.6955 (ptpt) cc_final: 0.6375 (ttpp) REVERT: D 262 ASN cc_start: 0.7584 (m-40) cc_final: 0.7246 (m-40) REVERT: D 303 ARG cc_start: 0.6844 (tpt170) cc_final: 0.5790 (mmt180) REVERT: D 355 GLN cc_start: 0.9283 (pt0) cc_final: 0.9079 (pt0) REVERT: E 14 GLN cc_start: 0.9152 (mt0) cc_final: 0.8874 (mt0) REVERT: E 46 TRP cc_start: 0.8563 (t-100) cc_final: 0.8091 (t-100) REVERT: E 47 MET cc_start: 0.8630 (tpt) cc_final: 0.8299 (tpp) REVERT: E 115 ASP cc_start: 0.8828 (t70) cc_final: 0.8525 (t0) REVERT: E 186 TYR cc_start: 0.7266 (t80) cc_final: 0.7044 (t80) REVERT: E 254 LYS cc_start: 0.6928 (ptpt) cc_final: 0.6354 (ttpp) REVERT: E 262 ASN cc_start: 0.7573 (m-40) cc_final: 0.7227 (m-40) REVERT: E 303 ARG cc_start: 0.6878 (tpt170) cc_final: 0.5821 (mmt180) REVERT: E 355 GLN cc_start: 0.9280 (pt0) cc_final: 0.9078 (pt0) REVERT: F 14 GLN cc_start: 0.9157 (mt0) cc_final: 0.8876 (mt0) REVERT: F 46 TRP cc_start: 0.8563 (t-100) cc_final: 0.8095 (t-100) REVERT: F 47 MET cc_start: 0.8631 (tpt) cc_final: 0.8307 (tpp) REVERT: F 115 ASP cc_start: 0.8848 (t70) cc_final: 0.8544 (t0) REVERT: F 186 TYR cc_start: 0.7256 (t80) cc_final: 0.7031 (t80) REVERT: F 254 LYS cc_start: 0.6939 (ptpt) cc_final: 0.6362 (ttpp) REVERT: F 262 ASN cc_start: 0.7572 (m-40) cc_final: 0.7231 (m-40) REVERT: F 303 ARG cc_start: 0.6860 (tpt170) cc_final: 0.5804 (mmt180) REVERT: F 355 GLN cc_start: 0.9284 (pt0) cc_final: 0.9083 (pt0) REVERT: G 14 GLN cc_start: 0.9161 (mt0) cc_final: 0.8884 (mt0) REVERT: G 46 TRP cc_start: 0.8561 (t-100) cc_final: 0.8091 (t-100) REVERT: G 47 MET cc_start: 0.8659 (tpt) cc_final: 0.8331 (tpp) REVERT: G 115 ASP cc_start: 0.8843 (t70) cc_final: 0.8541 (t0) REVERT: G 186 TYR cc_start: 0.7266 (t80) cc_final: 0.7046 (t80) REVERT: G 254 LYS cc_start: 0.6938 (ptpt) cc_final: 0.6365 (ttpp) REVERT: G 262 ASN cc_start: 0.7593 (m-40) cc_final: 0.7250 (m-40) REVERT: G 303 ARG cc_start: 0.6849 (tpt170) cc_final: 0.5811 (mmt180) REVERT: G 311 GLU cc_start: 0.7234 (tt0) cc_final: 0.6901 (mt-10) REVERT: G 355 GLN cc_start: 0.9284 (pt0) cc_final: 0.9082 (pt0) REVERT: H 14 GLN cc_start: 0.9148 (mt0) cc_final: 0.8870 (mt0) REVERT: H 46 TRP cc_start: 0.8551 (t-100) cc_final: 0.8077 (t-100) REVERT: H 47 MET cc_start: 0.8636 (tpt) cc_final: 0.8315 (tpp) REVERT: H 115 ASP cc_start: 0.8848 (t70) cc_final: 0.8542 (t0) REVERT: H 224 ASN cc_start: 0.7052 (t160) cc_final: 0.6510 (t0) REVERT: H 254 LYS cc_start: 0.6932 (ptpt) cc_final: 0.6366 (ttpp) REVERT: H 262 ASN cc_start: 0.7594 (m-40) cc_final: 0.7256 (m-40) REVERT: H 303 ARG cc_start: 0.6876 (tpt170) cc_final: 0.5829 (mmt180) REVERT: H 311 GLU cc_start: 0.7229 (tt0) cc_final: 0.6898 (mt-10) REVERT: H 355 GLN cc_start: 0.9279 (pt0) cc_final: 0.9077 (pt0) outliers start: 47 outliers final: 16 residues processed: 481 average time/residue: 0.6460 time to fit residues: 350.7885 Evaluate side-chains 447 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 431 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 302 ASN Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 10 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 179 optimal weight: 0.3980 chunk 267 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 179 GLN A 261 ASN A 352 GLN B 104 GLN B 179 GLN B 261 ASN B 352 GLN C 179 GLN C 261 ASN C 352 GLN D 179 GLN D 261 ASN D 352 GLN E 104 GLN E 179 GLN E 261 ASN E 352 GLN F 179 GLN F 261 ASN F 352 GLN G 179 GLN G 261 ASN G 352 GLN H 179 GLN H 261 ASN H 352 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.186071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115009 restraints weight = 110599.642| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 5.06 r_work: 0.2835 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 23584 Z= 0.136 Angle : 0.529 5.473 31840 Z= 0.288 Chirality : 0.043 0.140 3416 Planarity : 0.004 0.036 4240 Dihedral : 4.724 27.228 3392 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.04 % Allowed : 12.20 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 2968 helix: 1.15 (0.13), residues: 1464 sheet: -0.41 (0.23), residues: 456 loop : -1.89 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 109 TYR 0.015 0.001 TYR D 314 PHE 0.012 0.002 PHE D 99 TRP 0.001 0.000 TRP C 46 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00313 (23584) covalent geometry : angle 0.52903 (31840) hydrogen bonds : bond 0.03995 ( 1152) hydrogen bonds : angle 4.75021 ( 3336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 439 time to evaluate : 0.688 Fit side-chains REVERT: A 14 GLN cc_start: 0.9098 (mt0) cc_final: 0.8833 (mt0) REVERT: A 46 TRP cc_start: 0.8489 (t-100) cc_final: 0.8000 (t-100) REVERT: A 47 MET cc_start: 0.8611 (tpt) cc_final: 0.8230 (tpp) REVERT: A 95 MET cc_start: 0.8962 (ptp) cc_final: 0.8686 (ptp) REVERT: A 115 ASP cc_start: 0.8638 (t70) cc_final: 0.8325 (t0) REVERT: A 254 LYS cc_start: 0.6666 (ptpt) cc_final: 0.6076 (ttpp) REVERT: A 262 ASN cc_start: 0.7523 (m-40) cc_final: 0.7230 (m-40) REVERT: A 303 ARG cc_start: 0.6834 (tpt170) cc_final: 0.5929 (mmt180) REVERT: A 311 GLU cc_start: 0.7135 (tt0) cc_final: 0.6755 (mt-10) REVERT: B 14 GLN cc_start: 0.9090 (mt0) cc_final: 0.8829 (mt0) REVERT: B 46 TRP cc_start: 0.8485 (t-100) cc_final: 0.8000 (t-100) REVERT: B 47 MET cc_start: 0.8618 (tpt) cc_final: 0.8239 (tpp) REVERT: B 95 MET cc_start: 0.8960 (ptp) cc_final: 0.8686 (ptp) REVERT: B 115 ASP cc_start: 0.8635 (t70) cc_final: 0.8320 (t0) REVERT: B 224 ASN cc_start: 0.6782 (t160) cc_final: 0.6405 (t0) REVERT: B 254 LYS cc_start: 0.6680 (ptpt) cc_final: 0.6090 (ttpp) REVERT: B 262 ASN cc_start: 0.7525 (m-40) cc_final: 0.7260 (m-40) REVERT: B 303 ARG cc_start: 0.6836 (tpt170) cc_final: 0.5927 (mmt180) REVERT: B 311 GLU cc_start: 0.7282 (tt0) cc_final: 0.6904 (mt-10) REVERT: C 14 GLN cc_start: 0.9088 (mt0) cc_final: 0.8826 (mt0) REVERT: C 46 TRP cc_start: 0.8499 (t-100) cc_final: 0.8011 (t-100) REVERT: C 47 MET cc_start: 0.8611 (tpt) cc_final: 0.8231 (tpp) REVERT: C 95 MET cc_start: 0.8965 (ptp) cc_final: 0.8688 (ptp) REVERT: C 115 ASP cc_start: 0.8641 (t70) cc_final: 0.8325 (t0) REVERT: C 254 LYS cc_start: 0.6655 (ptpt) cc_final: 0.6068 (ttpp) REVERT: C 262 ASN cc_start: 0.7517 (m-40) cc_final: 0.7250 (m-40) REVERT: C 303 ARG cc_start: 0.6846 (tpt170) cc_final: 0.5938 (mmt180) REVERT: C 311 GLU cc_start: 0.7128 (tt0) cc_final: 0.6746 (mt-10) REVERT: D 14 GLN cc_start: 0.9087 (mt0) cc_final: 0.8827 (mt0) REVERT: D 46 TRP cc_start: 0.8502 (t-100) cc_final: 0.8014 (t-100) REVERT: D 47 MET cc_start: 0.8623 (tpt) cc_final: 0.8241 (tpp) REVERT: D 95 MET cc_start: 0.8959 (ptp) cc_final: 0.8681 (ptp) REVERT: D 115 ASP cc_start: 0.8638 (t70) cc_final: 0.8327 (t0) REVERT: D 254 LYS cc_start: 0.6711 (ptpt) cc_final: 0.6113 (ttpp) REVERT: D 262 ASN cc_start: 0.7516 (m-40) cc_final: 0.7254 (m-40) REVERT: D 303 ARG cc_start: 0.6793 (tpt170) cc_final: 0.5884 (mmt180) REVERT: D 311 GLU cc_start: 0.7133 (tt0) cc_final: 0.6753 (mt-10) REVERT: E 14 GLN cc_start: 0.9097 (mt0) cc_final: 0.8833 (mt0) REVERT: E 46 TRP cc_start: 0.8508 (t-100) cc_final: 0.8018 (t-100) REVERT: E 47 MET cc_start: 0.8597 (tpt) cc_final: 0.8211 (tpp) REVERT: E 95 MET cc_start: 0.8970 (ptp) cc_final: 0.8691 (ptp) REVERT: E 115 ASP cc_start: 0.8630 (t70) cc_final: 0.8317 (t0) REVERT: E 254 LYS cc_start: 0.6667 (ptpt) cc_final: 0.6072 (ttpp) REVERT: E 262 ASN cc_start: 0.7516 (m-40) cc_final: 0.7218 (m-40) REVERT: E 303 ARG cc_start: 0.6844 (tpt170) cc_final: 0.5924 (mmt180) REVERT: E 311 GLU cc_start: 0.7133 (tt0) cc_final: 0.6751 (mt-10) REVERT: F 14 GLN cc_start: 0.9090 (mt0) cc_final: 0.8826 (mt0) REVERT: F 46 TRP cc_start: 0.8516 (t-100) cc_final: 0.8027 (t-100) REVERT: F 47 MET cc_start: 0.8606 (tpt) cc_final: 0.8225 (tpp) REVERT: F 95 MET cc_start: 0.8958 (ptp) cc_final: 0.8684 (ptp) REVERT: F 115 ASP cc_start: 0.8630 (t70) cc_final: 0.8318 (t0) REVERT: F 254 LYS cc_start: 0.6706 (ptpt) cc_final: 0.6103 (ttpp) REVERT: F 262 ASN cc_start: 0.7508 (m-40) cc_final: 0.7243 (m-40) REVERT: F 303 ARG cc_start: 0.6843 (tpt170) cc_final: 0.5926 (mmt180) REVERT: F 311 GLU cc_start: 0.7158 (tt0) cc_final: 0.6777 (mt-10) REVERT: G 14 GLN cc_start: 0.9095 (mt0) cc_final: 0.8831 (mt0) REVERT: G 46 TRP cc_start: 0.8511 (t-100) cc_final: 0.8023 (t-100) REVERT: G 47 MET cc_start: 0.8622 (tpt) cc_final: 0.8238 (tpp) REVERT: G 95 MET cc_start: 0.8962 (ptp) cc_final: 0.8684 (ptp) REVERT: G 115 ASP cc_start: 0.8637 (t70) cc_final: 0.8322 (t0) REVERT: G 254 LYS cc_start: 0.6688 (ptpt) cc_final: 0.6093 (ttpp) REVERT: G 262 ASN cc_start: 0.7517 (m-40) cc_final: 0.7254 (m-40) REVERT: G 303 ARG cc_start: 0.6814 (tpt170) cc_final: 0.5903 (mmt180) REVERT: G 311 GLU cc_start: 0.7276 (tt0) cc_final: 0.6898 (mt-10) REVERT: H 14 GLN cc_start: 0.9092 (mt0) cc_final: 0.8829 (mt0) REVERT: H 46 TRP cc_start: 0.8496 (t-100) cc_final: 0.8006 (t-100) REVERT: H 47 MET cc_start: 0.8610 (tpt) cc_final: 0.8232 (tpp) REVERT: H 95 MET cc_start: 0.8961 (ptp) cc_final: 0.8685 (ptp) REVERT: H 115 ASP cc_start: 0.8643 (t70) cc_final: 0.8332 (t0) REVERT: H 224 ASN cc_start: 0.6767 (t160) cc_final: 0.6397 (t0) REVERT: H 254 LYS cc_start: 0.6693 (ptpt) cc_final: 0.6099 (ttpp) REVERT: H 262 ASN cc_start: 0.7536 (m-40) cc_final: 0.7286 (m-40) REVERT: H 303 ARG cc_start: 0.6856 (tpt170) cc_final: 0.5940 (mmt180) REVERT: H 311 GLU cc_start: 0.7282 (tt0) cc_final: 0.6902 (mt-10) outliers start: 56 outliers final: 8 residues processed: 463 average time/residue: 0.6872 time to fit residues: 356.9352 Evaluate side-chains 403 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 395 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 55 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 179 GLN A 224 ASN A 261 ASN A 352 GLN B 5 GLN B 179 GLN B 261 ASN B 352 GLN C 5 GLN C 104 GLN C 179 GLN C 224 ASN C 261 ASN C 352 GLN D 5 GLN D 179 GLN D 224 ASN D 261 ASN D 352 GLN E 5 GLN E 179 GLN E 224 ASN E 261 ASN E 352 GLN F 5 GLN F 179 GLN F 224 ASN F 261 ASN F 352 GLN G 5 GLN G 179 GLN G 224 ASN G 261 ASN G 352 GLN H 5 GLN H 104 GLN H 179 GLN H 261 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.185399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.111032 restraints weight = 112715.643| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 5.07 r_work: 0.2812 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 23584 Z= 0.204 Angle : 0.579 5.066 31840 Z= 0.313 Chirality : 0.046 0.145 3416 Planarity : 0.005 0.044 4240 Dihedral : 4.827 26.155 3392 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.08 % Allowed : 13.26 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 2968 helix: 1.13 (0.13), residues: 1472 sheet: -0.45 (0.24), residues: 456 loop : -1.89 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 109 TYR 0.022 0.002 TYR H 155 PHE 0.010 0.002 PHE C 99 TRP 0.001 0.000 TRP G 46 HIS 0.004 0.001 HIS G 359 Details of bonding type rmsd covalent geometry : bond 0.00484 (23584) covalent geometry : angle 0.57868 (31840) hydrogen bonds : bond 0.04640 ( 1152) hydrogen bonds : angle 4.74421 ( 3336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 415 time to evaluate : 0.836 Fit side-chains REVERT: A 14 GLN cc_start: 0.9156 (mt0) cc_final: 0.8883 (mt0) REVERT: A 46 TRP cc_start: 0.8435 (t-100) cc_final: 0.7955 (t-100) REVERT: A 47 MET cc_start: 0.8585 (tpt) cc_final: 0.8234 (tpp) REVERT: A 115 ASP cc_start: 0.8589 (t70) cc_final: 0.8277 (t0) REVERT: A 254 LYS cc_start: 0.6845 (ptpt) cc_final: 0.6366 (ttpp) REVERT: A 262 ASN cc_start: 0.7570 (m-40) cc_final: 0.7287 (m-40) REVERT: A 303 ARG cc_start: 0.6754 (tpt170) cc_final: 0.6029 (mmt180) REVERT: B 14 GLN cc_start: 0.9153 (mt0) cc_final: 0.8878 (mt0) REVERT: B 46 TRP cc_start: 0.8432 (t-100) cc_final: 0.7949 (t-100) REVERT: B 47 MET cc_start: 0.8593 (tpt) cc_final: 0.8247 (tpp) REVERT: B 115 ASP cc_start: 0.8600 (t70) cc_final: 0.8291 (t0) REVERT: B 224 ASN cc_start: 0.6796 (t160) cc_final: 0.6438 (t0) REVERT: B 254 LYS cc_start: 0.6841 (ptpt) cc_final: 0.6361 (ttpp) REVERT: B 262 ASN cc_start: 0.7581 (m-40) cc_final: 0.7300 (m-40) REVERT: B 303 ARG cc_start: 0.6741 (tpt170) cc_final: 0.6031 (mmt180) REVERT: C 14 GLN cc_start: 0.9149 (mt0) cc_final: 0.8877 (mt0) REVERT: C 46 TRP cc_start: 0.8444 (t-100) cc_final: 0.7964 (t-100) REVERT: C 47 MET cc_start: 0.8597 (tpt) cc_final: 0.8248 (tpp) REVERT: C 115 ASP cc_start: 0.8578 (t70) cc_final: 0.8268 (t0) REVERT: C 254 LYS cc_start: 0.6837 (ptpt) cc_final: 0.6361 (ttpp) REVERT: C 262 ASN cc_start: 0.7587 (m-40) cc_final: 0.7302 (m-40) REVERT: C 303 ARG cc_start: 0.6771 (tpt170) cc_final: 0.6052 (mmt180) REVERT: D 14 GLN cc_start: 0.9158 (mt0) cc_final: 0.8889 (mt0) REVERT: D 46 TRP cc_start: 0.8446 (t-100) cc_final: 0.7968 (t-100) REVERT: D 47 MET cc_start: 0.8611 (tpt) cc_final: 0.8264 (tpp) REVERT: D 115 ASP cc_start: 0.8581 (t70) cc_final: 0.8270 (t0) REVERT: D 254 LYS cc_start: 0.6879 (ptpt) cc_final: 0.6389 (ttpp) REVERT: D 262 ASN cc_start: 0.7576 (m-40) cc_final: 0.7291 (m-40) REVERT: D 303 ARG cc_start: 0.6732 (tpt170) cc_final: 0.6012 (mmt180) REVERT: E 14 GLN cc_start: 0.9153 (mt0) cc_final: 0.8887 (mt0) REVERT: E 46 TRP cc_start: 0.8446 (t-100) cc_final: 0.7966 (t-100) REVERT: E 47 MET cc_start: 0.8605 (tpt) cc_final: 0.8251 (tpp) REVERT: E 115 ASP cc_start: 0.8577 (t70) cc_final: 0.8267 (t0) REVERT: E 254 LYS cc_start: 0.6833 (ptpt) cc_final: 0.6348 (ttpp) REVERT: E 262 ASN cc_start: 0.7582 (m-40) cc_final: 0.7296 (m-40) REVERT: E 303 ARG cc_start: 0.6773 (tpt170) cc_final: 0.6039 (mmt180) REVERT: F 14 GLN cc_start: 0.9153 (mt0) cc_final: 0.8884 (mt0) REVERT: F 46 TRP cc_start: 0.8450 (t-100) cc_final: 0.7974 (t-100) REVERT: F 47 MET cc_start: 0.8608 (tpt) cc_final: 0.8259 (tpp) REVERT: F 115 ASP cc_start: 0.8580 (t70) cc_final: 0.8271 (t0) REVERT: F 254 LYS cc_start: 0.6851 (ptpt) cc_final: 0.6362 (ttpp) REVERT: F 262 ASN cc_start: 0.7576 (m-40) cc_final: 0.7293 (m-40) REVERT: F 303 ARG cc_start: 0.6758 (tpt170) cc_final: 0.6033 (mmt180) REVERT: G 14 GLN cc_start: 0.9157 (mt0) cc_final: 0.8887 (mt0) REVERT: G 46 TRP cc_start: 0.8445 (t-100) cc_final: 0.7964 (t-100) REVERT: G 47 MET cc_start: 0.8607 (tpt) cc_final: 0.8257 (tpp) REVERT: G 115 ASP cc_start: 0.8580 (t70) cc_final: 0.8269 (t0) REVERT: G 254 LYS cc_start: 0.6858 (ptpt) cc_final: 0.6370 (ttpp) REVERT: G 262 ASN cc_start: 0.7575 (m-40) cc_final: 0.7291 (m-40) REVERT: G 303 ARG cc_start: 0.6739 (tpt170) cc_final: 0.6016 (mmt180) REVERT: H 14 GLN cc_start: 0.9148 (mt0) cc_final: 0.8876 (mt0) REVERT: H 46 TRP cc_start: 0.8448 (t-100) cc_final: 0.7968 (t-100) REVERT: H 47 MET cc_start: 0.8591 (tpt) cc_final: 0.8247 (tpp) REVERT: H 115 ASP cc_start: 0.8587 (t70) cc_final: 0.8275 (t0) REVERT: H 224 ASN cc_start: 0.6779 (t160) cc_final: 0.6423 (t0) REVERT: H 254 LYS cc_start: 0.6839 (ptpt) cc_final: 0.6362 (ttpp) REVERT: H 262 ASN cc_start: 0.7601 (m-40) cc_final: 0.7316 (m-40) REVERT: H 303 ARG cc_start: 0.6772 (tpt170) cc_final: 0.6062 (mmt180) outliers start: 57 outliers final: 8 residues processed: 447 average time/residue: 0.6434 time to fit residues: 325.3871 Evaluate side-chains 405 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 397 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 41 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 179 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN B 179 GLN B 352 GLN C 5 GLN C 179 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN D 179 GLN ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 179 GLN ** E 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 179 GLN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 179 GLN G 352 GLN H 5 GLN H 179 GLN H 261 ASN ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.186334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111798 restraints weight = 112976.497| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 5.37 r_work: 0.2863 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23584 Z= 0.127 Angle : 0.518 5.633 31840 Z= 0.282 Chirality : 0.043 0.136 3416 Planarity : 0.004 0.030 4240 Dihedral : 4.611 26.849 3392 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.51 % Allowed : 14.40 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.15), residues: 2968 helix: 1.33 (0.13), residues: 1472 sheet: -0.34 (0.23), residues: 472 loop : -1.70 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 109 TYR 0.018 0.001 TYR H 155 PHE 0.010 0.002 PHE H 99 TRP 0.000 0.000 TRP H 46 HIS 0.004 0.001 HIS H 269 Details of bonding type rmsd covalent geometry : bond 0.00291 (23584) covalent geometry : angle 0.51820 (31840) hydrogen bonds : bond 0.03813 ( 1152) hydrogen bonds : angle 4.60606 ( 3336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 368 time to evaluate : 0.668 Fit side-chains REVERT: A 14 GLN cc_start: 0.9147 (mt0) cc_final: 0.8895 (mt0) REVERT: A 16 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8645 (tt) REVERT: A 46 TRP cc_start: 0.8437 (t-100) cc_final: 0.7976 (t-100) REVERT: A 47 MET cc_start: 0.8599 (tpt) cc_final: 0.8232 (tpp) REVERT: A 115 ASP cc_start: 0.8528 (t70) cc_final: 0.8220 (t0) REVERT: A 254 LYS cc_start: 0.6812 (ptpt) cc_final: 0.6247 (ttpp) REVERT: A 262 ASN cc_start: 0.7503 (m-40) cc_final: 0.7265 (m-40) REVERT: A 303 ARG cc_start: 0.6650 (tpt170) cc_final: 0.5949 (mmt180) REVERT: B 14 GLN cc_start: 0.9142 (mt0) cc_final: 0.8893 (mt0) REVERT: B 16 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8654 (tt) REVERT: B 46 TRP cc_start: 0.8451 (t-100) cc_final: 0.7990 (t-100) REVERT: B 47 MET cc_start: 0.8591 (tpt) cc_final: 0.8225 (tpp) REVERT: B 115 ASP cc_start: 0.8536 (t70) cc_final: 0.8227 (t0) REVERT: B 224 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.6379 (t0) REVERT: B 254 LYS cc_start: 0.6784 (ptpt) cc_final: 0.6223 (ttpp) REVERT: B 262 ASN cc_start: 0.7504 (m-40) cc_final: 0.7270 (m-40) REVERT: B 303 ARG cc_start: 0.6769 (tpt170) cc_final: 0.5975 (mmt180) REVERT: C 14 GLN cc_start: 0.9139 (mt0) cc_final: 0.8886 (mt0) REVERT: C 16 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8626 (tt) REVERT: C 46 TRP cc_start: 0.8444 (t-100) cc_final: 0.7985 (t-100) REVERT: C 47 MET cc_start: 0.8611 (tpt) cc_final: 0.8247 (tpp) REVERT: C 115 ASP cc_start: 0.8530 (t70) cc_final: 0.8227 (t0) REVERT: C 254 LYS cc_start: 0.6802 (ptpt) cc_final: 0.6235 (ttpp) REVERT: C 262 ASN cc_start: 0.7520 (m-40) cc_final: 0.7283 (m-40) REVERT: C 303 ARG cc_start: 0.6688 (tpt170) cc_final: 0.5992 (mmt180) REVERT: D 14 GLN cc_start: 0.9149 (mt0) cc_final: 0.8900 (mt0) REVERT: D 16 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8624 (tt) REVERT: D 46 TRP cc_start: 0.8456 (t-100) cc_final: 0.7997 (t-100) REVERT: D 47 MET cc_start: 0.8614 (tpt) cc_final: 0.8249 (tpp) REVERT: D 115 ASP cc_start: 0.8520 (t70) cc_final: 0.8211 (t0) REVERT: D 254 LYS cc_start: 0.6814 (ptpt) cc_final: 0.6244 (ttpp) REVERT: D 262 ASN cc_start: 0.7508 (m-40) cc_final: 0.7272 (m-40) REVERT: D 303 ARG cc_start: 0.6632 (tpt170) cc_final: 0.5926 (mmt180) REVERT: E 14 GLN cc_start: 0.9146 (mt0) cc_final: 0.8895 (mt0) REVERT: E 16 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8651 (tt) REVERT: E 46 TRP cc_start: 0.8459 (t-100) cc_final: 0.7996 (t-100) REVERT: E 47 MET cc_start: 0.8599 (tpt) cc_final: 0.8229 (tpp) REVERT: E 115 ASP cc_start: 0.8506 (t70) cc_final: 0.8193 (t0) REVERT: E 254 LYS cc_start: 0.6768 (ptpt) cc_final: 0.6199 (ttpp) REVERT: E 262 ASN cc_start: 0.7517 (m-40) cc_final: 0.7280 (m-40) REVERT: E 303 ARG cc_start: 0.6672 (tpt170) cc_final: 0.5956 (mmt180) REVERT: F 14 GLN cc_start: 0.9150 (mt0) cc_final: 0.8900 (mt0) REVERT: F 16 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8661 (tt) REVERT: F 46 TRP cc_start: 0.8460 (t-100) cc_final: 0.8003 (t-100) REVERT: F 47 MET cc_start: 0.8600 (tpt) cc_final: 0.8233 (tpp) REVERT: F 115 ASP cc_start: 0.8513 (t70) cc_final: 0.8204 (t0) REVERT: F 254 LYS cc_start: 0.6816 (ptpt) cc_final: 0.6249 (ttpp) REVERT: F 262 ASN cc_start: 0.7499 (m-40) cc_final: 0.7262 (m-40) REVERT: F 303 ARG cc_start: 0.6660 (tpt170) cc_final: 0.5948 (mmt180) REVERT: G 14 GLN cc_start: 0.9144 (mt0) cc_final: 0.8896 (mt0) REVERT: G 16 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8648 (tt) REVERT: G 46 TRP cc_start: 0.8451 (t-100) cc_final: 0.7995 (t-100) REVERT: G 47 MET cc_start: 0.8609 (tpt) cc_final: 0.8242 (tpp) REVERT: G 115 ASP cc_start: 0.8517 (t70) cc_final: 0.8203 (t0) REVERT: G 254 LYS cc_start: 0.6810 (ptpt) cc_final: 0.6246 (ttpp) REVERT: G 262 ASN cc_start: 0.7514 (m-40) cc_final: 0.7279 (m-40) REVERT: G 303 ARG cc_start: 0.6510 (tpt170) cc_final: 0.5815 (mmt180) REVERT: H 14 GLN cc_start: 0.9143 (mt0) cc_final: 0.8891 (mt0) REVERT: H 16 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8648 (tt) REVERT: H 46 TRP cc_start: 0.8458 (t-100) cc_final: 0.7996 (t-100) REVERT: H 47 MET cc_start: 0.8610 (tpt) cc_final: 0.8249 (tpp) REVERT: H 115 ASP cc_start: 0.8525 (t70) cc_final: 0.8216 (t0) REVERT: H 224 ASN cc_start: 0.6696 (OUTLIER) cc_final: 0.6366 (t0) REVERT: H 254 LYS cc_start: 0.6786 (ptpt) cc_final: 0.6215 (ttpp) REVERT: H 262 ASN cc_start: 0.7525 (m-40) cc_final: 0.7307 (m-40) REVERT: H 303 ARG cc_start: 0.6789 (tpt170) cc_final: 0.5988 (mmt180) outliers start: 67 outliers final: 8 residues processed: 402 average time/residue: 0.6366 time to fit residues: 289.4176 Evaluate side-chains 395 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 377 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 224 ASN Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 131 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 188 optimal weight: 0.0670 chunk 89 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 179 GLN A 224 ASN A 352 GLN B 5 GLN B 179 GLN B 352 GLN C 5 GLN C 179 GLN C 224 ASN C 352 GLN D 5 GLN D 179 GLN D 224 ASN D 352 GLN E 5 GLN E 179 GLN E 224 ASN E 352 GLN F 5 GLN F 179 GLN F 224 ASN F 352 GLN G 5 GLN G 179 GLN G 224 ASN G 352 GLN H 5 GLN H 179 GLN H 352 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.186501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.141158 restraints weight = 120941.103| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 7.72 r_work: 0.2702 rms_B_bonded: 6.10 restraints_weight: 2.0000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23584 Z= 0.142 Angle : 0.540 5.580 31840 Z= 0.292 Chirality : 0.044 0.146 3416 Planarity : 0.004 0.035 4240 Dihedral : 4.583 26.840 3392 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.79 % Allowed : 14.91 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.15), residues: 2968 helix: 1.40 (0.13), residues: 1472 sheet: -0.30 (0.24), residues: 472 loop : -1.59 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 109 TYR 0.022 0.002 TYR B 155 PHE 0.009 0.002 PHE H 99 TRP 0.001 0.000 TRP D 46 HIS 0.003 0.001 HIS H 269 Details of bonding type rmsd covalent geometry : bond 0.00332 (23584) covalent geometry : angle 0.53993 (31840) hydrogen bonds : bond 0.04009 ( 1152) hydrogen bonds : angle 4.58607 ( 3336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 384 time to evaluate : 0.852 Fit side-chains REVERT: A 14 GLN cc_start: 0.9271 (mt0) cc_final: 0.8978 (mt0) REVERT: A 16 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8784 (tt) REVERT: A 46 TRP cc_start: 0.8608 (t-100) cc_final: 0.8130 (t-100) REVERT: A 47 MET cc_start: 0.8795 (tpt) cc_final: 0.8436 (tpp) REVERT: A 115 ASP cc_start: 0.8687 (t70) cc_final: 0.8397 (t0) REVERT: A 254 LYS cc_start: 0.6886 (ptpt) cc_final: 0.6311 (ttpp) REVERT: A 262 ASN cc_start: 0.7606 (m-40) cc_final: 0.7367 (m-40) REVERT: A 303 ARG cc_start: 0.6881 (tpt170) cc_final: 0.6121 (mmt180) REVERT: B 14 GLN cc_start: 0.9280 (mt0) cc_final: 0.8983 (mt0) REVERT: B 16 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 46 TRP cc_start: 0.8627 (t-100) cc_final: 0.8153 (t-100) REVERT: B 47 MET cc_start: 0.8793 (tpt) cc_final: 0.8436 (tpp) REVERT: B 115 ASP cc_start: 0.8668 (t70) cc_final: 0.8367 (t0) REVERT: B 224 ASN cc_start: 0.6711 (OUTLIER) cc_final: 0.6358 (t0) REVERT: B 254 LYS cc_start: 0.6864 (ptpt) cc_final: 0.6293 (ttpp) REVERT: B 262 ASN cc_start: 0.7598 (m-40) cc_final: 0.7356 (m-40) REVERT: B 303 ARG cc_start: 0.6954 (tpt170) cc_final: 0.6065 (mmt180) REVERT: C 14 GLN cc_start: 0.9280 (mt0) cc_final: 0.8990 (mt0) REVERT: C 16 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8783 (tt) REVERT: C 46 TRP cc_start: 0.8637 (t-100) cc_final: 0.8163 (t-100) REVERT: C 47 MET cc_start: 0.8809 (tpt) cc_final: 0.8449 (tpp) REVERT: C 115 ASP cc_start: 0.8670 (t70) cc_final: 0.8373 (t0) REVERT: C 254 LYS cc_start: 0.6888 (ptpt) cc_final: 0.6315 (ttpp) REVERT: C 262 ASN cc_start: 0.7593 (m-40) cc_final: 0.7360 (m-40) REVERT: C 303 ARG cc_start: 0.6905 (tpt170) cc_final: 0.6144 (mmt180) REVERT: D 14 GLN cc_start: 0.9280 (mt0) cc_final: 0.8988 (mt0) REVERT: D 16 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8773 (tt) REVERT: D 46 TRP cc_start: 0.8631 (t-100) cc_final: 0.8162 (t-100) REVERT: D 47 MET cc_start: 0.8801 (tpt) cc_final: 0.8442 (tpp) REVERT: D 115 ASP cc_start: 0.8644 (t70) cc_final: 0.8339 (t0) REVERT: D 254 LYS cc_start: 0.6869 (ptpt) cc_final: 0.6299 (ttpp) REVERT: D 262 ASN cc_start: 0.7600 (m-40) cc_final: 0.7360 (m-40) REVERT: D 303 ARG cc_start: 0.6884 (tpt170) cc_final: 0.6118 (mmt180) REVERT: E 14 GLN cc_start: 0.9273 (mt0) cc_final: 0.8984 (mt0) REVERT: E 16 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8777 (tt) REVERT: E 46 TRP cc_start: 0.8649 (t-100) cc_final: 0.8178 (t-100) REVERT: E 47 MET cc_start: 0.8819 (tpt) cc_final: 0.8460 (tpp) REVERT: E 115 ASP cc_start: 0.8694 (t70) cc_final: 0.8402 (t0) REVERT: E 254 LYS cc_start: 0.6869 (ptpt) cc_final: 0.6298 (ttpp) REVERT: E 262 ASN cc_start: 0.7600 (m-40) cc_final: 0.7367 (m-40) REVERT: E 303 ARG cc_start: 0.6879 (tpt170) cc_final: 0.6114 (mmt180) REVERT: F 14 GLN cc_start: 0.9273 (mt0) cc_final: 0.8981 (mt0) REVERT: F 16 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8790 (tt) REVERT: F 46 TRP cc_start: 0.8642 (t-100) cc_final: 0.8175 (t-100) REVERT: F 47 MET cc_start: 0.8804 (tpt) cc_final: 0.8446 (tpp) REVERT: F 115 ASP cc_start: 0.8655 (t70) cc_final: 0.8351 (t0) REVERT: F 254 LYS cc_start: 0.6868 (ptpt) cc_final: 0.6291 (ttpp) REVERT: F 262 ASN cc_start: 0.7605 (m-40) cc_final: 0.7363 (m-40) REVERT: F 303 ARG cc_start: 0.6873 (tpt170) cc_final: 0.6106 (mmt180) REVERT: G 14 GLN cc_start: 0.9275 (mt0) cc_final: 0.8983 (mt0) REVERT: G 16 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8780 (tt) REVERT: G 46 TRP cc_start: 0.8625 (t-100) cc_final: 0.8151 (t-100) REVERT: G 47 MET cc_start: 0.8824 (tpt) cc_final: 0.8467 (tpp) REVERT: G 115 ASP cc_start: 0.8680 (t70) cc_final: 0.8386 (t0) REVERT: G 254 LYS cc_start: 0.6879 (ptpt) cc_final: 0.6310 (ttpp) REVERT: G 262 ASN cc_start: 0.7592 (m-40) cc_final: 0.7355 (m-40) REVERT: G 303 ARG cc_start: 0.6874 (tpt170) cc_final: 0.6114 (mmt180) REVERT: H 14 GLN cc_start: 0.9274 (mt0) cc_final: 0.8981 (mt0) REVERT: H 16 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8788 (tt) REVERT: H 46 TRP cc_start: 0.8630 (t-100) cc_final: 0.8154 (t-100) REVERT: H 47 MET cc_start: 0.8804 (tpt) cc_final: 0.8447 (tpp) REVERT: H 115 ASP cc_start: 0.8691 (t70) cc_final: 0.8403 (t0) REVERT: H 224 ASN cc_start: 0.6690 (OUTLIER) cc_final: 0.6339 (t0) REVERT: H 254 LYS cc_start: 0.6850 (ptpt) cc_final: 0.6279 (ttpp) REVERT: H 262 ASN cc_start: 0.7538 (m-40) cc_final: 0.7323 (m-40) REVERT: H 303 ARG cc_start: 0.6943 (tpt170) cc_final: 0.6058 (mmt180) outliers start: 50 outliers final: 8 residues processed: 408 average time/residue: 0.6268 time to fit residues: 290.2619 Evaluate side-chains 393 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 375 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 224 ASN Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 278 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 83 optimal weight: 0.0270 chunk 168 optimal weight: 0.0980 chunk 79 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 201 optimal weight: 0.0050 chunk 266 optimal weight: 6.9990 overall best weight: 0.3852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 179 GLN A 224 ASN A 261 ASN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN B 179 GLN B 261 ASN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 179 GLN C 224 ASN C 261 ASN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN D 179 GLN D 261 ASN ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 179 GLN E 261 ASN ** E 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 179 GLN F 224 ASN F 261 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 179 GLN ** G 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 179 GLN ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.191510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115858 restraints weight = 115273.696| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 5.26 r_work: 0.2889 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23584 Z= 0.090 Angle : 0.479 4.785 31840 Z= 0.264 Chirality : 0.042 0.136 3416 Planarity : 0.003 0.030 4240 Dihedral : 4.290 26.148 3392 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.52 % Allowed : 16.09 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 2968 helix: 1.59 (0.13), residues: 1480 sheet: -0.05 (0.24), residues: 472 loop : -1.55 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 109 TYR 0.015 0.001 TYR G 314 PHE 0.009 0.001 PHE A 99 TRP 0.000 0.000 TRP A 46 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00189 (23584) covalent geometry : angle 0.47931 (31840) hydrogen bonds : bond 0.03111 ( 1152) hydrogen bonds : angle 4.44247 ( 3336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 399 time to evaluate : 0.775 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 46 TRP cc_start: 0.8337 (t-100) cc_final: 0.7814 (t-100) REVERT: A 47 MET cc_start: 0.8464 (tpt) cc_final: 0.8009 (tpp) REVERT: A 186 TYR cc_start: 0.7023 (t80) cc_final: 0.6819 (t80) REVERT: A 254 LYS cc_start: 0.6708 (ptpt) cc_final: 0.6150 (ttpp) REVERT: A 303 ARG cc_start: 0.6630 (tpt170) cc_final: 0.5883 (mmt180) REVERT: A 311 GLU cc_start: 0.6972 (tt0) cc_final: 0.6687 (mt-10) REVERT: B 46 TRP cc_start: 0.8358 (t-100) cc_final: 0.7834 (t-100) REVERT: B 47 MET cc_start: 0.8453 (tpt) cc_final: 0.7998 (tpp) REVERT: B 224 ASN cc_start: 0.6634 (OUTLIER) cc_final: 0.6292 (t0) REVERT: B 254 LYS cc_start: 0.6704 (ptpt) cc_final: 0.6141 (ttpp) REVERT: B 303 ARG cc_start: 0.6635 (tpt170) cc_final: 0.5869 (mmt180) REVERT: B 311 GLU cc_start: 0.6980 (tt0) cc_final: 0.6691 (mt-10) REVERT: C 46 TRP cc_start: 0.8340 (t-100) cc_final: 0.7817 (t-100) REVERT: C 47 MET cc_start: 0.8474 (tpt) cc_final: 0.8017 (tpp) REVERT: C 254 LYS cc_start: 0.6702 (ptpt) cc_final: 0.6144 (ttpp) REVERT: C 303 ARG cc_start: 0.6638 (tpt170) cc_final: 0.5874 (mmt180) REVERT: C 311 GLU cc_start: 0.6965 (tt0) cc_final: 0.6678 (mt-10) REVERT: D 46 TRP cc_start: 0.8364 (t-100) cc_final: 0.7844 (t-100) REVERT: D 47 MET cc_start: 0.8465 (tpt) cc_final: 0.8009 (tpp) REVERT: D 186 TYR cc_start: 0.7014 (t80) cc_final: 0.6811 (t80) REVERT: D 254 LYS cc_start: 0.6713 (ptpt) cc_final: 0.6153 (ttpp) REVERT: D 303 ARG cc_start: 0.6622 (tpt170) cc_final: 0.5865 (mmt180) REVERT: D 311 GLU cc_start: 0.6974 (tt0) cc_final: 0.6686 (mt-10) REVERT: E 46 TRP cc_start: 0.8357 (t-100) cc_final: 0.7837 (t-100) REVERT: E 47 MET cc_start: 0.8454 (tpt) cc_final: 0.7997 (tpp) REVERT: E 114 GLU cc_start: 0.8439 (tt0) cc_final: 0.8238 (tt0) REVERT: E 254 LYS cc_start: 0.6699 (ptpt) cc_final: 0.6138 (ttpp) REVERT: E 303 ARG cc_start: 0.6631 (tpt170) cc_final: 0.5872 (mmt180) REVERT: E 311 GLU cc_start: 0.6956 (tt0) cc_final: 0.6666 (mt-10) REVERT: F 46 TRP cc_start: 0.8351 (t-100) cc_final: 0.7831 (t-100) REVERT: F 47 MET cc_start: 0.8470 (tpt) cc_final: 0.8014 (tpp) REVERT: F 254 LYS cc_start: 0.6706 (ptpt) cc_final: 0.6148 (ttpp) REVERT: F 303 ARG cc_start: 0.6621 (tpt170) cc_final: 0.5867 (mmt180) REVERT: F 311 GLU cc_start: 0.6960 (tt0) cc_final: 0.6668 (mt-10) REVERT: G 46 TRP cc_start: 0.8365 (t-100) cc_final: 0.7843 (t-100) REVERT: G 47 MET cc_start: 0.8451 (tpt) cc_final: 0.7992 (tpp) REVERT: G 254 LYS cc_start: 0.6709 (ptpt) cc_final: 0.6150 (ttpp) REVERT: G 303 ARG cc_start: 0.6627 (tpt170) cc_final: 0.5874 (mmt180) REVERT: G 311 GLU cc_start: 0.6939 (tt0) cc_final: 0.6686 (mt-10) REVERT: H 46 TRP cc_start: 0.8346 (t-100) cc_final: 0.7821 (t-100) REVERT: H 47 MET cc_start: 0.8463 (tpt) cc_final: 0.8005 (tpp) REVERT: H 224 ASN cc_start: 0.6636 (OUTLIER) cc_final: 0.6290 (t0) REVERT: H 254 LYS cc_start: 0.6695 (ptpt) cc_final: 0.6140 (ttpp) REVERT: H 303 ARG cc_start: 0.6637 (tpt170) cc_final: 0.5866 (mmt180) REVERT: H 311 GLU cc_start: 0.6974 (tt0) cc_final: 0.6684 (mt-10) outliers start: 20 outliers final: 0 residues processed: 407 average time/residue: 0.6664 time to fit residues: 304.3650 Evaluate side-chains 365 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 363 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain H residue 224 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 165 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 179 GLN A 352 GLN B 5 GLN B 179 GLN B 352 GLN C 5 GLN C 179 GLN C 352 GLN D 5 GLN D 179 GLN D 224 ASN D 352 GLN E 5 GLN E 179 GLN E 224 ASN E 352 GLN F 5 GLN F 179 GLN F 352 GLN G 5 GLN G 179 GLN G 224 ASN G 352 GLN H 5 GLN H 179 GLN H 352 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.182951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103226 restraints weight = 114159.525| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 5.28 r_work: 0.2765 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 23584 Z= 0.298 Angle : 0.649 6.232 31840 Z= 0.346 Chirality : 0.049 0.145 3416 Planarity : 0.006 0.055 4240 Dihedral : 4.875 27.074 3392 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.87 % Allowed : 15.84 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 2968 helix: 1.20 (0.13), residues: 1464 sheet: -0.31 (0.24), residues: 456 loop : -1.45 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 364 TYR 0.023 0.003 TYR B 155 PHE 0.012 0.002 PHE D 4 TRP 0.004 0.001 TRP H 46 HIS 0.005 0.001 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00717 (23584) covalent geometry : angle 0.64925 (31840) hydrogen bonds : bond 0.05219 ( 1152) hydrogen bonds : angle 4.73772 ( 3336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 375 time to evaluate : 0.852 Fit side-chains REVERT: A 46 TRP cc_start: 0.8414 (t-100) cc_final: 0.7919 (t-100) REVERT: A 47 MET cc_start: 0.8482 (tpt) cc_final: 0.8078 (tpp) REVERT: A 254 LYS cc_start: 0.6790 (ptpt) cc_final: 0.6167 (ttpp) REVERT: A 303 ARG cc_start: 0.6781 (tpt170) cc_final: 0.5887 (mmt180) REVERT: B 46 TRP cc_start: 0.8416 (t-100) cc_final: 0.7925 (t-100) REVERT: B 47 MET cc_start: 0.8472 (tpt) cc_final: 0.8072 (tpp) REVERT: B 224 ASN cc_start: 0.6673 (t160) cc_final: 0.6351 (t0) REVERT: B 254 LYS cc_start: 0.6790 (ptpt) cc_final: 0.6169 (ttpp) REVERT: B 303 ARG cc_start: 0.6785 (tpt170) cc_final: 0.5739 (mmt180) REVERT: C 46 TRP cc_start: 0.8426 (t-100) cc_final: 0.7930 (t-100) REVERT: C 47 MET cc_start: 0.8490 (tpt) cc_final: 0.8088 (tpp) REVERT: C 254 LYS cc_start: 0.6765 (ptpt) cc_final: 0.6151 (ttpp) REVERT: C 303 ARG cc_start: 0.6793 (tpt170) cc_final: 0.5902 (mmt180) REVERT: D 46 TRP cc_start: 0.8424 (t-100) cc_final: 0.7930 (t-100) REVERT: D 47 MET cc_start: 0.8498 (tpt) cc_final: 0.8097 (tpp) REVERT: D 254 LYS cc_start: 0.6764 (ptpt) cc_final: 0.6153 (ttpp) REVERT: D 303 ARG cc_start: 0.6767 (tpt170) cc_final: 0.5848 (mmt180) REVERT: E 46 TRP cc_start: 0.8436 (t-100) cc_final: 0.7944 (t-100) REVERT: E 47 MET cc_start: 0.8496 (tpt) cc_final: 0.8094 (tpp) REVERT: E 254 LYS cc_start: 0.6769 (ptpt) cc_final: 0.6153 (ttpp) REVERT: E 303 ARG cc_start: 0.6785 (tpt170) cc_final: 0.5886 (mmt180) REVERT: F 46 TRP cc_start: 0.8429 (t-100) cc_final: 0.7936 (t-100) REVERT: F 47 MET cc_start: 0.8497 (tpt) cc_final: 0.8096 (tpp) REVERT: F 254 LYS cc_start: 0.6777 (ptpt) cc_final: 0.6160 (ttpp) REVERT: F 303 ARG cc_start: 0.6765 (tpt170) cc_final: 0.5852 (mmt180) REVERT: G 46 TRP cc_start: 0.8424 (t-100) cc_final: 0.7929 (t-100) REVERT: G 47 MET cc_start: 0.8492 (tpt) cc_final: 0.8090 (tpp) REVERT: G 254 LYS cc_start: 0.6762 (ptpt) cc_final: 0.6149 (ttpp) REVERT: G 303 ARG cc_start: 0.6768 (tpt170) cc_final: 0.5874 (mmt180) REVERT: H 46 TRP cc_start: 0.8418 (t-100) cc_final: 0.7922 (t-100) REVERT: H 47 MET cc_start: 0.8482 (tpt) cc_final: 0.8082 (tpp) REVERT: H 254 LYS cc_start: 0.6782 (ptpt) cc_final: 0.6161 (ttpp) REVERT: H 303 ARG cc_start: 0.6796 (tpt170) cc_final: 0.5771 (mmt180) outliers start: 52 outliers final: 7 residues processed: 406 average time/residue: 0.6350 time to fit residues: 291.6287 Evaluate side-chains 390 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 383 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 222 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 179 GLN A 224 ASN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN B 179 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 179 GLN C 224 ASN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN D 179 GLN ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 179 GLN ** E 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 179 GLN F 224 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 179 GLN ** G 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 179 GLN ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.186705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107429 restraints weight = 108911.249| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 5.38 r_work: 0.2812 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23584 Z= 0.120 Angle : 0.515 5.283 31840 Z= 0.282 Chirality : 0.044 0.141 3416 Planarity : 0.003 0.028 4240 Dihedral : 4.507 26.128 3392 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.39 % Allowed : 17.06 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 2968 helix: 1.51 (0.13), residues: 1472 sheet: -0.25 (0.24), residues: 472 loop : -1.39 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 109 TYR 0.020 0.002 TYR B 155 PHE 0.009 0.001 PHE D 99 TRP 0.001 0.000 TRP H 46 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00271 (23584) covalent geometry : angle 0.51510 (31840) hydrogen bonds : bond 0.03716 ( 1152) hydrogen bonds : angle 4.50469 ( 3336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 410 time to evaluate : 0.839 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 9 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8122 (tptp) REVERT: A 16 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8716 (tt) REVERT: A 46 TRP cc_start: 0.8478 (t-100) cc_final: 0.8003 (t-100) REVERT: A 47 MET cc_start: 0.8541 (tpt) cc_final: 0.8164 (tpp) REVERT: A 254 LYS cc_start: 0.6840 (ptpt) cc_final: 0.6221 (ttpp) REVERT: A 303 ARG cc_start: 0.6841 (tpt170) cc_final: 0.5944 (mmt180) REVERT: B 9 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8125 (tptp) REVERT: B 16 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8721 (tt) REVERT: B 46 TRP cc_start: 0.8478 (t-100) cc_final: 0.8004 (t-100) REVERT: B 47 MET cc_start: 0.8543 (tpt) cc_final: 0.8170 (tpp) REVERT: B 224 ASN cc_start: 0.6686 (t160) cc_final: 0.6358 (t0) REVERT: B 254 LYS cc_start: 0.6862 (ptpt) cc_final: 0.6242 (ttpp) REVERT: B 303 ARG cc_start: 0.6714 (tpt170) cc_final: 0.5994 (mmt180) REVERT: C 9 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8136 (tptp) REVERT: C 16 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8706 (tt) REVERT: C 46 TRP cc_start: 0.8478 (t-100) cc_final: 0.7998 (t-100) REVERT: C 47 MET cc_start: 0.8555 (tpt) cc_final: 0.8177 (tpp) REVERT: C 254 LYS cc_start: 0.6838 (ptpt) cc_final: 0.6226 (ttpp) REVERT: C 303 ARG cc_start: 0.6839 (tpt170) cc_final: 0.5945 (mmt180) REVERT: D 9 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8125 (tptp) REVERT: D 16 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8715 (tt) REVERT: D 46 TRP cc_start: 0.8490 (t-100) cc_final: 0.8014 (t-100) REVERT: D 47 MET cc_start: 0.8567 (tpt) cc_final: 0.8192 (tpp) REVERT: D 254 LYS cc_start: 0.6848 (ptpt) cc_final: 0.6228 (ttpp) REVERT: D 303 ARG cc_start: 0.6833 (tpt170) cc_final: 0.5931 (mmt180) REVERT: E 9 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8135 (tptp) REVERT: E 16 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8698 (tt) REVERT: E 46 TRP cc_start: 0.8501 (t-100) cc_final: 0.8025 (t-100) REVERT: E 47 MET cc_start: 0.8572 (tpt) cc_final: 0.8196 (tpp) REVERT: E 254 LYS cc_start: 0.6830 (ptpt) cc_final: 0.6219 (ttpp) REVERT: E 303 ARG cc_start: 0.6841 (tpt170) cc_final: 0.5939 (mmt180) REVERT: F 9 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8128 (tptp) REVERT: F 16 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8714 (tt) REVERT: F 46 TRP cc_start: 0.8500 (t-100) cc_final: 0.8024 (t-100) REVERT: F 47 MET cc_start: 0.8570 (tpt) cc_final: 0.8194 (tpp) REVERT: F 254 LYS cc_start: 0.6845 (ptpt) cc_final: 0.6230 (ttpp) REVERT: F 303 ARG cc_start: 0.6836 (tpt170) cc_final: 0.5935 (mmt180) REVERT: G 9 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8134 (tptp) REVERT: G 16 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8708 (tt) REVERT: G 46 TRP cc_start: 0.8502 (t-100) cc_final: 0.8026 (t-100) REVERT: G 47 MET cc_start: 0.8586 (tpt) cc_final: 0.8210 (tpp) REVERT: G 254 LYS cc_start: 0.6819 (ptpt) cc_final: 0.6208 (ttpp) REVERT: G 303 ARG cc_start: 0.6841 (tpt170) cc_final: 0.5943 (mmt180) REVERT: H 9 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8136 (tptp) REVERT: H 16 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8713 (tt) REVERT: H 46 TRP cc_start: 0.8478 (t-100) cc_final: 0.7997 (t-100) REVERT: H 47 MET cc_start: 0.8540 (tpt) cc_final: 0.8165 (tpp) REVERT: H 224 ASN cc_start: 0.6658 (t160) cc_final: 0.6327 (t0) REVERT: H 254 LYS cc_start: 0.6852 (ptpt) cc_final: 0.6235 (ttpp) REVERT: H 303 ARG cc_start: 0.6699 (tpt170) cc_final: 0.5979 (mmt180) outliers start: 17 outliers final: 1 residues processed: 419 average time/residue: 0.6457 time to fit residues: 305.4102 Evaluate side-chains 391 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 382 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 190 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 22 optimal weight: 0.0670 chunk 266 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 269 optimal weight: 30.0000 chunk 136 optimal weight: 3.9990 chunk 276 optimal weight: 0.0770 overall best weight: 1.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 179 GLN A 352 GLN B 5 GLN B 179 GLN B 352 GLN C 5 GLN C 179 GLN C 352 GLN D 5 GLN D 179 GLN D 224 ASN D 352 GLN E 5 GLN E 179 GLN E 224 ASN E 352 GLN F 5 GLN F 179 GLN F 352 GLN G 5 GLN G 179 GLN G 224 ASN G 352 GLN H 5 GLN H 179 GLN H 352 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.185777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106036 restraints weight = 107485.218| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 5.18 r_work: 0.2801 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23584 Z= 0.150 Angle : 0.540 5.664 31840 Z= 0.292 Chirality : 0.044 0.140 3416 Planarity : 0.004 0.028 4240 Dihedral : 4.546 27.377 3392 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.24 % Allowed : 15.41 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 2968 helix: 1.53 (0.13), residues: 1472 sheet: -0.29 (0.24), residues: 472 loop : -1.38 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 109 TYR 0.023 0.002 TYR C 155 PHE 0.008 0.002 PHE E 99 TRP 0.002 0.000 TRP G 46 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00352 (23584) covalent geometry : angle 0.53995 (31840) hydrogen bonds : bond 0.03949 ( 1152) hydrogen bonds : angle 4.48675 ( 3336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8892.66 seconds wall clock time: 151 minutes 40.99 seconds (9100.99 seconds total)