Starting phenix.real_space_refine on Mon Aug 25 12:09:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ff5_29040/08_2025/8ff5_29040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ff5_29040/08_2025/8ff5_29040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ff5_29040/08_2025/8ff5_29040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ff5_29040/08_2025/8ff5_29040.map" model { file = "/net/cci-nas-00/data/ceres_data/8ff5_29040/08_2025/8ff5_29040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ff5_29040/08_2025/8ff5_29040.cif" } resolution = 3.13 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= 0.005 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 859 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 136 5.49 5 S 94 5.16 5 C 16944 2.51 5 N 4614 2.21 5 O 5336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27124 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1702 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2330 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "H" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 26, 'rna3p': 36} Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1079 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "O" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Time building chain proxies: 5.30, per 1000 atoms: 0.20 Number of scatterers: 27124 At special positions: 0 Unit cell: (110.67, 129.642, 219.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 136 15.00 O 5336 8.00 N 4614 7.00 C 16944 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: 1.85 Conformation dependent library (CDL) restraints added in 628.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5546 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 44 sheets defined 39.3% alpha, 21.2% beta 47 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.635A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.617A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 removed outlier: 3.873A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.898A pdb=" N GLY C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 285 removed outlier: 3.611A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.535A pdb=" N MET C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.645A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.752A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.018A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 removed outlier: 3.612A pdb=" N MET D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.586A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.772A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 285 removed outlier: 3.911A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 removed outlier: 3.645A pdb=" N MET E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.634A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.933A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.532A pdb=" N GLY F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.716A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 removed outlier: 3.542A pdb=" N MET F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 56 through 72 removed outlier: 3.749A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.671A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.518A pdb=" N ILE G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.950A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 Processing helix chain 'G' and resid 301 through 317 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 56 through 71 removed outlier: 3.526A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.672A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.886A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.946A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 Processing helix chain 'H' and resid 301 through 318 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 42 through 50 removed outlier: 5.246A pdb=" N GLY I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY I 48 " --> pdb=" O GLN I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.940A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 253 through 257 removed outlier: 3.572A pdb=" N PHE I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 253 through 257' Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 removed outlier: 3.642A pdb=" N SER I 346 " --> pdb=" O ASN I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 367 Processing helix chain 'I' and resid 373 through 393 removed outlier: 3.956A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY I 385 " --> pdb=" O SER I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 421 removed outlier: 4.545A pdb=" N TYR I 399 " --> pdb=" O GLU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 Processing helix chain 'I' and resid 445 through 461 removed outlier: 3.755A pdb=" N GLY I 461 " --> pdb=" O LEU I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 5 through 33 Processing helix chain 'J' and resid 41 through 54 Processing helix chain 'J' and resid 58 through 73 removed outlier: 6.086A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'J' and resid 93 through 108 Processing helix chain 'J' and resid 109 through 112 Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 Processing helix chain 'K' and resid 58 through 73 removed outlier: 6.029A pdb=" N TYR K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 81 removed outlier: 3.769A pdb=" N HIS K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 91 removed outlier: 4.059A pdb=" N ILE K 85 " --> pdb=" O HIS K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 109 removed outlier: 4.606A pdb=" N LYS K 109 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.800A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 removed outlier: 3.550A pdb=" N HIS L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 92 Processing helix chain 'L' and resid 93 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.984A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.568A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 160 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.994A pdb=" N ILE A 6 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP A 104 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 8 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 102 " --> pdb=" O TYR A 8 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP A 10 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 100 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.489A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.489A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 removed outlier: 6.294A pdb=" N PHE B 177 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 119 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB4, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 225 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 276 " --> pdb=" O TYR D 299 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 156 Processing sheet with id=AB9, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.620A pdb=" N SER E 225 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 276 " --> pdb=" O TYR E 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.565A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'E' and resid 155 through 159 Processing sheet with id=AC7, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR F 182 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 15 " --> pdb=" O TRP F 230 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TRP F 230 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR F 17 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE F 228 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR F 19 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU F 226 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU F 21 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 276 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.690A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD3, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.398A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR G 183 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA G 145 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLN G 181 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 225 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.782A pdb=" N GLY G 25 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'G' and resid 77 through 80 Processing sheet with id=AD7, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD8, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE2, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE3, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.081A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 61 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 11 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AE5, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.592A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AE7, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.376A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 332 through 333 1087 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 5.16 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8138 1.34 - 1.46: 7686 1.46 - 1.59: 11827 1.59 - 1.71: 266 1.71 - 1.84: 149 Bond restraints: 28066 Sorted by residual: bond pdb=" CA ASP D 246 " pdb=" C ASP D 246 " ideal model delta sigma weight residual 1.524 1.508 0.016 8.10e-03 1.52e+04 3.84e+00 bond pdb=" O3' DC N 50 " pdb=" P DT N 51 " ideal model delta sigma weight residual 1.607 1.635 -0.028 1.50e-02 4.44e+03 3.51e+00 bond pdb=" C PRO A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.329 1.350 -0.020 1.25e-02 6.40e+03 2.60e+00 bond pdb=" CA VAL I 205 " pdb=" C VAL I 205 " ideal model delta sigma weight residual 1.520 1.534 -0.014 8.80e-03 1.29e+04 2.49e+00 bond pdb=" C LEU I 379 " pdb=" O LEU I 379 " ideal model delta sigma weight residual 1.236 1.219 0.018 1.15e-02 7.56e+03 2.45e+00 ... (remaining 28061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 37684 2.02 - 4.03: 725 4.03 - 6.05: 87 6.05 - 8.06: 16 8.06 - 10.08: 2 Bond angle restraints: 38514 Sorted by residual: angle pdb=" C THR B 157 " pdb=" N PRO B 158 " pdb=" CA PRO B 158 " ideal model delta sigma weight residual 119.76 115.31 4.45 1.03e+00 9.43e-01 1.87e+01 angle pdb=" N GLY I 355 " pdb=" CA GLY I 355 " pdb=" C GLY I 355 " ideal model delta sigma weight residual 115.21 109.83 5.38 1.30e+00 5.92e-01 1.71e+01 angle pdb=" C ILE B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 120.49 126.34 -5.85 1.42e+00 4.96e-01 1.70e+01 angle pdb=" C PRO A 200 " pdb=" N PRO A 201 " pdb=" CA PRO A 201 " ideal model delta sigma weight residual 120.14 115.79 4.35 1.06e+00 8.90e-01 1.68e+01 angle pdb=" N GLN I 45 " pdb=" CA GLN I 45 " pdb=" C GLN I 45 " ideal model delta sigma weight residual 112.23 107.18 5.05 1.26e+00 6.30e-01 1.61e+01 ... (remaining 38509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 15733 35.81 - 71.62: 822 71.62 - 107.43: 60 107.43 - 143.24: 4 143.24 - 179.04: 5 Dihedral angle restraints: 16624 sinusoidal: 7965 harmonic: 8659 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 20.96 179.04 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 60.29 139.71 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual 232.00 66.54 165.46 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 16621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3317 0.046 - 0.091: 623 0.091 - 0.137: 174 0.137 - 0.183: 14 0.183 - 0.228: 5 Chirality restraints: 4133 Sorted by residual: chirality pdb=" C3' A M 38 " pdb=" C4' A M 38 " pdb=" O3' A M 38 " pdb=" C2' A M 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE J 13 " pdb=" CA ILE J 13 " pdb=" CG1 ILE J 13 " pdb=" CG2 ILE J 13 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA MET A 1 " pdb=" N MET A 1 " pdb=" C MET A 1 " pdb=" CB MET A 1 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4130 not shown) Planarity restraints: 4439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " 0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO F 247 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C PHE J 61 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 246 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO E 247 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 247 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 247 " 0.041 5.00e-02 4.00e+02 ... (remaining 4436 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 190 2.49 - 3.09: 19801 3.09 - 3.69: 44453 3.69 - 4.30: 65577 4.30 - 4.90: 104498 Nonbonded interactions: 234519 Sorted by model distance: nonbonded pdb=" C5' DG O 10 " pdb=" O6 DG O 11 " model vdw 1.886 3.440 nonbonded pdb=" O4 U M 35 " pdb=" N6 A M 36 " model vdw 2.163 3.120 nonbonded pdb=" O4 U M 23 " pdb=" N6 A M 24 " model vdw 2.164 3.120 nonbonded pdb=" C5' DG O 10 " pdb=" C6 DG O 11 " model vdw 2.185 3.660 nonbonded pdb=" OG SER E 28 " pdb=" O GLU E 174 " model vdw 2.211 3.040 ... (remaining 234514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.930 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 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 : 0.003 0.060 28066 Z= 0.165 Angle : 0.657 10.079 38514 Z= 0.377 Chirality : 0.040 0.228 4133 Planarity : 0.005 0.088 4439 Dihedral : 19.538 179.045 11078 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.16 % Favored : 92.16 % Rotamer: Outliers : 0.95 % Allowed : 20.05 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.20 (0.16), residues: 2921 helix: 1.34 (0.16), residues: 1001 sheet: -0.86 (0.20), residues: 619 loop : -0.87 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 213 TYR 0.038 0.001 TYR C 244 PHE 0.019 0.001 PHE G 234 TRP 0.038 0.001 TRP I 63 HIS 0.005 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00323 (28066) covalent geometry : angle 0.65709 (38514) hydrogen bonds : bond 0.18246 ( 1150) hydrogen bonds : angle 6.85381 ( 3233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 368 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASN cc_start: 0.8214 (m-40) cc_final: 0.7877 (p0) REVERT: C 155 VAL cc_start: 0.8718 (p) cc_final: 0.8509 (p) REVERT: C 172 PHE cc_start: 0.6419 (m-10) cc_final: 0.5925 (m-10) REVERT: E 15 TYR cc_start: 0.8489 (m-80) cc_final: 0.8186 (m-80) REVERT: E 108 LEU cc_start: 0.8204 (tt) cc_final: 0.7872 (tt) REVERT: E 248 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7475 (mptt) REVERT: F 48 ASN cc_start: 0.8678 (m-40) cc_final: 0.8408 (t0) REVERT: F 144 MET cc_start: 0.8830 (mtm) cc_final: 0.8242 (mtm) REVERT: F 205 MET cc_start: 0.8489 (mmp) cc_final: 0.8078 (mmm) REVERT: G 135 GLN cc_start: 0.8447 (pt0) cc_final: 0.8182 (pt0) REVERT: I 310 ILE cc_start: 0.7768 (mt) cc_final: 0.6967 (mm) REVERT: I 443 CYS cc_start: 0.8878 (m) cc_final: 0.8653 (m) REVERT: J 38 ASP cc_start: 0.6373 (t0) cc_final: 0.6117 (m-30) REVERT: J 53 ASN cc_start: 0.7992 (t0) cc_final: 0.7588 (m-40) REVERT: K 38 ASP cc_start: 0.8389 (t0) cc_final: 0.8141 (t0) REVERT: K 47 ARG cc_start: 0.8730 (ttt90) cc_final: 0.8433 (ttt90) REVERT: L 43 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8659 (tppt) REVERT: L 51 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7974 (mm-30) REVERT: L 80 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8273 (mt-10) REVERT: L 96 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8363 (mp0) outliers start: 25 outliers final: 3 residues processed: 387 average time/residue: 0.1815 time to fit residues: 106.8858 Evaluate side-chains 218 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain I residue 358 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 193 GLN B 195 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 ASN ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.102513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.074435 restraints weight = 98095.655| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.14 r_work: 0.3326 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28066 Z= 0.195 Angle : 0.648 7.676 38514 Z= 0.347 Chirality : 0.042 0.238 4133 Planarity : 0.005 0.093 4439 Dihedral : 19.347 175.763 5061 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.85 % Favored : 92.64 % Rotamer: Outliers : 3.12 % Allowed : 17.91 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.09 (0.16), residues: 2921 helix: 1.62 (0.16), residues: 1008 sheet: -0.68 (0.22), residues: 563 loop : -0.78 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 98 TYR 0.025 0.002 TYR A 175 PHE 0.020 0.002 PHE G 234 TRP 0.027 0.001 TRP I 73 HIS 0.010 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00436 (28066) covalent geometry : angle 0.64765 (38514) hydrogen bonds : bond 0.04510 ( 1150) hydrogen bonds : angle 5.01401 ( 3233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 218 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7510 (t0) cc_final: 0.6973 (t70) REVERT: A 167 ASN cc_start: 0.8242 (m-40) cc_final: 0.7768 (p0) REVERT: B 98 PHE cc_start: 0.4771 (OUTLIER) cc_final: 0.4383 (t80) REVERT: B 116 TYR cc_start: 0.0868 (OUTLIER) cc_final: 0.0618 (t80) REVERT: E 137 MET cc_start: 0.8629 (tpt) cc_final: 0.8382 (tpt) REVERT: F 144 MET cc_start: 0.9076 (mtm) cc_final: 0.8830 (mtp) REVERT: F 205 MET cc_start: 0.8423 (mmp) cc_final: 0.8067 (mmm) REVERT: G 32 ASP cc_start: 0.8174 (p0) cc_final: 0.7958 (p0) REVERT: G 137 MET cc_start: 0.8611 (tpp) cc_final: 0.8254 (tpp) REVERT: G 160 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8460 (mttp) REVERT: G 170 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7356 (pt) REVERT: G 221 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7939 (t80) REVERT: H 250 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7257 (mtmm) REVERT: I 74 LEU cc_start: 0.9556 (tp) cc_final: 0.9216 (pp) REVERT: I 187 GLN cc_start: 0.8943 (pm20) cc_final: 0.8483 (pp30) REVERT: I 323 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7767 (mmtt) REVERT: J 38 ASP cc_start: 0.6454 (t0) cc_final: 0.6047 (m-30) REVERT: K 38 ASP cc_start: 0.8495 (t0) cc_final: 0.8206 (t0) REVERT: K 47 ARG cc_start: 0.8897 (ttt90) cc_final: 0.8598 (ttt90) REVERT: L 51 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8308 (mm-30) REVERT: L 97 ILE cc_start: 0.9311 (mm) cc_final: 0.9015 (mt) outliers start: 82 outliers final: 20 residues processed: 292 average time/residue: 0.1701 time to fit residues: 77.0140 Evaluate side-chains 217 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 261 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 276 optimal weight: 0.4980 chunk 289 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS E 135 GLN E 266 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN F 233 HIS ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.098437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069490 restraints weight = 98793.116| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.02 r_work: 0.3208 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 28066 Z= 0.309 Angle : 0.725 10.116 38514 Z= 0.386 Chirality : 0.045 0.210 4133 Planarity : 0.006 0.093 4439 Dihedral : 19.402 172.579 5055 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.09 % Favored : 92.37 % Rotamer: Outliers : 3.28 % Allowed : 17.68 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.11 (0.16), residues: 2921 helix: 1.25 (0.16), residues: 1012 sheet: -0.85 (0.22), residues: 564 loop : -0.68 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 46 TYR 0.027 0.002 TYR F 244 PHE 0.025 0.002 PHE L 26 TRP 0.030 0.002 TRP A 104 HIS 0.006 0.001 HIS F 171 Details of bonding type rmsd covalent geometry : bond 0.00694 (28066) covalent geometry : angle 0.72486 (38514) hydrogen bonds : bond 0.04839 ( 1150) hydrogen bonds : angle 4.99928 ( 3233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 200 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7451 (tpp) REVERT: A 113 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8898 (mm-40) REVERT: A 166 ASP cc_start: 0.7915 (t0) cc_final: 0.7442 (t0) REVERT: A 167 ASN cc_start: 0.8333 (m-40) cc_final: 0.7846 (p0) REVERT: B 98 PHE cc_start: 0.4753 (OUTLIER) cc_final: 0.4441 (t80) REVERT: B 116 TYR cc_start: 0.0536 (OUTLIER) cc_final: 0.0170 (t80) REVERT: C 295 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8663 (tptp) REVERT: D 137 MET cc_start: 0.8238 (tpp) cc_final: 0.7869 (tpp) REVERT: D 305 MET cc_start: 0.8122 (tmm) cc_final: 0.7871 (tmm) REVERT: F 205 MET cc_start: 0.8536 (mmp) cc_final: 0.8291 (mmm) REVERT: G 137 MET cc_start: 0.8726 (tpp) cc_final: 0.8462 (tpp) REVERT: G 170 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7458 (pt) REVERT: H 140 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8155 (tp) REVERT: I 323 LYS cc_start: 0.8454 (mmmt) cc_final: 0.7997 (mmtt) REVERT: I 358 TRP cc_start: 0.6154 (OUTLIER) cc_final: 0.5879 (p90) REVERT: J 38 ASP cc_start: 0.6525 (t0) cc_final: 0.6065 (m-30) REVERT: J 67 ASP cc_start: 0.7778 (m-30) cc_final: 0.7570 (t0) REVERT: K 38 ASP cc_start: 0.8538 (t0) cc_final: 0.8221 (t0) REVERT: L 51 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8204 (mm-30) outliers start: 86 outliers final: 38 residues processed: 274 average time/residue: 0.1793 time to fit residues: 75.7328 Evaluate side-chains 214 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 181 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 238 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 255 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 23 optimal weight: 50.0000 chunk 282 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 292 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN J 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.099316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070658 restraints weight = 97462.107| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.07 r_work: 0.3246 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28066 Z= 0.194 Angle : 0.623 9.793 38514 Z= 0.334 Chirality : 0.041 0.187 4133 Planarity : 0.005 0.091 4439 Dihedral : 19.262 168.976 5055 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.02 % Favored : 92.47 % Rotamer: Outliers : 2.36 % Allowed : 18.52 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.07 (0.16), residues: 2921 helix: 1.40 (0.16), residues: 1017 sheet: -0.94 (0.21), residues: 578 loop : -0.71 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 98 TYR 0.020 0.002 TYR E 244 PHE 0.013 0.001 PHE G 234 TRP 0.033 0.001 TRP I 73 HIS 0.007 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00433 (28066) covalent geometry : angle 0.62279 (38514) hydrogen bonds : bond 0.03878 ( 1150) hydrogen bonds : angle 4.71752 ( 3233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.898 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 24 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7158 (tpp) REVERT: A 166 ASP cc_start: 0.7887 (t0) cc_final: 0.7677 (t0) REVERT: B 98 PHE cc_start: 0.4738 (OUTLIER) cc_final: 0.4454 (t80) REVERT: D 135 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: D 305 MET cc_start: 0.8197 (tmm) cc_final: 0.7953 (tmm) REVERT: F 166 ASP cc_start: 0.8098 (t0) cc_final: 0.7852 (t0) REVERT: G 137 MET cc_start: 0.8740 (tpp) cc_final: 0.8478 (tpp) REVERT: G 170 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7364 (pt) REVERT: I 21 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6742 (ttm) REVERT: I 187 GLN cc_start: 0.9038 (pm20) cc_final: 0.8584 (pp30) REVERT: I 303 MET cc_start: 0.8158 (mmm) cc_final: 0.7885 (mmm) REVERT: I 323 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8011 (mmtt) REVERT: I 389 MET cc_start: 0.3109 (ttm) cc_final: 0.2408 (ttp) REVERT: I 439 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8001 (tp30) REVERT: J 38 ASP cc_start: 0.6443 (t0) cc_final: 0.5984 (m-30) REVERT: J 67 ASP cc_start: 0.7772 (m-30) cc_final: 0.7508 (t0) REVERT: J 71 ARG cc_start: 0.8398 (mtt180) cc_final: 0.7743 (mtt-85) REVERT: K 38 ASP cc_start: 0.8565 (t0) cc_final: 0.8275 (t0) REVERT: L 47 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8678 (tpt-90) outliers start: 62 outliers final: 29 residues processed: 234 average time/residue: 0.1715 time to fit residues: 63.3832 Evaluate side-chains 206 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 300 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 234 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 251 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS E 42 GLN E 284 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.098094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.069351 restraints weight = 98067.781| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.01 r_work: 0.3208 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28066 Z= 0.276 Angle : 0.661 11.134 38514 Z= 0.352 Chirality : 0.042 0.207 4133 Planarity : 0.005 0.091 4439 Dihedral : 19.267 166.274 5055 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.46 % Favored : 92.02 % Rotamer: Outliers : 3.09 % Allowed : 18.37 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.20 (0.16), residues: 2921 helix: 1.24 (0.16), residues: 1019 sheet: -0.95 (0.21), residues: 579 loop : -0.76 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 71 TYR 0.023 0.002 TYR L 11 PHE 0.018 0.002 PHE J 78 TRP 0.031 0.002 TRP I 73 HIS 0.006 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00622 (28066) covalent geometry : angle 0.66063 (38514) hydrogen bonds : bond 0.04187 ( 1150) hydrogen bonds : angle 4.76417 ( 3233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 169 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: D 305 MET cc_start: 0.8272 (tmm) cc_final: 0.8059 (tmm) REVERT: F 166 ASP cc_start: 0.8214 (t0) cc_final: 0.7883 (t0) REVERT: G 137 MET cc_start: 0.8708 (tpp) cc_final: 0.8447 (tpp) REVERT: G 170 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7429 (pt) REVERT: H 140 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8157 (tp) REVERT: I 21 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6587 (ttm) REVERT: I 389 MET cc_start: 0.3291 (ttm) cc_final: 0.2592 (ttp) REVERT: I 439 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8037 (tp30) REVERT: J 38 ASP cc_start: 0.6528 (t0) cc_final: 0.6025 (m-30) REVERT: J 67 ASP cc_start: 0.7874 (m-30) cc_final: 0.7668 (t0) REVERT: J 71 ARG cc_start: 0.8546 (mtt180) cc_final: 0.7986 (mtt-85) REVERT: K 38 ASP cc_start: 0.8526 (t0) cc_final: 0.8244 (t0) REVERT: L 47 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8609 (tpt-90) outliers start: 81 outliers final: 52 residues processed: 234 average time/residue: 0.1560 time to fit residues: 59.0471 Evaluate side-chains 217 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 135 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 30 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.098845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.070337 restraints weight = 97651.668| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.06 r_work: 0.3241 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28066 Z= 0.190 Angle : 0.616 11.187 38514 Z= 0.328 Chirality : 0.041 0.189 4133 Planarity : 0.005 0.090 4439 Dihedral : 19.225 169.565 5055 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.98 % Favored : 92.54 % Rotamer: Outliers : 2.32 % Allowed : 19.32 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.09 (0.16), residues: 2921 helix: 1.34 (0.16), residues: 1020 sheet: -0.88 (0.22), residues: 578 loop : -0.73 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 71 TYR 0.017 0.001 TYR L 11 PHE 0.027 0.001 PHE B 98 TRP 0.021 0.001 TRP I 359 HIS 0.007 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00430 (28066) covalent geometry : angle 0.61637 (38514) hydrogen bonds : bond 0.03752 ( 1150) hydrogen bonds : angle 4.63628 ( 3233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 1.041 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 24 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: A 140 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7814 (tp30) REVERT: D 305 MET cc_start: 0.8311 (tmm) cc_final: 0.8074 (tmm) REVERT: F 77 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8441 (mtm110) REVERT: F 108 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8791 (tt) REVERT: F 166 ASP cc_start: 0.8091 (t0) cc_final: 0.7784 (t0) REVERT: G 170 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7345 (pt) REVERT: I 21 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6660 (ttm) REVERT: I 389 MET cc_start: 0.3599 (ttm) cc_final: 0.2896 (ttp) REVERT: I 439 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8016 (tp30) REVERT: J 38 ASP cc_start: 0.6357 (t0) cc_final: 0.5928 (m-30) REVERT: J 67 ASP cc_start: 0.7896 (m-30) cc_final: 0.7658 (t0) REVERT: J 71 ARG cc_start: 0.8440 (mtt180) cc_final: 0.7884 (mtt-85) REVERT: J 112 ASP cc_start: 0.3953 (OUTLIER) cc_final: 0.2661 (p0) REVERT: K 38 ASP cc_start: 0.8629 (t0) cc_final: 0.8350 (t0) REVERT: L 47 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8625 (tpt-90) outliers start: 61 outliers final: 38 residues processed: 218 average time/residue: 0.1732 time to fit residues: 59.5594 Evaluate side-chains 205 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 219 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 214 optimal weight: 50.0000 chunk 160 optimal weight: 6.9990 chunk 38 optimal weight: 40.0000 chunk 237 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 226 optimal weight: 0.2980 chunk 224 optimal weight: 20.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 30 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.097738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.069244 restraints weight = 97755.158| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.03 r_work: 0.3205 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 28066 Z= 0.259 Angle : 0.650 9.945 38514 Z= 0.345 Chirality : 0.042 0.202 4133 Planarity : 0.005 0.089 4439 Dihedral : 19.219 171.089 5055 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.70 % Favored : 91.82 % Rotamer: Outliers : 2.86 % Allowed : 19.36 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.19 (0.16), residues: 2921 helix: 1.22 (0.16), residues: 1025 sheet: -0.86 (0.22), residues: 575 loop : -0.78 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 71 TYR 0.020 0.002 TYR G 182 PHE 0.020 0.002 PHE B 98 TRP 0.021 0.001 TRP I 359 HIS 0.006 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00585 (28066) covalent geometry : angle 0.65022 (38514) hydrogen bonds : bond 0.04083 ( 1150) hydrogen bonds : angle 4.69866 ( 3233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7173 (tpp) REVERT: D 305 MET cc_start: 0.8364 (tmm) cc_final: 0.8130 (tmm) REVERT: F 77 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8458 (mtm110) REVERT: F 166 ASP cc_start: 0.8180 (t0) cc_final: 0.7903 (t0) REVERT: G 170 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7376 (pt) REVERT: I 21 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6637 (ttm) REVERT: I 187 GLN cc_start: 0.9096 (pm20) cc_final: 0.8657 (pp30) REVERT: I 358 TRP cc_start: 0.6282 (OUTLIER) cc_final: 0.5840 (p90) REVERT: I 439 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8089 (tp30) REVERT: J 22 MET cc_start: 0.7558 (ppp) cc_final: 0.7279 (ppp) REVERT: J 38 ASP cc_start: 0.6318 (t0) cc_final: 0.5900 (m-30) REVERT: J 41 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6467 (pp) REVERT: J 67 ASP cc_start: 0.7893 (m-30) cc_final: 0.7691 (t0) REVERT: J 71 ARG cc_start: 0.8452 (mtt180) cc_final: 0.7945 (mtt-85) REVERT: J 112 ASP cc_start: 0.4164 (OUTLIER) cc_final: 0.2619 (p0) REVERT: K 38 ASP cc_start: 0.8635 (t0) cc_final: 0.8342 (t0) REVERT: L 47 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8626 (tpt-90) outliers start: 75 outliers final: 52 residues processed: 229 average time/residue: 0.1616 time to fit residues: 58.7600 Evaluate side-chains 217 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 157 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 252 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 41 optimal weight: 40.0000 chunk 163 optimal weight: 8.9990 chunk 280 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 251 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 162 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 30 ASN C 215 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.098721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070361 restraints weight = 97400.595| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.04 r_work: 0.3236 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28066 Z= 0.180 Angle : 0.612 10.994 38514 Z= 0.325 Chirality : 0.040 0.216 4133 Planarity : 0.005 0.088 4439 Dihedral : 19.166 171.932 5055 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.22 % Favored : 92.30 % Rotamer: Outliers : 2.55 % Allowed : 20.16 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.07 (0.16), residues: 2921 helix: 1.38 (0.16), residues: 1022 sheet: -0.88 (0.21), residues: 581 loop : -0.73 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 71 TYR 0.018 0.001 TYR G 182 PHE 0.020 0.001 PHE F 234 TRP 0.021 0.001 TRP I 359 HIS 0.006 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00409 (28066) covalent geometry : angle 0.61167 (38514) hydrogen bonds : bond 0.03696 ( 1150) hydrogen bonds : angle 4.59189 ( 3233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7062 (tpp) REVERT: A 140 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7781 (tp30) REVERT: C 224 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8067 (p0) REVERT: D 305 MET cc_start: 0.8376 (tmm) cc_final: 0.8135 (tmm) REVERT: F 77 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8439 (mtm110) REVERT: F 108 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8847 (tt) REVERT: F 166 ASP cc_start: 0.7959 (t0) cc_final: 0.7675 (t0) REVERT: G 170 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7304 (pt) REVERT: I 21 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6697 (ttm) REVERT: I 303 MET cc_start: 0.8384 (mmm) cc_final: 0.8014 (mmm) REVERT: I 358 TRP cc_start: 0.6243 (OUTLIER) cc_final: 0.5787 (p90) REVERT: I 359 TRP cc_start: 0.6179 (t-100) cc_final: 0.5948 (t-100) REVERT: I 439 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8057 (tp30) REVERT: J 22 MET cc_start: 0.7695 (ppp) cc_final: 0.7359 (ppp) REVERT: J 71 ARG cc_start: 0.8645 (mtt180) cc_final: 0.8168 (mtt-85) REVERT: J 112 ASP cc_start: 0.4309 (OUTLIER) cc_final: 0.2833 (p0) REVERT: K 38 ASP cc_start: 0.8589 (t0) cc_final: 0.8275 (t0) REVERT: L 47 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8636 (tpt-90) outliers start: 67 outliers final: 47 residues processed: 229 average time/residue: 0.1711 time to fit residues: 60.8081 Evaluate side-chains 223 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 95 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 171 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN F 30 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.097882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.069341 restraints weight = 97637.344| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.05 r_work: 0.3213 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28066 Z= 0.233 Angle : 0.642 11.832 38514 Z= 0.340 Chirality : 0.041 0.227 4133 Planarity : 0.005 0.088 4439 Dihedral : 19.143 172.257 5055 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.50 % Favored : 92.02 % Rotamer: Outliers : 2.48 % Allowed : 20.35 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.15 (0.16), residues: 2921 helix: 1.29 (0.16), residues: 1026 sheet: -0.89 (0.22), residues: 570 loop : -0.77 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 71 TYR 0.017 0.002 TYR L 11 PHE 0.018 0.001 PHE B 98 TRP 0.037 0.001 TRP I 73 HIS 0.006 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00530 (28066) covalent geometry : angle 0.64154 (38514) hydrogen bonds : bond 0.03947 ( 1150) hydrogen bonds : angle 4.64352 ( 3233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 0.796 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 24 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7171 (tpp) REVERT: A 140 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7773 (tp30) REVERT: D 205 MET cc_start: 0.8680 (mmm) cc_final: 0.8462 (mmm) REVERT: D 305 MET cc_start: 0.8358 (tmm) cc_final: 0.8155 (tmm) REVERT: F 77 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8424 (mtm110) REVERT: F 166 ASP cc_start: 0.8088 (t0) cc_final: 0.7847 (t0) REVERT: G 81 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8749 (pm20) REVERT: G 170 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7364 (pt) REVERT: I 21 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6595 (ttm) REVERT: I 42 LEU cc_start: 0.8847 (mt) cc_final: 0.8612 (tp) REVERT: I 74 LEU cc_start: 0.9524 (tp) cc_final: 0.9156 (pp) REVERT: I 303 MET cc_start: 0.8296 (mmm) cc_final: 0.7937 (mmm) REVERT: I 358 TRP cc_start: 0.6312 (OUTLIER) cc_final: 0.5793 (p90) REVERT: I 439 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8056 (tp30) REVERT: J 22 MET cc_start: 0.7586 (ppp) cc_final: 0.7259 (ppp) REVERT: J 71 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8063 (mtt90) REVERT: K 38 ASP cc_start: 0.8591 (t0) cc_final: 0.8274 (t0) REVERT: L 47 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8618 (tpt-90) outliers start: 65 outliers final: 52 residues processed: 215 average time/residue: 0.1639 time to fit residues: 54.9912 Evaluate side-chains 220 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain I residue 410 MET Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 72 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 15 optimal weight: 0.2980 chunk 1 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN C 30 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.098125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069757 restraints weight = 97745.692| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.03 r_work: 0.3221 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28066 Z= 0.212 Angle : 0.634 12.930 38514 Z= 0.336 Chirality : 0.041 0.242 4133 Planarity : 0.005 0.087 4439 Dihedral : 19.106 172.523 5055 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.43 % Favored : 92.09 % Rotamer: Outliers : 2.48 % Allowed : 20.54 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.14 (0.16), residues: 2921 helix: 1.29 (0.16), residues: 1027 sheet: -0.91 (0.22), residues: 570 loop : -0.76 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 71 TYR 0.017 0.002 TYR L 11 PHE 0.027 0.001 PHE J 78 TRP 0.033 0.001 TRP I 73 HIS 0.007 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00481 (28066) covalent geometry : angle 0.63415 (38514) hydrogen bonds : bond 0.03818 ( 1150) hydrogen bonds : angle 4.62952 ( 3233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7187 (tpp) REVERT: A 140 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7800 (tp30) REVERT: C 200 MET cc_start: 0.8741 (mtm) cc_final: 0.8200 (mpp) REVERT: D 205 MET cc_start: 0.8654 (mmm) cc_final: 0.8436 (mmm) REVERT: D 305 MET cc_start: 0.8365 (tmm) cc_final: 0.8157 (tmm) REVERT: F 77 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8446 (mtm110) REVERT: F 108 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8861 (tt) REVERT: F 166 ASP cc_start: 0.7994 (t0) cc_final: 0.7717 (t0) REVERT: G 81 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: G 170 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7365 (pt) REVERT: I 21 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6720 (ttm) REVERT: I 42 LEU cc_start: 0.8799 (mt) cc_final: 0.8570 (tp) REVERT: I 74 LEU cc_start: 0.9472 (tp) cc_final: 0.9092 (pp) REVERT: I 303 MET cc_start: 0.8495 (mmm) cc_final: 0.8095 (mmm) REVERT: I 358 TRP cc_start: 0.6263 (OUTLIER) cc_final: 0.5334 (p90) REVERT: I 439 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8040 (tp30) REVERT: J 22 MET cc_start: 0.7640 (ppp) cc_final: 0.7300 (ppp) REVERT: J 71 ARG cc_start: 0.8472 (mtt180) cc_final: 0.8138 (mtt90) REVERT: K 38 ASP cc_start: 0.8582 (t0) cc_final: 0.8257 (t0) REVERT: L 47 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8586 (tpt-90) outliers start: 65 outliers final: 54 residues processed: 216 average time/residue: 0.1484 time to fit residues: 50.3347 Evaluate side-chains 226 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain H residue 312 VAL Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain I residue 410 MET Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 39 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 297 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 293 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 244 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.098182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069795 restraints weight = 96850.533| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.05 r_work: 0.3224 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 28066 Z= 0.232 Angle : 0.788 59.179 38514 Z= 0.435 Chirality : 0.046 1.295 4133 Planarity : 0.006 0.167 4439 Dihedral : 19.108 172.513 5055 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.33 % Favored : 92.19 % Rotamer: Outliers : 2.59 % Allowed : 20.54 % Favored : 76.87 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.93 % 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: -0.13 (0.16), residues: 2921 helix: 1.29 (0.16), residues: 1027 sheet: -0.90 (0.22), residues: 575 loop : -0.75 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 71 TYR 0.017 0.001 TYR L 11 PHE 0.017 0.001 PHE J 78 TRP 0.034 0.001 TRP I 359 HIS 0.057 0.001 HIS I 357 Details of bonding type rmsd covalent geometry : bond 0.00504 (28066) covalent geometry : angle 0.78759 (38514) hydrogen bonds : bond 0.03803 ( 1150) hydrogen bonds : angle 4.62848 ( 3233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7506.49 seconds wall clock time: 129 minutes 12.27 seconds (7752.27 seconds total)