Starting phenix.real_space_refine on Wed Jan 14 23:44:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ded_27390/01_2026/8ded_27390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ded_27390/01_2026/8ded_27390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ded_27390/01_2026/8ded_27390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ded_27390/01_2026/8ded_27390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ded_27390/01_2026/8ded_27390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ded_27390/01_2026/8ded_27390.map" } resolution = 4.1 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= -0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 12931 2.51 5 N 3530 2.21 5 O 3868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20450 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2989 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2611 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 20, 'TRANS': 310} Chain: "F" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2989 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "G" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2611 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 20, 'TRANS': 310} Chain: "J" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2989 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "K" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2611 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 20, 'TRANS': 310} Chain: "H" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 982 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "L" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 843 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "U" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 982 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "V" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 843 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Time building chain proxies: 4.71, per 1000 atoms: 0.23 Number of scatterers: 20450 At special positions: 0 Unit cell: (171.81, 174.3, 169.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 121 16.00 O 3868 8.00 N 3530 7.00 C 12931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.08 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.04 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 108 " distance=2.01 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 204 " - pdb=" SG CYS B 229 " distance=2.04 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.04 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.05 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.09 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.03 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 269 " distance=2.03 Simple disulfide: pdb=" SG CYS G 204 " - pdb=" SG CYS G 229 " distance=2.04 Simple disulfide: pdb=" SG CYS G 206 " - pdb=" SG CYS G 223 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.06 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.05 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 127 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 28 " distance=2.02 Simple disulfide: pdb=" SG CYS K 94 " - pdb=" SG CYS K 108 " distance=2.03 Simple disulfide: pdb=" SG CYS K 155 " - pdb=" SG CYS K 269 " distance=2.02 Simple disulfide: pdb=" SG CYS K 204 " - pdb=" SG CYS K 229 " distance=2.04 Simple disulfide: pdb=" SG CYS K 206 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 109 " distance=2.07 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 95 " distance=2.02 Simple disulfide: pdb=" SG CYS U 104 " - pdb=" SG CYS U 109 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 93 " distance=2.05 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: 1.61 Conformation dependent library (CDL) restraints added in 929.6 milliseconds 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4914 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 66 sheets defined 4.5% alpha, 50.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.544A pdb=" N THR A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 removed outlier: 4.076A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.947A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'G' and resid 225 through 229 removed outlier: 3.699A pdb=" N CYS G 229 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 255 removed outlier: 3.651A pdb=" N THR J 254 " --> pdb=" O PRO J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 259 removed outlier: 4.051A pdb=" N CYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 256 through 259' Processing helix chain 'J' and resid 283 through 287 Processing helix chain 'J' and resid 289 through 293 Processing helix chain 'K' and resid 225 through 227 No H-bonds generated for 'chain 'K' and resid 225 through 227' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.645A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 84 through 88 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.572A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 64 removed outlier: 3.535A pdb=" N LYS U 64 " --> pdb=" O ASP U 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 61 through 64' Processing helix chain 'U' and resid 86 through 90 Processing helix chain 'V' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 4.271A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 5.488A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.763A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 306 removed outlier: 5.293A pdb=" N SER A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.287A pdb=" N LEU B 288 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE B 322 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU B 290 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG B 320 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA B 292 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR B 318 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG B 294 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY B 316 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB4, first strand: chain 'B' and resid 34 through 38 removed outlier: 8.729A pdb=" N ILE B 34 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER B 51 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 49 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 16.814A pdb=" N GLN B 49 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 14.184A pdb=" N TYR B 69 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 12.826A pdb=" N SER B 51 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 11.853A pdb=" N PHE B 67 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N GLN B 53 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N THR B 65 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY B 55 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 38 removed outlier: 8.729A pdb=" N ILE B 34 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER B 51 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 49 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 50 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR B 102 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N ALA B 52 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LYS B 100 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N PHE B 54 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLY B 98 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 16.299A pdb=" N TYR B 56 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 18.242A pdb=" N ARG B 96 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 88 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ARG B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 11.700A pdb=" N ILE B 86 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP B 112 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 151 through 158 Processing sheet with id=AB7, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AB8, first strand: chain 'B' and resid 183 through 186 Processing sheet with id=AB9, first strand: chain 'B' and resid 209 through 214 Processing sheet with id=AC1, first strand: chain 'F' and resid 2 through 8 removed outlier: 3.975A pdb=" N LYS F 160 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 14 through 19 removed outlier: 5.496A pdb=" N ILE F 31 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL F 33 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG F 134 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER F 41 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR F 126 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN F 43 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL F 124 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU F 45 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU F 122 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 47 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL F 120 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 140 through 147 removed outlier: 6.741A pdb=" N VAL F 120 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 47 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU F 122 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU F 45 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL F 124 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN F 43 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR F 126 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER F 41 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG F 134 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL F 33 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE F 31 " --> pdb=" O VAL F 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC5, first strand: chain 'F' and resid 51 through 54 removed outlier: 4.850A pdb=" N VAL F 108 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASP F 75 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AC7, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AC8, first strand: chain 'F' and resid 296 through 306 removed outlier: 5.295A pdb=" N SER F 315 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 330 through 332 Processing sheet with id=AD1, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD2, first strand: chain 'F' and resid 387 through 388 removed outlier: 7.252A pdb=" N LEU G 288 " --> pdb=" O PHE G 322 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE G 322 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU G 290 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG G 320 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA G 292 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR G 318 " --> pdb=" O ALA G 292 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG G 294 " --> pdb=" O GLY G 316 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY G 316 " --> pdb=" O ARG G 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AD4, first strand: chain 'G' and resid 34 through 38 removed outlier: 4.212A pdb=" N ASN G 36 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN G 49 " --> pdb=" O ASN G 36 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE G 103 " --> pdb=" O HIS G 99 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N HIS G 99 " --> pdb=" O PHE G 103 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU G 105 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE G 88 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG G 96 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N ILE G 86 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP G 112 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 66 through 70 Processing sheet with id=AD6, first strand: chain 'G' and resid 151 through 158 Processing sheet with id=AD7, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AD8, first strand: chain 'G' and resid 183 through 186 Processing sheet with id=AD9, first strand: chain 'G' and resid 209 through 214 Processing sheet with id=AE1, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.961A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 14 through 19 removed outlier: 5.501A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.745A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AE5, first strand: chain 'J' and resid 51 through 54 removed outlier: 4.838A pdb=" N VAL J 108 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP J 75 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AE7, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AE8, first strand: chain 'J' and resid 296 through 306 removed outlier: 5.271A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 330 through 332 Processing sheet with id=AF1, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AF2, first strand: chain 'J' and resid 387 through 388 removed outlier: 7.259A pdb=" N LEU K 288 " --> pdb=" O PHE K 322 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE K 322 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU K 290 " --> pdb=" O ARG K 320 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ARG K 320 " --> pdb=" O LEU K 290 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA K 292 " --> pdb=" O THR K 318 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR K 318 " --> pdb=" O ALA K 292 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG K 294 " --> pdb=" O GLY K 316 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY K 316 " --> pdb=" O ARG K 294 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AF4, first strand: chain 'K' and resid 34 through 38 removed outlier: 7.599A pdb=" N GLN K 49 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL K 37 " --> pdb=" O ARG K 47 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG K 47 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL K 50 " --> pdb=" O TYR K 102 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR K 102 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ALA K 52 " --> pdb=" O LYS K 100 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LYS K 100 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N PHE K 54 " --> pdb=" O GLY K 98 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N GLY K 98 " --> pdb=" O PHE K 54 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE K 88 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ARG K 96 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 11.268A pdb=" N ILE K 86 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP K 112 " --> pdb=" O LYS K 131 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 66 through 70 Processing sheet with id=AF6, first strand: chain 'K' and resid 151 through 158 Processing sheet with id=AF7, first strand: chain 'K' and resid 240 through 241 Processing sheet with id=AF8, first strand: chain 'K' and resid 183 through 186 Processing sheet with id=AF9, first strand: chain 'K' and resid 209 through 214 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.259A pdb=" N GLY H 10 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.259A pdb=" N GLY H 10 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 104 through 105 removed outlier: 3.519A pdb=" N GLY H 108 " --> pdb=" O THR H 105 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.912A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.304A pdb=" N GLY U 10 " --> pdb=" O THR U 127 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET U 34 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.304A pdb=" N GLY U 10 " --> pdb=" O THR U 127 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 104 through 105 Processing sheet with id=AH2, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AH3, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.517A pdb=" N GLU V 110 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU V 38 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR V 54 " --> pdb=" O LEU V 38 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP V 40 " --> pdb=" O LEU V 52 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.16: 1 1.16 - 1.37: 6886 1.37 - 1.58: 13954 1.58 - 1.78: 36 1.78 - 1.99: 113 Bond restraints: 20990 Sorted by residual: bond pdb=" CB PRO J 294 " pdb=" CG PRO J 294 " ideal model delta sigma weight residual 1.492 0.953 0.539 5.00e-02 4.00e+02 1.16e+02 bond pdb=" CG PRO J 294 " pdb=" CD PRO J 294 " ideal model delta sigma weight residual 1.503 1.262 0.241 3.40e-02 8.65e+02 5.03e+01 bond pdb=" CB VAL J 136 " pdb=" CG1 VAL J 136 " ideal model delta sigma weight residual 1.521 1.289 0.232 3.30e-02 9.18e+02 4.94e+01 bond pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " ideal model delta sigma weight residual 1.808 1.612 0.196 3.30e-02 9.18e+02 3.52e+01 bond pdb=" CD1 TYR B 102 " pdb=" CE1 TYR B 102 " ideal model delta sigma weight residual 1.382 1.213 0.169 3.00e-02 1.11e+03 3.19e+01 ... (remaining 20985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 28561 14.77 - 29.53: 4 29.53 - 44.30: 0 44.30 - 59.06: 0 59.06 - 73.83: 1 Bond angle restraints: 28566 Sorted by residual: angle pdb=" CB PRO J 294 " pdb=" CG PRO J 294 " pdb=" CD PRO J 294 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO J 294 " pdb=" CD PRO J 294 " pdb=" CG PRO J 294 " ideal model delta sigma weight residual 103.20 77.16 26.04 1.50e+00 4.44e-01 3.01e+02 angle pdb=" CA PRO J 294 " pdb=" CB PRO J 294 " pdb=" CG PRO J 294 " ideal model delta sigma weight residual 104.50 76.27 28.23 1.90e+00 2.77e-01 2.21e+02 angle pdb=" CA CYS B 108 " pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " ideal model delta sigma weight residual 114.40 136.80 -22.40 2.30e+00 1.89e-01 9.48e+01 angle pdb=" N CYS B 108 " pdb=" CA CYS B 108 " pdb=" C CYS B 108 " ideal model delta sigma weight residual 108.07 114.67 -6.60 8.90e-01 1.26e+00 5.50e+01 ... (remaining 28561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11497 17.92 - 35.83: 892 35.83 - 53.74: 169 53.74 - 71.66: 22 71.66 - 89.57: 8 Dihedral angle restraints: 12588 sinusoidal: 4908 harmonic: 7680 Sorted by residual: dihedral pdb=" CA GLN L 55 " pdb=" C GLN L 55 " pdb=" N VAL L 56 " pdb=" CA VAL L 56 " ideal model delta harmonic sigma weight residual -180.00 -131.69 -48.31 0 5.00e+00 4.00e-02 9.33e+01 dihedral pdb=" CB CYS H 104 " pdb=" SG CYS H 104 " pdb=" SG CYS H 109 " pdb=" CB CYS H 109 " ideal model delta sinusoidal sigma weight residual 93.00 7.90 85.10 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CA GLN V 55 " pdb=" C GLN V 55 " pdb=" N VAL V 56 " pdb=" CA VAL V 56 " ideal model delta harmonic sigma weight residual -180.00 -133.16 -46.84 0 5.00e+00 4.00e-02 8.78e+01 ... (remaining 12585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2911 0.097 - 0.194: 265 0.194 - 0.291: 7 0.291 - 0.388: 1 0.388 - 0.485: 1 Chirality restraints: 3185 Sorted by residual: chirality pdb=" CB VAL J 136 " pdb=" CA VAL J 136 " pdb=" CG1 VAL J 136 " pdb=" CG2 VAL J 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CA CYS H 104 " pdb=" N CYS H 104 " pdb=" C CYS H 104 " pdb=" CB CYS H 104 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA CYS F 328 " pdb=" N CYS F 328 " pdb=" C CYS F 328 " pdb=" CB CYS F 328 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 3182 not shown) Planarity restraints: 3669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 53 " 0.041 2.00e-02 2.50e+03 9.04e-02 8.17e+01 pdb=" CD GLN B 53 " -0.156 2.00e-02 2.50e+03 pdb=" OE1 GLN B 53 " 0.060 2.00e-02 2.50e+03 pdb=" NE2 GLN B 53 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 21 " 0.073 2.00e-02 2.50e+03 3.87e-02 2.99e+01 pdb=" CG TYR K 21 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR K 21 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR K 21 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR K 21 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR K 21 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR K 21 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR K 21 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR V 14 " -0.089 5.00e-02 4.00e+02 1.34e-01 2.86e+01 pdb=" N PRO V 15 " 0.231 5.00e-02 4.00e+02 pdb=" CA PRO V 15 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO V 15 " -0.071 5.00e-02 4.00e+02 ... (remaining 3666 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 282 2.61 - 3.19: 18264 3.19 - 3.76: 31877 3.76 - 4.33: 43594 4.33 - 4.90: 72649 Nonbonded interactions: 166666 Sorted by model distance: nonbonded pdb=" OE1 GLU G 203 " pdb=" OH TYR G 209 " model vdw 2.042 3.040 nonbonded pdb=" OG SER J 309 " pdb=" OD1 ASP J 311 " model vdw 2.100 3.040 nonbonded pdb=" OG SER A 309 " pdb=" OD1 ASP A 311 " model vdw 2.105 3.040 nonbonded pdb=" O GLU J 292 " pdb=" NH2 ARG J 324 " model vdw 2.115 3.120 nonbonded pdb=" OG SER F 309 " pdb=" OD1 ASP F 311 " model vdw 2.146 3.040 ... (remaining 166661 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'V' } 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 group one per residue 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: 47.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.000 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.009 0.539 21035 Z= 0.339 Angle : 1.130 73.830 28656 Z= 0.564 Chirality : 0.054 0.485 3185 Planarity : 0.007 0.134 3669 Dihedral : 12.795 89.574 7539 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2642 helix: -0.32 (0.75), residues: 45 sheet: -0.52 (0.15), residues: 1087 loop : -0.66 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 180 TYR 0.073 0.003 TYR K 21 PHE 0.029 0.002 PHE A 81 TRP 0.056 0.002 TRP B 313 HIS 0.012 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00914 (20990) covalent geometry : angle 1.08999 (28566) SS BOND : bond 0.01566 ( 45) SS BOND : angle 5.44715 ( 90) hydrogen bonds : bond 0.12086 ( 694) hydrogen bonds : angle 7.37740 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 0.800 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: A 246 ASN cc_start: 0.8419 (t0) cc_final: 0.8072 (t0) REVERT: A 305 ASP cc_start: 0.8221 (t0) cc_final: 0.7848 (t0) REVERT: B 49 GLN cc_start: 0.8109 (tt0) cc_final: 0.7714 (tt0) REVERT: B 278 THR cc_start: 0.9438 (m) cc_final: 0.8915 (p) REVERT: B 283 PHE cc_start: 0.7250 (t80) cc_final: 0.6734 (t80) REVERT: B 308 ASP cc_start: 0.8264 (t70) cc_final: 0.8009 (t0) REVERT: F 9 ASN cc_start: 0.9313 (t0) cc_final: 0.8697 (t0) REVERT: F 100 ASN cc_start: 0.8524 (t0) cc_final: 0.7729 (t0) REVERT: F 204 GLN cc_start: 0.9098 (mt0) cc_final: 0.8753 (mt0) REVERT: G 49 GLN cc_start: 0.8570 (tt0) cc_final: 0.8052 (tt0) REVERT: G 125 ASN cc_start: 0.8064 (m110) cc_final: 0.7615 (m-40) REVERT: G 247 ILE cc_start: 0.8631 (mp) cc_final: 0.8401 (mp) REVERT: J 56 PRO cc_start: 0.9195 (Cg_exo) cc_final: 0.8844 (Cg_endo) REVERT: J 257 PHE cc_start: 0.8821 (m-80) cc_final: 0.8415 (m-10) REVERT: J 388 ILE cc_start: 0.8740 (tp) cc_final: 0.8499 (mp) REVERT: K 112 ASP cc_start: 0.8086 (m-30) cc_final: 0.7755 (m-30) REVERT: K 203 GLU cc_start: 0.8013 (pp20) cc_final: 0.7514 (pp20) REVERT: K 344 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6469 (mm-40) REVERT: L 42 GLN cc_start: 0.7474 (tt0) cc_final: 0.6978 (tt0) REVERT: L 76 PHE cc_start: 0.8467 (m-80) cc_final: 0.7579 (m-10) REVERT: U 39 GLN cc_start: 0.7295 (tt0) cc_final: 0.6784 (tt0) REVERT: U 66 ARG cc_start: 0.7077 (mtm110) cc_final: 0.6592 (mtm-85) REVERT: U 67 PHE cc_start: 0.7357 (m-80) cc_final: 0.7059 (m-80) REVERT: V 54 TYR cc_start: 0.8332 (p90) cc_final: 0.7627 (p90) REVERT: V 55 GLN cc_start: 0.6236 (tt0) cc_final: 0.5673 (tt0) REVERT: V 58 ASN cc_start: 0.8460 (m110) cc_final: 0.8084 (m110) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.1439 time to fit residues: 118.5476 Evaluate side-chains 393 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN F 331 HIS G 58 GLN G 259 HIS G 335 ASN J 59 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN J 186 ASN K 74 HIS H 39 GLN H 76 ASN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 GLN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.159144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120696 restraints weight = 39743.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119271 restraints weight = 24750.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120775 restraints weight = 24965.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.121021 restraints weight = 16310.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121450 restraints weight = 14676.466| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21035 Z= 0.208 Angle : 0.736 10.662 28656 Z= 0.383 Chirality : 0.050 0.209 3185 Planarity : 0.006 0.144 3669 Dihedral : 5.885 51.994 2878 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 0.53 % Allowed : 4.51 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.16), residues: 2642 helix: -0.54 (0.74), residues: 45 sheet: -0.44 (0.15), residues: 1116 loop : -0.58 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 82 TYR 0.053 0.002 TYR K 21 PHE 0.022 0.002 PHE H 29 TRP 0.029 0.003 TRP V 40 HIS 0.011 0.001 HIS K 74 Details of bonding type rmsd covalent geometry : bond 0.00481 (20990) covalent geometry : angle 0.72765 (28566) SS BOND : bond 0.00508 ( 45) SS BOND : angle 2.05431 ( 90) hydrogen bonds : bond 0.03782 ( 694) hydrogen bonds : angle 6.11695 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 503 time to evaluate : 0.705 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: A 195 MET cc_start: 0.8825 (mpp) cc_final: 0.8598 (mpp) REVERT: A 246 ASN cc_start: 0.8672 (t0) cc_final: 0.8161 (t0) REVERT: A 305 ASP cc_start: 0.8364 (t0) cc_final: 0.8077 (t0) REVERT: B 43 ASP cc_start: 0.8471 (p0) cc_final: 0.8208 (p0) REVERT: B 45 SER cc_start: 0.9524 (m) cc_final: 0.9051 (m) REVERT: B 103 PHE cc_start: 0.9170 (m-80) cc_final: 0.8439 (m-10) REVERT: B 228 GLN cc_start: 0.8330 (tt0) cc_final: 0.7997 (tt0) REVERT: B 278 THR cc_start: 0.9412 (m) cc_final: 0.8960 (p) REVERT: B 283 PHE cc_start: 0.7405 (t80) cc_final: 0.6804 (t80) REVERT: B 308 ASP cc_start: 0.8226 (t70) cc_final: 0.7924 (t0) REVERT: B 333 TRP cc_start: 0.9490 (t-100) cc_final: 0.9016 (t-100) REVERT: F 373 LYS cc_start: 0.9218 (mmtp) cc_final: 0.8903 (mmtp) REVERT: G 46 ILE cc_start: 0.9035 (mm) cc_final: 0.8741 (pt) REVERT: G 70 MET cc_start: 0.8867 (tpp) cc_final: 0.8572 (tpp) REVERT: G 97 LEU cc_start: 0.9241 (mt) cc_final: 0.8911 (mt) REVERT: G 283 PHE cc_start: 0.7505 (t80) cc_final: 0.7283 (t80) REVERT: G 287 THR cc_start: 0.9389 (m) cc_final: 0.9180 (p) REVERT: J 24 TYR cc_start: 0.7221 (m-80) cc_final: 0.7015 (m-80) REVERT: J 171 SER cc_start: 0.9175 (t) cc_final: 0.8944 (m) REVERT: J 246 ASN cc_start: 0.8922 (t0) cc_final: 0.8643 (t0) REVERT: J 257 PHE cc_start: 0.8773 (m-80) cc_final: 0.8165 (m-10) REVERT: K 49 GLN cc_start: 0.8479 (tt0) cc_final: 0.8118 (tt0) REVERT: K 112 ASP cc_start: 0.7944 (m-30) cc_final: 0.7691 (m-30) REVERT: K 177 HIS cc_start: 0.8295 (t-170) cc_final: 0.8070 (t70) REVERT: K 203 GLU cc_start: 0.8044 (pp20) cc_final: 0.7513 (pp20) REVERT: H 59 TYR cc_start: 0.7008 (m-80) cc_final: 0.6744 (m-80) REVERT: L 40 TRP cc_start: 0.8157 (m100) cc_final: 0.7638 (m100) REVERT: L 42 GLN cc_start: 0.7716 (tt0) cc_final: 0.7265 (tt0) REVERT: L 50 ARG cc_start: 0.7705 (tmt170) cc_final: 0.7497 (tmt170) REVERT: U 32 TYR cc_start: 0.8331 (m-80) cc_final: 0.8055 (m-10) REVERT: U 39 GLN cc_start: 0.7079 (tt0) cc_final: 0.6813 (tt0) REVERT: U 66 ARG cc_start: 0.6792 (mtm110) cc_final: 0.6561 (mtp-110) REVERT: U 67 PHE cc_start: 0.7502 (m-80) cc_final: 0.7049 (m-80) REVERT: V 36 THR cc_start: 0.8216 (m) cc_final: 0.7556 (m) REVERT: V 54 TYR cc_start: 0.8650 (p90) cc_final: 0.8063 (p90) REVERT: V 82 ARG cc_start: 0.7211 (ptm-80) cc_final: 0.6778 (ttp80) outliers start: 12 outliers final: 2 residues processed: 514 average time/residue: 0.1521 time to fit residues: 120.4923 Evaluate side-chains 358 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 356 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 103 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 125 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 100 ASN B 53 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 230 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN ** V 95 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 = 0.3912 r_free = 0.3912 target = 0.155667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116848 restraints weight = 39449.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115209 restraints weight = 25794.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116942 restraints weight = 26226.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117055 restraints weight = 16484.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117701 restraints weight = 15144.982| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21035 Z= 0.225 Angle : 0.720 13.520 28656 Z= 0.374 Chirality : 0.048 0.214 3185 Planarity : 0.005 0.058 3669 Dihedral : 5.805 52.988 2878 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.21 % Rotamer: Outliers : 0.31 % Allowed : 4.25 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2642 helix: -0.70 (0.72), residues: 45 sheet: -0.43 (0.15), residues: 1159 loop : -0.73 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 21 TYR 0.058 0.002 TYR K 21 PHE 0.017 0.002 PHE F 95 TRP 0.028 0.002 TRP B 239 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00525 (20990) covalent geometry : angle 0.70964 (28566) SS BOND : bond 0.00608 ( 45) SS BOND : angle 2.32596 ( 90) hydrogen bonds : bond 0.03710 ( 694) hydrogen bonds : angle 6.02813 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 476 time to evaluate : 0.739 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: A 246 ASN cc_start: 0.8768 (t0) cc_final: 0.8450 (t0) REVERT: A 305 ASP cc_start: 0.8475 (t0) cc_final: 0.8179 (t0) REVERT: A 352 ILE cc_start: 0.7574 (mt) cc_final: 0.6746 (mt) REVERT: B 103 PHE cc_start: 0.9165 (m-80) cc_final: 0.8666 (m-80) REVERT: B 283 PHE cc_start: 0.7277 (t80) cc_final: 0.6756 (t80) REVERT: B 308 ASP cc_start: 0.8196 (t70) cc_final: 0.7856 (t0) REVERT: F 100 ASN cc_start: 0.8433 (t0) cc_final: 0.8024 (t0) REVERT: F 134 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7778 (ttm-80) REVERT: F 149 ASN cc_start: 0.8347 (p0) cc_final: 0.8117 (p0) REVERT: F 246 ASN cc_start: 0.9020 (m-40) cc_final: 0.8475 (t0) REVERT: F 321 LYS cc_start: 0.8699 (tttt) cc_final: 0.8400 (tttp) REVERT: F 373 LYS cc_start: 0.9263 (mmtp) cc_final: 0.8877 (mmtp) REVERT: F 377 ASN cc_start: 0.7947 (m-40) cc_final: 0.7682 (m-40) REVERT: G 46 ILE cc_start: 0.9055 (mm) cc_final: 0.8737 (pt) REVERT: G 97 LEU cc_start: 0.9171 (mt) cc_final: 0.8928 (mt) REVERT: G 125 ASN cc_start: 0.8209 (m110) cc_final: 0.7732 (m-40) REVERT: G 287 THR cc_start: 0.9394 (m) cc_final: 0.9173 (p) REVERT: G 330 GLU cc_start: 0.8174 (tt0) cc_final: 0.7895 (tt0) REVERT: J 65 SER cc_start: 0.8562 (t) cc_final: 0.8355 (t) REVERT: J 134 ARG cc_start: 0.8507 (ttp80) cc_final: 0.7821 (ttp80) REVERT: J 186 ASN cc_start: 0.8570 (m110) cc_final: 0.8304 (m-40) REVERT: J 214 VAL cc_start: 0.9637 (m) cc_final: 0.9283 (t) REVERT: J 246 ASN cc_start: 0.9003 (t0) cc_final: 0.8737 (t0) REVERT: J 257 PHE cc_start: 0.8768 (m-80) cc_final: 0.8212 (m-10) REVERT: J 385 ASP cc_start: 0.7528 (t0) cc_final: 0.7318 (t0) REVERT: K 25 SER cc_start: 0.8414 (t) cc_final: 0.8027 (t) REVERT: K 49 GLN cc_start: 0.8629 (tt0) cc_final: 0.8301 (tt0) REVERT: K 83 MET cc_start: 0.7102 (mmt) cc_final: 0.6843 (mmt) REVERT: K 112 ASP cc_start: 0.8112 (m-30) cc_final: 0.7905 (m-30) REVERT: K 203 GLU cc_start: 0.8222 (pp20) cc_final: 0.7671 (pp20) REVERT: K 209 TYR cc_start: 0.7052 (t80) cc_final: 0.6798 (t80) REVERT: H 3 GLN cc_start: 0.8382 (tp40) cc_final: 0.7789 (tm-30) REVERT: H 28 THR cc_start: 0.7870 (m) cc_final: 0.7137 (m) REVERT: L 40 TRP cc_start: 0.8155 (m100) cc_final: 0.7629 (m100) REVERT: U 39 GLN cc_start: 0.7005 (tt0) cc_final: 0.6715 (tt0) REVERT: U 66 ARG cc_start: 0.7062 (mtm110) cc_final: 0.6829 (mtp-110) REVERT: U 67 PHE cc_start: 0.7368 (m-80) cc_final: 0.7012 (m-80) REVERT: U 116 TRP cc_start: 0.7793 (p90) cc_final: 0.7471 (p90) REVERT: V 27 GLN cc_start: 0.7768 (mt0) cc_final: 0.6957 (mp10) REVERT: V 54 TYR cc_start: 0.8665 (p90) cc_final: 0.7916 (p90) REVERT: V 55 GLN cc_start: 0.5065 (tt0) cc_final: 0.4516 (tt0) REVERT: V 58 ASN cc_start: 0.8608 (m110) cc_final: 0.8310 (m110) outliers start: 7 outliers final: 1 residues processed: 482 average time/residue: 0.1504 time to fit residues: 110.8076 Evaluate side-chains 359 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 169 optimal weight: 0.5980 chunk 193 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 156 optimal weight: 0.0980 chunk 227 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 ASN J 186 ASN J 235 GLN H 3 GLN H 76 ASN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118162 restraints weight = 39484.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115761 restraints weight = 25049.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117497 restraints weight = 26233.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117843 restraints weight = 16835.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119095 restraints weight = 15067.767| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21035 Z= 0.155 Angle : 0.677 12.433 28656 Z= 0.349 Chirality : 0.047 0.242 3185 Planarity : 0.005 0.048 3669 Dihedral : 5.618 50.929 2878 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.51 % Rotamer: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2642 helix: -0.77 (0.70), residues: 45 sheet: -0.39 (0.15), residues: 1133 loop : -0.78 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 135 TYR 0.026 0.002 TYR A 240 PHE 0.019 0.001 PHE F 95 TRP 0.015 0.001 TRP V 40 HIS 0.010 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00365 (20990) covalent geometry : angle 0.66653 (28566) SS BOND : bond 0.00578 ( 45) SS BOND : angle 2.23062 ( 90) hydrogen bonds : bond 0.03350 ( 694) hydrogen bonds : angle 5.81620 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 491 time to evaluate : 0.762 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: A 75 ASP cc_start: 0.8755 (t0) cc_final: 0.8302 (t0) REVERT: A 93 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7666 (tp40) REVERT: A 246 ASN cc_start: 0.8811 (t0) cc_final: 0.8400 (t0) REVERT: A 305 ASP cc_start: 0.8404 (t0) cc_final: 0.8056 (t0) REVERT: A 352 ILE cc_start: 0.7445 (mt) cc_final: 0.6450 (mt) REVERT: B 83 MET cc_start: 0.8222 (tpt) cc_final: 0.7695 (tpt) REVERT: B 95 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7658 (ttp80) REVERT: B 97 LEU cc_start: 0.8781 (mp) cc_final: 0.8370 (mt) REVERT: B 103 PHE cc_start: 0.9140 (m-80) cc_final: 0.8668 (m-80) REVERT: B 283 PHE cc_start: 0.7343 (t80) cc_final: 0.6754 (t80) REVERT: B 308 ASP cc_start: 0.8199 (t70) cc_final: 0.7846 (t0) REVERT: F 149 ASN cc_start: 0.8375 (p0) cc_final: 0.8105 (p0) REVERT: F 246 ASN cc_start: 0.8987 (m-40) cc_final: 0.8421 (t0) REVERT: F 341 GLU cc_start: 0.7870 (mp0) cc_final: 0.7602 (mp0) REVERT: F 377 ASN cc_start: 0.7925 (m-40) cc_final: 0.7668 (m-40) REVERT: G 46 ILE cc_start: 0.9106 (mm) cc_final: 0.8738 (pt) REVERT: G 97 LEU cc_start: 0.9021 (mt) cc_final: 0.8811 (mt) REVERT: G 125 ASN cc_start: 0.8197 (m110) cc_final: 0.7729 (m-40) REVERT: G 128 THR cc_start: 0.9361 (m) cc_final: 0.8844 (p) REVERT: G 220 MET cc_start: 0.8992 (mmm) cc_final: 0.8515 (mmm) REVERT: G 275 HIS cc_start: 0.8475 (t70) cc_final: 0.8251 (t70) REVERT: G 282 TRP cc_start: 0.9339 (p-90) cc_final: 0.8647 (p-90) REVERT: G 287 THR cc_start: 0.9410 (m) cc_final: 0.9026 (p) REVERT: J 134 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8125 (ttp80) REVERT: J 246 ASN cc_start: 0.9014 (t0) cc_final: 0.8691 (t0) REVERT: J 257 PHE cc_start: 0.8796 (m-80) cc_final: 0.8185 (m-10) REVERT: J 385 ASP cc_start: 0.7724 (t0) cc_final: 0.7482 (t0) REVERT: K 25 SER cc_start: 0.8198 (t) cc_final: 0.7535 (t) REVERT: K 203 GLU cc_start: 0.7978 (pp20) cc_final: 0.7514 (pp20) REVERT: K 209 TYR cc_start: 0.6967 (t80) cc_final: 0.6658 (t80) REVERT: K 220 MET cc_start: 0.7616 (mmt) cc_final: 0.6835 (mmt) REVERT: H 3 GLN cc_start: 0.8376 (tp-100) cc_final: 0.7897 (tm-30) REVERT: H 28 THR cc_start: 0.8042 (m) cc_final: 0.7756 (m) REVERT: L 40 TRP cc_start: 0.8058 (m100) cc_final: 0.7512 (m100) REVERT: L 55 GLN cc_start: 0.6879 (mm-40) cc_final: 0.6274 (mm-40) REVERT: L 76 PHE cc_start: 0.8050 (m-80) cc_final: 0.7268 (m-80) REVERT: U 3 GLN cc_start: 0.7346 (tm-30) cc_final: 0.7023 (tm-30) REVERT: U 39 GLN cc_start: 0.7047 (tt0) cc_final: 0.6674 (tt0) REVERT: U 66 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6853 (mtp-110) REVERT: U 67 PHE cc_start: 0.7311 (m-80) cc_final: 0.6992 (m-80) REVERT: V 54 TYR cc_start: 0.8588 (p90) cc_final: 0.8042 (p90) REVERT: V 55 GLN cc_start: 0.4268 (tt0) cc_final: 0.3686 (tt0) REVERT: V 58 ASN cc_start: 0.8591 (m110) cc_final: 0.8265 (m110) REVERT: V 76 PHE cc_start: 0.7694 (m-10) cc_final: 0.6957 (m-10) REVERT: V 92 TYR cc_start: 0.5740 (m-80) cc_final: 0.5126 (m-80) outliers start: 2 outliers final: 0 residues processed: 491 average time/residue: 0.1513 time to fit residues: 113.7670 Evaluate side-chains 364 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 109 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 189 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 235 GLN B 58 GLN B 228 GLN F 93 GLN F 143 HIS ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 ASN H 76 ASN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110885 restraints weight = 39201.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111852 restraints weight = 28588.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112150 restraints weight = 21764.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112474 restraints weight = 17265.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112788 restraints weight = 14339.351| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21035 Z= 0.198 Angle : 0.699 11.661 28656 Z= 0.361 Chirality : 0.048 0.199 3185 Planarity : 0.005 0.050 3669 Dihedral : 5.652 50.798 2878 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.60 % Favored : 94.36 % Rotamer: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2642 helix: -0.75 (0.71), residues: 45 sheet: -0.45 (0.15), residues: 1166 loop : -0.85 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 135 TYR 0.044 0.002 TYR A 46 PHE 0.023 0.002 PHE H 29 TRP 0.019 0.002 TRP V 40 HIS 0.010 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00471 (20990) covalent geometry : angle 0.68975 (28566) SS BOND : bond 0.00496 ( 45) SS BOND : angle 2.16884 ( 90) hydrogen bonds : bond 0.03548 ( 694) hydrogen bonds : angle 5.77739 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 478 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8157 (ptm) cc_final: 0.7348 (ptm) REVERT: A 246 ASN cc_start: 0.8698 (t0) cc_final: 0.8368 (t0) REVERT: A 305 ASP cc_start: 0.8263 (t0) cc_final: 0.7979 (t0) REVERT: A 352 ILE cc_start: 0.7427 (mt) cc_final: 0.6071 (mt) REVERT: B 83 MET cc_start: 0.7808 (tpt) cc_final: 0.7228 (tpt) REVERT: B 95 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7697 (ttp80) REVERT: B 97 LEU cc_start: 0.8827 (mp) cc_final: 0.8438 (mt) REVERT: B 228 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7828 (tp40) REVERT: B 283 PHE cc_start: 0.7529 (t80) cc_final: 0.6843 (t80) REVERT: B 308 ASP cc_start: 0.8193 (t70) cc_final: 0.7797 (t0) REVERT: F 61 LYS cc_start: 0.7910 (tppt) cc_final: 0.7632 (ttmt) REVERT: F 149 ASN cc_start: 0.8334 (p0) cc_final: 0.7873 (p0) REVERT: F 174 ASP cc_start: 0.8362 (m-30) cc_final: 0.7557 (m-30) REVERT: F 246 ASN cc_start: 0.9050 (m-40) cc_final: 0.8512 (t0) REVERT: F 281 ASP cc_start: 0.8329 (t70) cc_final: 0.8127 (t0) REVERT: F 373 LYS cc_start: 0.9277 (mmtp) cc_final: 0.8853 (mmtp) REVERT: F 377 ASN cc_start: 0.8199 (m-40) cc_final: 0.7928 (m-40) REVERT: G 46 ILE cc_start: 0.9192 (mm) cc_final: 0.8890 (pt) REVERT: G 70 MET cc_start: 0.8740 (tpp) cc_final: 0.8532 (tpp) REVERT: G 125 ASN cc_start: 0.8204 (m110) cc_final: 0.7651 (m-40) REVERT: G 220 MET cc_start: 0.9072 (mmm) cc_final: 0.8654 (mmm) REVERT: G 282 TRP cc_start: 0.9393 (p-90) cc_final: 0.8590 (p-90) REVERT: G 287 THR cc_start: 0.9448 (m) cc_final: 0.9030 (p) REVERT: J 65 SER cc_start: 0.8540 (t) cc_final: 0.8320 (t) REVERT: J 88 MET cc_start: 0.8254 (tmm) cc_final: 0.7882 (tmm) REVERT: J 134 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8175 (ttp80) REVERT: J 160 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8292 (tppp) REVERT: J 246 ASN cc_start: 0.9109 (t0) cc_final: 0.8758 (t0) REVERT: J 257 PHE cc_start: 0.8856 (m-80) cc_final: 0.8262 (m-10) REVERT: J 385 ASP cc_start: 0.7685 (t0) cc_final: 0.7429 (t0) REVERT: J 388 ILE cc_start: 0.8902 (mm) cc_final: 0.8677 (mm) REVERT: K 25 SER cc_start: 0.8251 (t) cc_final: 0.7636 (t) REVERT: K 83 MET cc_start: 0.7551 (mmt) cc_final: 0.7309 (mmm) REVERT: K 112 ASP cc_start: 0.8154 (m-30) cc_final: 0.7923 (m-30) REVERT: K 203 GLU cc_start: 0.8077 (pp20) cc_final: 0.7510 (pp20) REVERT: K 209 TYR cc_start: 0.6959 (t80) cc_final: 0.6642 (t80) REVERT: H 51 ILE cc_start: 0.8869 (tt) cc_final: 0.8423 (tp) REVERT: H 97 LYS cc_start: 0.6420 (tttm) cc_final: 0.6019 (tttm) REVERT: L 40 TRP cc_start: 0.7994 (m100) cc_final: 0.7553 (m100) REVERT: L 55 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6552 (mm-40) REVERT: L 76 PHE cc_start: 0.7956 (m-80) cc_final: 0.7294 (m-80) REVERT: U 39 GLN cc_start: 0.7033 (tt0) cc_final: 0.6665 (tt0) REVERT: U 66 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6453 (mtp-110) REVERT: U 67 PHE cc_start: 0.7379 (m-80) cc_final: 0.7004 (m-80) REVERT: V 5 THR cc_start: 0.7565 (p) cc_final: 0.7321 (p) REVERT: V 54 TYR cc_start: 0.8595 (p90) cc_final: 0.7921 (p90) REVERT: V 55 GLN cc_start: 0.3963 (tt0) cc_final: 0.3181 (tt0) REVERT: V 58 ASN cc_start: 0.8480 (m110) cc_final: 0.8067 (m110) REVERT: V 76 PHE cc_start: 0.7820 (m-10) cc_final: 0.6571 (m-10) REVERT: V 92 TYR cc_start: 0.5709 (m-80) cc_final: 0.5077 (m-80) outliers start: 1 outliers final: 0 residues processed: 479 average time/residue: 0.1549 time to fit residues: 113.4524 Evaluate side-chains 352 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 15 optimal weight: 0.0770 chunk 165 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 218 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN F 143 HIS F 230 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 230 HIS H 76 ASN V 31 HIS ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 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 = 0.3892 r_free = 0.3892 target = 0.153785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112515 restraints weight = 39175.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112944 restraints weight = 27207.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113240 restraints weight = 20061.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113782 restraints weight = 16625.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113992 restraints weight = 14532.784| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21035 Z= 0.159 Angle : 0.679 10.868 28656 Z= 0.348 Chirality : 0.047 0.211 3185 Planarity : 0.005 0.057 3669 Dihedral : 5.565 50.004 2878 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2642 helix: -0.70 (0.70), residues: 45 sheet: -0.40 (0.15), residues: 1160 loop : -0.85 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 135 TYR 0.028 0.002 TYR K 21 PHE 0.058 0.002 PHE V 76 TRP 0.020 0.001 TRP A 89 HIS 0.009 0.001 HIS V 31 Details of bonding type rmsd covalent geometry : bond 0.00379 (20990) covalent geometry : angle 0.66795 (28566) SS BOND : bond 0.00544 ( 45) SS BOND : angle 2.25283 ( 90) hydrogen bonds : bond 0.03341 ( 694) hydrogen bonds : angle 5.66638 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.794 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: A 88 MET cc_start: 0.8379 (ptm) cc_final: 0.8094 (ppp) REVERT: A 246 ASN cc_start: 0.8785 (t0) cc_final: 0.8336 (t0) REVERT: A 305 ASP cc_start: 0.8192 (t0) cc_final: 0.7969 (t0) REVERT: A 352 ILE cc_start: 0.7575 (mt) cc_final: 0.6333 (mt) REVERT: B 83 MET cc_start: 0.7875 (tpt) cc_final: 0.7388 (tpt) REVERT: B 95 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7547 (ttp80) REVERT: B 97 LEU cc_start: 0.8810 (mp) cc_final: 0.8419 (mt) REVERT: B 203 GLU cc_start: 0.8058 (pp20) cc_final: 0.7815 (pp20) REVERT: B 228 GLN cc_start: 0.8276 (tp-100) cc_final: 0.7913 (tp40) REVERT: B 283 PHE cc_start: 0.7534 (t80) cc_final: 0.6835 (t80) REVERT: B 308 ASP cc_start: 0.8193 (t70) cc_final: 0.7855 (t0) REVERT: F 61 LYS cc_start: 0.7815 (tppt) cc_final: 0.7487 (ttmt) REVERT: F 116 ILE cc_start: 0.9209 (tp) cc_final: 0.8862 (mm) REVERT: F 134 ARG cc_start: 0.8346 (ttm110) cc_final: 0.7897 (ttm-80) REVERT: F 188 ASP cc_start: 0.8062 (t0) cc_final: 0.7832 (t0) REVERT: F 246 ASN cc_start: 0.8937 (m-40) cc_final: 0.8438 (t0) REVERT: F 377 ASN cc_start: 0.8154 (m-40) cc_final: 0.7906 (m-40) REVERT: G 46 ILE cc_start: 0.9159 (mm) cc_final: 0.8850 (pt) REVERT: G 125 ASN cc_start: 0.8185 (m110) cc_final: 0.7612 (m-40) REVERT: G 220 MET cc_start: 0.9072 (mmm) cc_final: 0.8681 (mmm) REVERT: G 275 HIS cc_start: 0.8490 (t70) cc_final: 0.8090 (t-90) REVERT: G 282 TRP cc_start: 0.9414 (p-90) cc_final: 0.8646 (p-90) REVERT: J 65 SER cc_start: 0.8414 (t) cc_final: 0.8208 (t) REVERT: J 160 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8298 (tppp) REVERT: J 246 ASN cc_start: 0.9125 (t0) cc_final: 0.8746 (t0) REVERT: J 257 PHE cc_start: 0.8853 (m-80) cc_final: 0.8242 (m-10) REVERT: J 385 ASP cc_start: 0.7688 (t0) cc_final: 0.7389 (t0) REVERT: J 387 ILE cc_start: 0.8373 (tp) cc_final: 0.7651 (tp) REVERT: K 25 SER cc_start: 0.8420 (t) cc_final: 0.7607 (t) REVERT: K 83 MET cc_start: 0.7681 (mmt) cc_final: 0.7451 (mmm) REVERT: K 161 LEU cc_start: 0.9157 (mt) cc_final: 0.8947 (tp) REVERT: K 203 GLU cc_start: 0.8040 (pp20) cc_final: 0.7493 (pp20) REVERT: K 209 TYR cc_start: 0.6848 (t80) cc_final: 0.6534 (t80) REVERT: H 51 ILE cc_start: 0.8924 (tt) cc_final: 0.8413 (tp) REVERT: L 40 TRP cc_start: 0.7918 (m100) cc_final: 0.7491 (m100) REVERT: L 55 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6593 (mm-40) REVERT: L 76 PHE cc_start: 0.7905 (m-80) cc_final: 0.7280 (m-80) REVERT: U 3 GLN cc_start: 0.7379 (tm-30) cc_final: 0.7102 (tm-30) REVERT: U 29 PHE cc_start: 0.8155 (t80) cc_final: 0.7886 (t80) REVERT: U 39 GLN cc_start: 0.7011 (tt0) cc_final: 0.6695 (tt0) REVERT: U 66 ARG cc_start: 0.7119 (mtm110) cc_final: 0.6625 (mtp-110) REVERT: U 67 PHE cc_start: 0.7493 (m-80) cc_final: 0.7051 (m-80) REVERT: V 5 THR cc_start: 0.7599 (p) cc_final: 0.7354 (p) REVERT: V 27 GLN cc_start: 0.7606 (mt0) cc_final: 0.7335 (mt0) REVERT: V 54 TYR cc_start: 0.8622 (p90) cc_final: 0.7867 (p90) REVERT: V 55 GLN cc_start: 0.3957 (tt0) cc_final: 0.3179 (tt0) REVERT: V 58 ASN cc_start: 0.8477 (m110) cc_final: 0.8179 (m110) REVERT: V 92 TYR cc_start: 0.5770 (m-80) cc_final: 0.5341 (m-80) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.1521 time to fit residues: 109.8216 Evaluate side-chains 363 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 100 optimal weight: 0.0770 chunk 59 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 15 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN V 31 HIS V 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112449 restraints weight = 39162.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113647 restraints weight = 26843.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113670 restraints weight = 20247.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114281 restraints weight = 15488.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114476 restraints weight = 13714.468| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21035 Z= 0.154 Angle : 0.668 10.172 28656 Z= 0.343 Chirality : 0.047 0.195 3185 Planarity : 0.005 0.050 3669 Dihedral : 5.498 49.728 2878 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.51 % Rotamer: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2642 helix: -0.64 (0.70), residues: 45 sheet: -0.37 (0.15), residues: 1142 loop : -0.80 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 135 TYR 0.030 0.001 TYR K 21 PHE 0.034 0.002 PHE H 114 TRP 0.027 0.002 TRP G 282 HIS 0.007 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00367 (20990) covalent geometry : angle 0.65979 (28566) SS BOND : bond 0.00613 ( 45) SS BOND : angle 2.02783 ( 90) hydrogen bonds : bond 0.03283 ( 694) hydrogen bonds : angle 5.57425 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 471 time to evaluate : 0.824 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: A 88 MET cc_start: 0.8298 (ptm) cc_final: 0.7984 (ppp) REVERT: A 89 TRP cc_start: 0.7933 (t-100) cc_final: 0.7659 (t-100) REVERT: A 246 ASN cc_start: 0.8789 (t0) cc_final: 0.8443 (t0) REVERT: B 83 MET cc_start: 0.7962 (tpt) cc_final: 0.6956 (tpp) REVERT: B 95 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7726 (ttp80) REVERT: B 97 LEU cc_start: 0.8825 (mp) cc_final: 0.8479 (mt) REVERT: B 283 PHE cc_start: 0.7922 (t80) cc_final: 0.7269 (t80) REVERT: B 308 ASP cc_start: 0.8140 (t70) cc_final: 0.7799 (t0) REVERT: F 47 VAL cc_start: 0.9706 (m) cc_final: 0.9358 (t) REVERT: F 61 LYS cc_start: 0.7896 (tppt) cc_final: 0.7489 (ttmt) REVERT: F 114 CYS cc_start: 0.6066 (m) cc_final: 0.5848 (m) REVERT: F 116 ILE cc_start: 0.9178 (tp) cc_final: 0.8808 (mm) REVERT: F 149 ASN cc_start: 0.8335 (p0) cc_final: 0.7877 (p0) REVERT: F 246 ASN cc_start: 0.8971 (m-40) cc_final: 0.8476 (t0) REVERT: F 281 ASP cc_start: 0.8429 (t0) cc_final: 0.8203 (t0) REVERT: G 46 ILE cc_start: 0.9135 (mm) cc_final: 0.8891 (pt) REVERT: G 125 ASN cc_start: 0.8180 (m110) cc_final: 0.7635 (m-40) REVERT: G 202 TYR cc_start: 0.8347 (p90) cc_final: 0.7818 (p90) REVERT: G 275 HIS cc_start: 0.8515 (t70) cc_final: 0.8098 (t-90) REVERT: J 65 SER cc_start: 0.8419 (t) cc_final: 0.8189 (t) REVERT: J 160 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8162 (tppp) REVERT: J 246 ASN cc_start: 0.9091 (t0) cc_final: 0.8718 (t0) REVERT: J 257 PHE cc_start: 0.8885 (m-80) cc_final: 0.8251 (m-10) REVERT: J 385 ASP cc_start: 0.7381 (t0) cc_final: 0.7109 (t0) REVERT: J 387 ILE cc_start: 0.8426 (tp) cc_final: 0.7553 (mm) REVERT: J 388 ILE cc_start: 0.8780 (mm) cc_final: 0.8561 (mm) REVERT: K 177 HIS cc_start: 0.8090 (t-90) cc_final: 0.7842 (t-90) REVERT: K 203 GLU cc_start: 0.8115 (pp20) cc_final: 0.7533 (pp20) REVERT: L 40 TRP cc_start: 0.7856 (m100) cc_final: 0.7478 (m100) REVERT: L 55 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6577 (mm-40) REVERT: L 76 PHE cc_start: 0.7889 (m-80) cc_final: 0.7312 (m-80) REVERT: U 3 GLN cc_start: 0.7195 (tm-30) cc_final: 0.6930 (tm-30) REVERT: U 29 PHE cc_start: 0.8074 (t80) cc_final: 0.7843 (t80) REVERT: U 39 GLN cc_start: 0.7019 (tt0) cc_final: 0.6684 (tt0) REVERT: U 66 ARG cc_start: 0.7113 (mtm110) cc_final: 0.6595 (mtp-110) REVERT: U 67 PHE cc_start: 0.7397 (m-80) cc_final: 0.7014 (m-80) REVERT: V 5 THR cc_start: 0.7362 (p) cc_final: 0.7088 (p) REVERT: V 54 TYR cc_start: 0.8474 (p90) cc_final: 0.7440 (p90) REVERT: V 58 ASN cc_start: 0.8444 (m110) cc_final: 0.8205 (m110) REVERT: V 76 PHE cc_start: 0.8017 (m-80) cc_final: 0.7450 (m-80) REVERT: V 92 TYR cc_start: 0.5918 (m-80) cc_final: 0.5461 (m-80) outliers start: 1 outliers final: 1 residues processed: 472 average time/residue: 0.1486 time to fit residues: 107.4130 Evaluate side-chains 369 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 83 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 162 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 chunk 176 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 228 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 230 HIS J 364 ASN ** K 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN V 27 GLN ** V 95 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 = 0.3880 r_free = 0.3880 target = 0.152664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111067 restraints weight = 39231.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111672 restraints weight = 24956.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111930 restraints weight = 18810.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112454 restraints weight = 15403.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112593 restraints weight = 13639.204| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21035 Z= 0.173 Angle : 0.688 11.070 28656 Z= 0.354 Chirality : 0.047 0.188 3185 Planarity : 0.005 0.051 3669 Dihedral : 5.595 49.356 2878 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2642 helix: -0.73 (0.70), residues: 45 sheet: -0.34 (0.15), residues: 1172 loop : -0.77 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 135 TYR 0.046 0.002 TYR K 209 PHE 0.021 0.001 PHE V 76 TRP 0.026 0.002 TRP G 282 HIS 0.007 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00411 (20990) covalent geometry : angle 0.67817 (28566) SS BOND : bond 0.00522 ( 45) SS BOND : angle 2.22102 ( 90) hydrogen bonds : bond 0.03373 ( 694) hydrogen bonds : angle 5.58980 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 454 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7978 (ptm) cc_final: 0.7764 (ppp) REVERT: A 246 ASN cc_start: 0.8823 (t0) cc_final: 0.8437 (t0) REVERT: B 83 MET cc_start: 0.7842 (tpt) cc_final: 0.6832 (tpp) REVERT: B 95 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7567 (ttp80) REVERT: B 203 GLU cc_start: 0.8111 (pp20) cc_final: 0.7846 (pp20) REVERT: B 282 TRP cc_start: 0.8856 (p-90) cc_final: 0.8599 (p-90) REVERT: B 283 PHE cc_start: 0.8013 (t80) cc_final: 0.7384 (t80) REVERT: B 308 ASP cc_start: 0.8224 (t70) cc_final: 0.7913 (t0) REVERT: F 47 VAL cc_start: 0.9689 (m) cc_final: 0.9384 (t) REVERT: F 61 LYS cc_start: 0.8186 (tppt) cc_final: 0.7716 (ttmt) REVERT: F 116 ILE cc_start: 0.9188 (tp) cc_final: 0.8807 (mm) REVERT: G 46 ILE cc_start: 0.9205 (mm) cc_final: 0.8937 (pt) REVERT: G 125 ASN cc_start: 0.8228 (m110) cc_final: 0.7710 (m-40) REVERT: G 275 HIS cc_start: 0.8593 (t70) cc_final: 0.8207 (t-90) REVERT: J 65 SER cc_start: 0.8397 (t) cc_final: 0.8185 (t) REVERT: J 160 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8164 (tppp) REVERT: J 246 ASN cc_start: 0.9114 (t0) cc_final: 0.8744 (t0) REVERT: J 257 PHE cc_start: 0.8861 (m-80) cc_final: 0.8333 (m-10) REVERT: J 388 ILE cc_start: 0.8820 (mm) cc_final: 0.8618 (mm) REVERT: K 23 ARG cc_start: 0.8164 (tpt170) cc_final: 0.7911 (tpt170) REVERT: K 141 GLU cc_start: 0.7965 (pm20) cc_final: 0.7595 (pm20) REVERT: K 177 HIS cc_start: 0.8176 (t-90) cc_final: 0.7910 (t-90) REVERT: K 203 GLU cc_start: 0.8044 (pp20) cc_final: 0.7459 (pp20) REVERT: K 209 TYR cc_start: 0.6623 (t80) cc_final: 0.6186 (t80) REVERT: K 220 MET cc_start: 0.7922 (mmt) cc_final: 0.7644 (mmt) REVERT: L 4 MET cc_start: 0.6674 (tpt) cc_final: 0.6317 (tmm) REVERT: L 40 TRP cc_start: 0.7891 (m100) cc_final: 0.7436 (m100) REVERT: L 55 GLN cc_start: 0.6992 (mm-40) cc_final: 0.6615 (mm-40) REVERT: L 76 PHE cc_start: 0.7941 (m-80) cc_final: 0.7394 (m-80) REVERT: U 3 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6886 (tm-30) REVERT: U 29 PHE cc_start: 0.8174 (t80) cc_final: 0.7919 (t80) REVERT: U 39 GLN cc_start: 0.7094 (tt0) cc_final: 0.6775 (tt0) REVERT: U 66 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6752 (mtp-110) REVERT: U 67 PHE cc_start: 0.7474 (m-80) cc_final: 0.6857 (m-80) REVERT: V 5 THR cc_start: 0.7403 (p) cc_final: 0.7132 (p) REVERT: V 50 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.8234 (tmm-80) REVERT: V 55 GLN cc_start: 0.4172 (tt0) cc_final: 0.3251 (tt0) REVERT: V 58 ASN cc_start: 0.8393 (m110) cc_final: 0.8029 (m110) REVERT: V 76 PHE cc_start: 0.7836 (m-80) cc_final: 0.7485 (m-80) REVERT: V 92 TYR cc_start: 0.6119 (m-80) cc_final: 0.5711 (m-80) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.1466 time to fit residues: 102.0860 Evaluate side-chains 362 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 125 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 199 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 220 optimal weight: 0.4980 chunk 48 optimal weight: 0.0670 chunk 170 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 228 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** V 95 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 = 0.3894 r_free = 0.3894 target = 0.153902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112587 restraints weight = 38810.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113628 restraints weight = 26605.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113745 restraints weight = 19175.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114286 restraints weight = 15861.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114443 restraints weight = 14034.108| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21035 Z= 0.145 Angle : 0.678 10.672 28656 Z= 0.347 Chirality : 0.047 0.186 3185 Planarity : 0.005 0.057 3669 Dihedral : 5.529 49.023 2878 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.16), residues: 2642 helix: -0.73 (0.70), residues: 45 sheet: -0.34 (0.15), residues: 1158 loop : -0.81 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 135 TYR 0.033 0.002 TYR F 46 PHE 0.020 0.002 PHE B 29 TRP 0.013 0.001 TRP G 282 HIS 0.012 0.001 HIS K 172 Details of bonding type rmsd covalent geometry : bond 0.00347 (20990) covalent geometry : angle 0.66760 (28566) SS BOND : bond 0.00606 ( 45) SS BOND : angle 2.20776 ( 90) hydrogen bonds : bond 0.03272 ( 694) hydrogen bonds : angle 5.52981 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.816 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: A 9 ASN cc_start: 0.8776 (t0) cc_final: 0.8534 (t0) REVERT: A 246 ASN cc_start: 0.8837 (t0) cc_final: 0.8455 (t0) REVERT: B 83 MET cc_start: 0.7978 (tpt) cc_final: 0.7144 (tpp) REVERT: B 95 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7565 (ttp80) REVERT: B 203 GLU cc_start: 0.8034 (pp20) cc_final: 0.7756 (pp20) REVERT: B 282 TRP cc_start: 0.8830 (p-90) cc_final: 0.8589 (p-90) REVERT: B 283 PHE cc_start: 0.7960 (t80) cc_final: 0.7319 (t80) REVERT: B 308 ASP cc_start: 0.8312 (t70) cc_final: 0.7979 (t0) REVERT: F 100 ASN cc_start: 0.8547 (t0) cc_final: 0.7948 (t0) REVERT: F 116 ILE cc_start: 0.9106 (tp) cc_final: 0.8762 (mm) REVERT: F 149 ASN cc_start: 0.8423 (p0) cc_final: 0.8027 (p0) REVERT: F 174 ASP cc_start: 0.8417 (m-30) cc_final: 0.7596 (m-30) REVERT: F 246 ASN cc_start: 0.8902 (m-40) cc_final: 0.8448 (t0) REVERT: F 377 ASN cc_start: 0.8336 (m-40) cc_final: 0.7902 (p0) REVERT: G 125 ASN cc_start: 0.8095 (m110) cc_final: 0.7580 (m-40) REVERT: G 202 TYR cc_start: 0.8500 (p90) cc_final: 0.8024 (p90) REVERT: G 228 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8199 (mp10) REVERT: G 275 HIS cc_start: 0.8560 (t70) cc_final: 0.8197 (t-90) REVERT: G 282 TRP cc_start: 0.9086 (p-90) cc_final: 0.8548 (p-90) REVERT: J 160 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8223 (tppp) REVERT: J 246 ASN cc_start: 0.9129 (t0) cc_final: 0.8720 (t0) REVERT: J 257 PHE cc_start: 0.8881 (m-80) cc_final: 0.8390 (m-10) REVERT: J 336 THR cc_start: 0.8607 (m) cc_final: 0.8332 (m) REVERT: K 141 GLU cc_start: 0.7972 (pm20) cc_final: 0.7570 (pm20) REVERT: K 177 HIS cc_start: 0.8087 (t-90) cc_final: 0.7816 (t-90) REVERT: K 203 GLU cc_start: 0.8081 (pp20) cc_final: 0.7498 (pp20) REVERT: K 209 TYR cc_start: 0.6526 (t80) cc_final: 0.6138 (t80) REVERT: K 220 MET cc_start: 0.8030 (mmt) cc_final: 0.7608 (mmt) REVERT: K 283 PHE cc_start: 0.6321 (t80) cc_final: 0.6114 (t80) REVERT: H 51 ILE cc_start: 0.8811 (tt) cc_final: 0.8454 (tp) REVERT: L 40 TRP cc_start: 0.7814 (m100) cc_final: 0.7418 (m100) REVERT: L 55 GLN cc_start: 0.6932 (mm-40) cc_final: 0.6566 (mm-40) REVERT: L 76 PHE cc_start: 0.7880 (m-80) cc_final: 0.7303 (m-80) REVERT: U 3 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6889 (tm-30) REVERT: U 29 PHE cc_start: 0.7967 (t80) cc_final: 0.7748 (t80) REVERT: U 39 GLN cc_start: 0.7019 (tt0) cc_final: 0.6738 (tt0) REVERT: U 66 ARG cc_start: 0.7172 (mtm110) cc_final: 0.6637 (mtp-110) REVERT: U 67 PHE cc_start: 0.7417 (m-80) cc_final: 0.6899 (m-80) REVERT: V 5 THR cc_start: 0.7363 (p) cc_final: 0.7118 (p) REVERT: V 53 ILE cc_start: 0.9053 (mp) cc_final: 0.8182 (mp) REVERT: V 55 GLN cc_start: 0.4093 (tt0) cc_final: 0.3135 (tt0) REVERT: V 58 ASN cc_start: 0.8374 (m110) cc_final: 0.8117 (m110) REVERT: V 76 PHE cc_start: 0.7789 (m-80) cc_final: 0.7384 (m-80) REVERT: V 78 LEU cc_start: 0.6720 (tp) cc_final: 0.6485 (tp) REVERT: V 92 TYR cc_start: 0.6045 (m-80) cc_final: 0.5674 (m-80) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1558 time to fit residues: 107.4136 Evaluate side-chains 352 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 148 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 254 optimal weight: 0.0980 chunk 78 optimal weight: 0.0030 chunk 125 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 228 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 HIS ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN L 35 ASN ** V 95 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 = 0.3889 r_free = 0.3889 target = 0.153395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112326 restraints weight = 38996.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112417 restraints weight = 25871.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112662 restraints weight = 20408.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113244 restraints weight = 16345.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113555 restraints weight = 14268.585| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21035 Z= 0.150 Angle : 0.688 14.528 28656 Z= 0.351 Chirality : 0.047 0.223 3185 Planarity : 0.005 0.059 3669 Dihedral : 5.496 48.951 2878 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.16), residues: 2642 helix: -0.77 (0.69), residues: 45 sheet: -0.36 (0.15), residues: 1158 loop : -0.78 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 135 TYR 0.036 0.002 TYR K 21 PHE 0.019 0.002 PHE B 145 TRP 0.039 0.002 TRP H 36 HIS 0.009 0.001 HIS K 172 Details of bonding type rmsd covalent geometry : bond 0.00357 (20990) covalent geometry : angle 0.67434 (28566) SS BOND : bond 0.00574 ( 45) SS BOND : angle 2.49185 ( 90) hydrogen bonds : bond 0.03325 ( 694) hydrogen bonds : angle 5.49160 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8761 (t0) cc_final: 0.8554 (t0) REVERT: A 246 ASN cc_start: 0.8782 (t0) cc_final: 0.8406 (t0) REVERT: A 352 ILE cc_start: 0.8054 (mt) cc_final: 0.6961 (mt) REVERT: B 83 MET cc_start: 0.8052 (tpt) cc_final: 0.7313 (tpp) REVERT: B 95 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7571 (ttp80) REVERT: B 203 GLU cc_start: 0.8051 (pp20) cc_final: 0.7790 (pp20) REVERT: B 283 PHE cc_start: 0.7915 (t80) cc_final: 0.7296 (t80) REVERT: B 308 ASP cc_start: 0.8273 (t70) cc_final: 0.7937 (t0) REVERT: F 100 ASN cc_start: 0.8410 (t0) cc_final: 0.7950 (t0) REVERT: F 188 ASP cc_start: 0.8087 (t70) cc_final: 0.7764 (t0) REVERT: F 246 ASN cc_start: 0.8914 (m-40) cc_final: 0.8460 (t0) REVERT: G 125 ASN cc_start: 0.8117 (m110) cc_final: 0.7668 (m-40) REVERT: G 213 ILE cc_start: 0.8325 (mp) cc_final: 0.8055 (mp) REVERT: G 220 MET cc_start: 0.9075 (mmm) cc_final: 0.8770 (mmm) REVERT: G 275 HIS cc_start: 0.8587 (t70) cc_final: 0.8248 (t-90) REVERT: G 282 TRP cc_start: 0.9175 (p-90) cc_final: 0.8732 (p-90) REVERT: J 160 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8351 (tppp) REVERT: J 257 PHE cc_start: 0.8842 (m-80) cc_final: 0.8399 (m-10) REVERT: J 336 THR cc_start: 0.8628 (m) cc_final: 0.8395 (m) REVERT: K 57 ASN cc_start: 0.8525 (p0) cc_final: 0.8270 (p0) REVERT: K 141 GLU cc_start: 0.7958 (pm20) cc_final: 0.7588 (pm20) REVERT: K 177 HIS cc_start: 0.7909 (t-90) cc_final: 0.7624 (t-90) REVERT: K 203 GLU cc_start: 0.8082 (pp20) cc_final: 0.7462 (pp20) REVERT: K 209 TYR cc_start: 0.6477 (t80) cc_final: 0.5980 (t80) REVERT: K 220 MET cc_start: 0.7997 (mmt) cc_final: 0.7733 (mmt) REVERT: H 51 ILE cc_start: 0.8966 (tt) cc_final: 0.8685 (tp) REVERT: L 40 TRP cc_start: 0.7973 (m100) cc_final: 0.7676 (m100) REVERT: L 55 GLN cc_start: 0.6907 (mm-40) cc_final: 0.6542 (mm-40) REVERT: L 76 PHE cc_start: 0.7972 (m-80) cc_final: 0.7370 (m-80) REVERT: U 3 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6857 (tm-30) REVERT: U 4 LEU cc_start: 0.7388 (mt) cc_final: 0.7151 (mp) REVERT: U 66 ARG cc_start: 0.7218 (mtm110) cc_final: 0.6603 (mtp-110) REVERT: U 67 PHE cc_start: 0.7428 (m-80) cc_final: 0.6898 (m-80) REVERT: V 5 THR cc_start: 0.7310 (p) cc_final: 0.7046 (p) REVERT: V 53 ILE cc_start: 0.9060 (mp) cc_final: 0.8836 (mt) REVERT: V 54 TYR cc_start: 0.8552 (p90) cc_final: 0.7916 (p90) REVERT: V 55 GLN cc_start: 0.4117 (tt0) cc_final: 0.3803 (tt0) REVERT: V 59 ARG cc_start: 0.6796 (mmt-90) cc_final: 0.6494 (mmt-90) REVERT: V 76 PHE cc_start: 0.7950 (m-80) cc_final: 0.7612 (m-80) REVERT: V 92 TYR cc_start: 0.6130 (m-80) cc_final: 0.5701 (m-80) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1531 time to fit residues: 101.5783 Evaluate side-chains 347 residues out of total 2260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 128 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 146 optimal weight: 0.0470 chunk 204 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 251 optimal weight: 0.0770 chunk 127 optimal weight: 0.7980 chunk 138 optimal weight: 0.4980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 228 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 HIS G 221 ASN ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 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 = 0.3898 r_free = 0.3898 target = 0.154180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113115 restraints weight = 39202.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113420 restraints weight = 28174.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113628 restraints weight = 20932.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114280 restraints weight = 16823.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114637 restraints weight = 14739.563| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21035 Z= 0.140 Angle : 0.682 13.161 28656 Z= 0.348 Chirality : 0.047 0.246 3185 Planarity : 0.005 0.061 3669 Dihedral : 5.480 49.154 2878 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2642 helix: -0.74 (0.69), residues: 45 sheet: -0.31 (0.15), residues: 1158 loop : -0.76 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 135 TYR 0.029 0.001 TYR K 21 PHE 0.030 0.002 PHE B 29 TRP 0.024 0.002 TRP K 282 HIS 0.015 0.001 HIS G 172 Details of bonding type rmsd covalent geometry : bond 0.00334 (20990) covalent geometry : angle 0.66950 (28566) SS BOND : bond 0.00554 ( 45) SS BOND : angle 2.44757 ( 90) hydrogen bonds : bond 0.03298 ( 694) hydrogen bonds : angle 5.43892 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4259.31 seconds wall clock time: 74 minutes 45.34 seconds (4485.34 seconds total)