Starting phenix.real_space_refine on Sun Aug 24 09:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6j_27920/08_2025/8e6j_27920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6j_27920/08_2025/8e6j_27920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e6j_27920/08_2025/8e6j_27920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6j_27920/08_2025/8e6j_27920.map" model { file = "/net/cci-nas-00/data/ceres_data/8e6j_27920/08_2025/8e6j_27920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6j_27920/08_2025/8e6j_27920.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 112 5.16 5 C 11944 2.51 5 N 3224 2.21 5 O 3728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19008 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Restraints were copied for chains: B, C, D, I, J, K, E, F, G Time building chain proxies: 3.24, per 1000 atoms: 0.17 Number of scatterers: 19008 At special positions: 0 Unit cell: (151.525, 151.525, 87, 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 112 16.00 O 3728 8.00 N 3224 7.00 C 11944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.04 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.04 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 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: 1.55 Conformation dependent library (CDL) restraints added in 820.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 48 sheets defined 3.4% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 412A through 414 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.388A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.693A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.481A pdb=" N ALA A 203 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 205 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.982A pdb=" N TYR A 252 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU A 267 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 254 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS A 256 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.843A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS A 280 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.621A pdb=" N PHE A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 363 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 372 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 392 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.234A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.247A pdb=" N SER H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL H 96 " --> pdb=" O LEU H 100H" (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU H 100H" --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.388A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.693A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.481A pdb=" N ALA B 203 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 205 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.982A pdb=" N TYR B 252 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B 267 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 254 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS B 256 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.843A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS B 280 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.621A pdb=" N PHE B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 363 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER B 372 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 399 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 392 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR I 13 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR I 13 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.234A pdb=" N TRP E 35A" --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.247A pdb=" N SER E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL E 96 " --> pdb=" O LEU E 100H" (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU E 100H" --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.388A pdb=" N SER C 445 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.693A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.481A pdb=" N ALA C 203 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR C 214 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 205 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 231 through 233 removed outlier: 6.982A pdb=" N TYR C 252 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 267 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 254 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS C 256 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 276 through 283 removed outlier: 4.843A pdb=" N CYS C 278 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS C 280 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.621A pdb=" N PHE C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 363 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER C 372 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA C 399 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 392 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR J 13 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR J 13 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'F' and resid 11 through 12 removed outlier: 7.234A pdb=" N TRP F 35A" --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.247A pdb=" N SER F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL F 96 " --> pdb=" O LEU F 100H" (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU F 100H" --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.388A pdb=" N SER D 445 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.693A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.481A pdb=" N ALA D 203 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR D 214 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU D 205 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 231 through 233 removed outlier: 6.982A pdb=" N TYR D 252 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU D 267 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 254 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS D 256 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 276 through 283 removed outlier: 4.843A pdb=" N CYS D 278 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS D 280 " --> pdb=" O MET D 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.621A pdb=" N PHE D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 363 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER D 372 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA D 399 " --> pdb=" O SER D 372 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 392 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR K 13 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR K 13 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.234A pdb=" N TRP G 35A" --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.247A pdb=" N SER G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL G 96 " --> pdb=" O LEU G 100H" (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU G 100H" --> pdb=" O VAL G 96 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1776 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: 3.93 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6028 1.34 - 1.47: 5264 1.47 - 1.59: 8072 1.59 - 1.72: 0 1.72 - 1.84: 140 Bond restraints: 19504 Sorted by residual: bond pdb=" N CYS B 318 " pdb=" CA CYS B 318 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.64e+00 bond pdb=" N CYS C 318 " pdb=" CA CYS C 318 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.64e+00 bond pdb=" N CYS A 318 " pdb=" CA CYS A 318 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.64e+00 bond pdb=" N CYS D 318 " pdb=" CA CYS D 318 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.64e+00 bond pdb=" N LYS I 42 " pdb=" CA LYS I 42 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.27e-02 6.20e+03 6.59e+00 ... (remaining 19499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 22040 1.42 - 2.83: 3464 2.83 - 4.25: 804 4.25 - 5.67: 180 5.67 - 7.08: 44 Bond angle restraints: 26532 Sorted by residual: angle pdb=" N CYS B 336 " pdb=" CA CYS B 336 " pdb=" C CYS B 336 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N CYS A 336 " pdb=" CA CYS A 336 " pdb=" C CYS A 336 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N CYS C 336 " pdb=" CA CYS C 336 " pdb=" C CYS C 336 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N CYS D 336 " pdb=" CA CYS D 336 " pdb=" C CYS D 336 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N SER C 442 " pdb=" CA SER C 442 " pdb=" C SER C 442 " ideal model delta sigma weight residual 109.14 102.33 6.81 1.49e+00 4.50e-01 2.09e+01 ... (remaining 26527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 10756 17.54 - 35.08: 484 35.08 - 52.63: 152 52.63 - 70.17: 48 70.17 - 87.71: 20 Dihedral angle restraints: 11460 sinusoidal: 4444 harmonic: 7016 Sorted by residual: dihedral pdb=" CB CYS B 183 " pdb=" SG CYS B 183 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual 93.00 179.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS D 183 " pdb=" SG CYS D 183 " pdb=" SG CYS D 230 " pdb=" CB CYS D 230 " ideal model delta sinusoidal sigma weight residual 93.00 179.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS A 183 " pdb=" SG CYS A 183 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual 93.00 179.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 ... (remaining 11457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1732 0.049 - 0.097: 772 0.097 - 0.146: 268 0.146 - 0.195: 64 0.195 - 0.243: 24 Chirality restraints: 2860 Sorted by residual: chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE B 222 " pdb=" CA ILE B 222 " pdb=" CG1 ILE B 222 " pdb=" CG2 ILE B 222 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE C 222 " pdb=" CA ILE C 222 " pdb=" CG1 ILE C 222 " pdb=" CG2 ILE C 222 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2857 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 222 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE D 222 " -0.068 2.00e-02 2.50e+03 pdb=" O ILE D 222 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU D 223 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 222 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE C 222 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE C 222 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU C 223 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 222 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE A 222 " -0.068 2.00e-02 2.50e+03 pdb=" O ILE A 222 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU A 223 " 0.023 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 692 2.69 - 3.24: 17468 3.24 - 3.79: 31924 3.79 - 4.35: 45276 4.35 - 4.90: 74768 Nonbonded interactions: 170128 Sorted by model distance: nonbonded pdb=" O ASP A 113 " pdb=" OG SER A 168 " model vdw 2.136 3.040 nonbonded pdb=" O ASP C 113 " pdb=" OG SER C 168 " model vdw 2.136 3.040 nonbonded pdb=" O ASP D 113 " pdb=" OG SER D 168 " model vdw 2.136 3.040 nonbonded pdb=" O ASP B 113 " pdb=" OG SER B 168 " model vdw 2.136 3.040 nonbonded pdb=" OG SER A 298 " pdb=" O SER A 343 " model vdw 2.230 3.040 ... (remaining 170123 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'L' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.007 0.089 19544 Z= 0.310 Angle : 1.182 7.899 26612 Z= 0.689 Chirality : 0.064 0.243 2860 Planarity : 0.006 0.039 3408 Dihedral : 12.050 87.709 6884 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.19 % Allowed : 7.87 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.17), residues: 2444 helix: 0.36 (0.79), residues: 24 sheet: 0.71 (0.17), residues: 884 loop : 0.15 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 66 TYR 0.043 0.004 TYR E 34 PHE 0.022 0.004 PHE B 446 TRP 0.028 0.004 TRP I 35 HIS 0.012 0.003 HIS D 412A Details of bonding type rmsd covalent geometry : bond 0.00679 (19504) covalent geometry : angle 1.17136 (26532) SS BOND : bond 0.00851 ( 40) SS BOND : angle 3.08168 ( 80) hydrogen bonds : bond 0.13507 ( 672) hydrogen bonds : angle 7.89538 ( 1776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.736 Fit side-chains REVERT: A 358 ASN cc_start: 0.7852 (m110) cc_final: 0.7544 (t0) REVERT: H 100 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7630 (mmt90) REVERT: B 358 ASN cc_start: 0.7853 (m110) cc_final: 0.7544 (t0) REVERT: E 100 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7631 (mmt90) REVERT: C 358 ASN cc_start: 0.7852 (m110) cc_final: 0.7541 (t0) REVERT: F 100 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7632 (mmt90) REVERT: D 358 ASN cc_start: 0.7849 (m110) cc_final: 0.7538 (t0) REVERT: G 100 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7631 (mmt90) outliers start: 4 outliers final: 0 residues processed: 248 average time/residue: 0.3672 time to fit residues: 108.0470 Evaluate side-chains 192 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 274 HIS A 347 ASN A 450 ASN H 81 ASN B 226 GLN B 274 HIS B 347 ASN B 450 ASN E 81 ASN C 226 GLN C 274 HIS C 347 ASN C 450 ASN F 81 ASN D 226 GLN D 274 HIS D 347 ASN D 450 ASN G 81 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121646 restraints weight = 21880.816| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.36 r_work: 0.3204 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19544 Z= 0.260 Angle : 0.705 9.323 26612 Z= 0.388 Chirality : 0.051 0.166 2860 Planarity : 0.005 0.038 3408 Dihedral : 5.679 22.118 2664 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.62 % Allowed : 8.43 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2444 helix: -0.40 (0.72), residues: 28 sheet: 0.51 (0.15), residues: 992 loop : 0.18 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 300 TYR 0.018 0.003 TYR A 169A PHE 0.021 0.003 PHE D 115 TRP 0.020 0.002 TRP D 97 HIS 0.011 0.004 HIS D 412A Details of bonding type rmsd covalent geometry : bond 0.00590 (19504) covalent geometry : angle 0.70250 (26532) SS BOND : bond 0.00532 ( 40) SS BOND : angle 1.30711 ( 80) hydrogen bonds : bond 0.05230 ( 672) hydrogen bonds : angle 6.82175 ( 1776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.705 Fit side-chains REVERT: A 358 ASN cc_start: 0.7809 (m110) cc_final: 0.7519 (t0) REVERT: B 358 ASN cc_start: 0.7805 (m110) cc_final: 0.7521 (t0) REVERT: C 358 ASN cc_start: 0.7798 (m110) cc_final: 0.7514 (t0) REVERT: D 358 ASN cc_start: 0.7806 (m110) cc_final: 0.7522 (t0) outliers start: 56 outliers final: 20 residues processed: 240 average time/residue: 0.5393 time to fit residues: 147.5432 Evaluate side-chains 220 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 105 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 66 optimal weight: 7.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 294 ASN A 313 GLN A 347 ASN L 89 GLN H 81 ASN B 226 GLN B 294 ASN B 313 GLN B 347 ASN I 89 GLN E 81 ASN C 226 GLN C 294 ASN C 313 GLN C 347 ASN J 89 GLN F 81 ASN D 226 GLN D 294 ASN D 313 GLN D 347 ASN K 89 GLN G 81 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125622 restraints weight = 21937.417| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.39 r_work: 0.3300 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 19544 Z= 0.134 Angle : 0.612 15.495 26612 Z= 0.325 Chirality : 0.047 0.169 2860 Planarity : 0.004 0.035 3408 Dihedral : 5.368 39.180 2664 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.29 % Favored : 97.55 % Rotamer: Outliers : 1.69 % Allowed : 11.24 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.17), residues: 2444 helix: -0.54 (0.68), residues: 28 sheet: 0.49 (0.16), residues: 992 loop : 0.24 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 61 TYR 0.013 0.001 TYR E 34 PHE 0.014 0.002 PHE F 78 TRP 0.016 0.001 TRP E 47 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00314 (19504) covalent geometry : angle 0.60474 (26532) SS BOND : bond 0.00921 ( 40) SS BOND : angle 1.81417 ( 80) hydrogen bonds : bond 0.03913 ( 672) hydrogen bonds : angle 6.36407 ( 1776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.652 Fit side-chains REVERT: A 172 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7316 (ttm170) REVERT: A 358 ASN cc_start: 0.7744 (m110) cc_final: 0.7524 (t0) REVERT: A 396 ASP cc_start: 0.8812 (m-30) cc_final: 0.8605 (m-30) REVERT: B 172 ARG cc_start: 0.7629 (ttp-170) cc_final: 0.7319 (ttm170) REVERT: B 358 ASN cc_start: 0.7742 (m110) cc_final: 0.7524 (t0) REVERT: B 396 ASP cc_start: 0.8802 (m-30) cc_final: 0.8594 (m-30) REVERT: C 172 ARG cc_start: 0.7639 (ttp-170) cc_final: 0.7330 (ttm170) REVERT: C 358 ASN cc_start: 0.7741 (m110) cc_final: 0.7517 (t0) REVERT: C 396 ASP cc_start: 0.8811 (m-30) cc_final: 0.8599 (m-30) REVERT: D 172 ARG cc_start: 0.7634 (ttp-170) cc_final: 0.7323 (ttm170) REVERT: D 358 ASN cc_start: 0.7741 (m110) cc_final: 0.7523 (t0) REVERT: D 396 ASP cc_start: 0.8812 (m-30) cc_final: 0.8603 (m-30) outliers start: 36 outliers final: 8 residues processed: 252 average time/residue: 0.4593 time to fit residues: 134.0960 Evaluate side-chains 200 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain G residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 79 optimal weight: 0.9990 chunk 237 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 0.0000 chunk 166 optimal weight: 1.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 294 ASN A 296 HIS A 313 GLN L 89 GLN H 81 ASN B 226 GLN B 294 ASN B 296 HIS B 313 GLN I 89 GLN E 81 ASN C 226 GLN C 294 ASN C 296 HIS C 313 GLN J 89 GLN F 81 ASN D 226 GLN D 294 ASN D 296 HIS D 313 GLN K 89 GLN G 81 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.160474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123510 restraints weight = 21959.845| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.40 r_work: 0.3269 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19544 Z= 0.173 Angle : 0.630 14.212 26612 Z= 0.334 Chirality : 0.047 0.180 2860 Planarity : 0.004 0.040 3408 Dihedral : 5.495 40.529 2664 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.05 % Rotamer: Outliers : 3.18 % Allowed : 11.42 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.17), residues: 2444 helix: -0.82 (0.73), residues: 28 sheet: 0.46 (0.16), residues: 968 loop : 0.14 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 364 TYR 0.011 0.002 TYR A 252 PHE 0.018 0.002 PHE D 121 TRP 0.012 0.002 TRP F 47 HIS 0.005 0.001 HIS G 95 Details of bonding type rmsd covalent geometry : bond 0.00407 (19504) covalent geometry : angle 0.61673 (26532) SS BOND : bond 0.00585 ( 40) SS BOND : angle 2.42415 ( 80) hydrogen bonds : bond 0.03943 ( 672) hydrogen bonds : angle 6.40646 ( 1776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.737 Fit side-chains REVERT: A 172 ARG cc_start: 0.7622 (ttp-170) cc_final: 0.7419 (ttp-170) REVERT: A 358 ASN cc_start: 0.7883 (m110) cc_final: 0.7593 (t0) REVERT: A 396 ASP cc_start: 0.8821 (m-30) cc_final: 0.8607 (m-30) REVERT: B 358 ASN cc_start: 0.7880 (m110) cc_final: 0.7591 (t0) REVERT: B 396 ASP cc_start: 0.8811 (m-30) cc_final: 0.8597 (m-30) REVERT: C 172 ARG cc_start: 0.7629 (ttp-170) cc_final: 0.7429 (ttp-170) REVERT: C 358 ASN cc_start: 0.7876 (m110) cc_final: 0.7590 (t0) REVERT: C 396 ASP cc_start: 0.8811 (m-30) cc_final: 0.8595 (m-30) REVERT: D 172 ARG cc_start: 0.7619 (ttp-170) cc_final: 0.7417 (ttp-170) REVERT: D 358 ASN cc_start: 0.7881 (m110) cc_final: 0.7596 (t0) REVERT: D 396 ASP cc_start: 0.8821 (m-30) cc_final: 0.8608 (m-30) outliers start: 68 outliers final: 48 residues processed: 256 average time/residue: 0.4525 time to fit residues: 134.2882 Evaluate side-chains 248 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 144 optimal weight: 0.2980 chunk 99 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 226 GLN A 296 HIS A 313 GLN L 89 GLN H 81 ASN B 136 GLN B 226 GLN B 296 HIS B 313 GLN I 89 GLN E 81 ASN C 136 GLN C 226 GLN C 296 HIS C 313 GLN J 89 GLN F 81 ASN D 136 GLN D 226 GLN D 296 HIS D 313 GLN K 89 GLN G 81 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.157611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121803 restraints weight = 22027.947| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.42 r_work: 0.3252 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 19544 Z= 0.249 Angle : 0.695 13.813 26612 Z= 0.370 Chirality : 0.050 0.168 2860 Planarity : 0.005 0.045 3408 Dihedral : 5.739 41.361 2664 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Rotamer: Outliers : 3.56 % Allowed : 12.17 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2444 helix: -1.01 (0.86), residues: 24 sheet: 0.41 (0.16), residues: 976 loop : 0.03 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 224 TYR 0.013 0.002 TYR E 100G PHE 0.023 0.003 PHE C 410 TRP 0.014 0.002 TRP A 97 HIS 0.006 0.002 HIS G 95 Details of bonding type rmsd covalent geometry : bond 0.00586 (19504) covalent geometry : angle 0.67932 (26532) SS BOND : bond 0.00493 ( 40) SS BOND : angle 2.78044 ( 80) hydrogen bonds : bond 0.04338 ( 672) hydrogen bonds : angle 6.45390 ( 1776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 188 time to evaluate : 0.547 Fit side-chains REVERT: A 358 ASN cc_start: 0.7813 (m110) cc_final: 0.7579 (t0) REVERT: B 358 ASN cc_start: 0.7789 (m110) cc_final: 0.7562 (t0) REVERT: C 358 ASN cc_start: 0.7789 (m110) cc_final: 0.7565 (t0) REVERT: D 358 ASN cc_start: 0.7811 (m110) cc_final: 0.7580 (t0) outliers start: 76 outliers final: 44 residues processed: 236 average time/residue: 0.5024 time to fit residues: 135.3162 Evaluate side-chains 224 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 0.3980 chunk 153 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 130 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 226 GLN A 296 HIS A 313 GLN L 89 GLN H 81 ASN B 136 GLN B 226 GLN B 296 HIS B 313 GLN I 89 GLN E 81 ASN C 136 GLN C 226 GLN C 296 HIS C 313 GLN J 89 GLN F 81 ASN D 136 GLN D 226 GLN D 296 HIS D 313 GLN K 89 GLN G 81 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.161967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124727 restraints weight = 21738.744| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.41 r_work: 0.3297 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19544 Z= 0.114 Angle : 0.571 11.886 26612 Z= 0.304 Chirality : 0.046 0.160 2860 Planarity : 0.004 0.037 3408 Dihedral : 5.241 38.616 2664 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.38 % Rotamer: Outliers : 3.37 % Allowed : 12.55 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2444 helix: -1.09 (0.70), residues: 28 sheet: 0.55 (0.16), residues: 976 loop : 0.10 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.012 0.001 TYR G 34 PHE 0.017 0.002 PHE B 410 TRP 0.014 0.001 TRP E 47 HIS 0.002 0.000 HIS G 95 Details of bonding type rmsd covalent geometry : bond 0.00267 (19504) covalent geometry : angle 0.56202 (26532) SS BOND : bond 0.00408 ( 40) SS BOND : angle 1.94035 ( 80) hydrogen bonds : bond 0.03464 ( 672) hydrogen bonds : angle 6.09387 ( 1776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 192 time to evaluate : 0.630 Fit side-chains REVERT: A 358 ASN cc_start: 0.7863 (m110) cc_final: 0.7610 (t0) REVERT: H 3 GLN cc_start: 0.8000 (mt0) cc_final: 0.7770 (mm110) REVERT: B 358 ASN cc_start: 0.7852 (m110) cc_final: 0.7595 (t0) REVERT: E 3 GLN cc_start: 0.8012 (mt0) cc_final: 0.7778 (mm110) REVERT: C 358 ASN cc_start: 0.7864 (m110) cc_final: 0.7607 (t0) REVERT: F 3 GLN cc_start: 0.7997 (mt0) cc_final: 0.7770 (mm110) REVERT: D 358 ASN cc_start: 0.7851 (m110) cc_final: 0.7608 (t0) REVERT: G 3 GLN cc_start: 0.8011 (mt0) cc_final: 0.7783 (mm110) outliers start: 72 outliers final: 44 residues processed: 252 average time/residue: 0.4964 time to fit residues: 144.3807 Evaluate side-chains 232 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 123 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 226 GLN A 296 HIS A 313 GLN L 89 GLN H 81 ASN B 136 GLN B 226 GLN B 296 HIS B 313 GLN I 89 GLN E 81 ASN C 136 GLN C 226 GLN C 296 HIS C 313 GLN J 89 GLN F 81 ASN D 136 GLN D 226 GLN D 296 HIS D 313 GLN K 89 GLN G 81 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119970 restraints weight = 22039.265| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.39 r_work: 0.3224 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 19544 Z= 0.278 Angle : 0.682 12.765 26612 Z= 0.365 Chirality : 0.050 0.169 2860 Planarity : 0.005 0.047 3408 Dihedral : 5.725 39.134 2664 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.40 % Rotamer: Outliers : 3.56 % Allowed : 12.92 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.17), residues: 2444 helix: -1.10 (0.85), residues: 24 sheet: 0.35 (0.16), residues: 976 loop : -0.07 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 152 TYR 0.013 0.002 TYR H 100G PHE 0.025 0.003 PHE B 121 TRP 0.016 0.002 TRP A 97 HIS 0.006 0.002 HIS G 95 Details of bonding type rmsd covalent geometry : bond 0.00648 (19504) covalent geometry : angle 0.67023 (26532) SS BOND : bond 0.00504 ( 40) SS BOND : angle 2.38141 ( 80) hydrogen bonds : bond 0.04343 ( 672) hydrogen bonds : angle 6.39097 ( 1776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 0.527 Fit side-chains REVERT: A 358 ASN cc_start: 0.7853 (m110) cc_final: 0.7576 (t0) REVERT: B 358 ASN cc_start: 0.7841 (m110) cc_final: 0.7568 (t0) REVERT: C 358 ASN cc_start: 0.7838 (m110) cc_final: 0.7568 (t0) REVERT: D 358 ASN cc_start: 0.7858 (m110) cc_final: 0.7583 (t0) outliers start: 76 outliers final: 44 residues processed: 220 average time/residue: 0.4541 time to fit residues: 116.2549 Evaluate side-chains 204 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 234 optimal weight: 10.0000 chunk 94 optimal weight: 0.4980 chunk 48 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 170 ASN A 226 GLN A 296 HIS A 313 GLN L 89 GLN H 81 ASN B 136 GLN B 170 ASN B 226 GLN B 296 HIS B 313 GLN I 89 GLN E 81 ASN C 136 GLN C 170 ASN C 226 GLN C 296 HIS C 313 GLN J 89 GLN F 81 ASN D 136 GLN D 170 ASN D 226 GLN D 296 HIS D 313 GLN K 89 GLN G 81 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124627 restraints weight = 21924.330| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.41 r_work: 0.3295 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19544 Z= 0.119 Angle : 0.581 10.582 26612 Z= 0.309 Chirality : 0.046 0.155 2860 Planarity : 0.004 0.036 3408 Dihedral : 5.203 34.249 2664 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.38 % Rotamer: Outliers : 2.81 % Allowed : 13.30 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2444 helix: -0.76 (0.78), residues: 24 sheet: 0.49 (0.16), residues: 976 loop : 0.06 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.012 0.001 TYR G 34 PHE 0.016 0.002 PHE C 410 TRP 0.015 0.001 TRP D 178 HIS 0.002 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00270 (19504) covalent geometry : angle 0.57077 (26532) SS BOND : bond 0.00419 ( 40) SS BOND : angle 2.04365 ( 80) hydrogen bonds : bond 0.03426 ( 672) hydrogen bonds : angle 6.01966 ( 1776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 0.874 Fit side-chains REVERT: A 304 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8088 (p) REVERT: A 358 ASN cc_start: 0.7867 (m110) cc_final: 0.7570 (t0) REVERT: A 418 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7438 (mpp) REVERT: A 430 GLN cc_start: 0.8292 (mm110) cc_final: 0.8071 (mt0) REVERT: H 3 GLN cc_start: 0.8015 (mt0) cc_final: 0.7768 (mm110) REVERT: B 304 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8078 (p) REVERT: B 358 ASN cc_start: 0.7854 (m110) cc_final: 0.7557 (t0) REVERT: B 418 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7435 (mpp) REVERT: B 430 GLN cc_start: 0.8292 (mm110) cc_final: 0.8071 (mt0) REVERT: E 3 GLN cc_start: 0.8024 (mt0) cc_final: 0.7774 (mm110) REVERT: C 304 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8080 (p) REVERT: C 358 ASN cc_start: 0.7857 (m110) cc_final: 0.7568 (t0) REVERT: C 418 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7447 (mpp) REVERT: C 430 GLN cc_start: 0.8274 (mm110) cc_final: 0.8056 (mt0) REVERT: F 3 GLN cc_start: 0.8010 (mt0) cc_final: 0.7774 (mm110) REVERT: D 304 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8079 (p) REVERT: D 358 ASN cc_start: 0.7859 (m110) cc_final: 0.7572 (t0) REVERT: D 418 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7452 (mpp) REVERT: D 430 GLN cc_start: 0.8300 (mm110) cc_final: 0.8076 (mt0) REVERT: G 3 GLN cc_start: 0.8017 (mt0) cc_final: 0.7778 (mm110) outliers start: 60 outliers final: 32 residues processed: 232 average time/residue: 0.5273 time to fit residues: 141.7386 Evaluate side-chains 216 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 228 optimal weight: 0.0010 chunk 147 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 226 GLN A 296 HIS A 347 ASN L 89 GLN H 81 ASN B 136 GLN B 226 GLN B 296 HIS B 347 ASN I 89 GLN E 81 ASN C 136 GLN C 226 GLN C 296 HIS C 347 ASN J 89 GLN F 81 ASN D 136 GLN D 226 GLN D 296 HIS D 347 ASN K 89 GLN G 81 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122205 restraints weight = 21898.673| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.40 r_work: 0.3265 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19544 Z= 0.162 Angle : 0.597 10.258 26612 Z= 0.317 Chirality : 0.047 0.160 2860 Planarity : 0.004 0.040 3408 Dihedral : 5.258 32.124 2664 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Rotamer: Outliers : 2.39 % Allowed : 14.28 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2444 helix: -0.95 (0.78), residues: 24 sheet: 0.45 (0.16), residues: 976 loop : 0.01 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 364 TYR 0.012 0.001 TYR I 49 PHE 0.020 0.002 PHE A 121 TRP 0.010 0.001 TRP D 178 HIS 0.004 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00379 (19504) covalent geometry : angle 0.58491 (26532) SS BOND : bond 0.00414 ( 40) SS BOND : angle 2.25429 ( 80) hydrogen bonds : bond 0.03656 ( 672) hydrogen bonds : angle 6.01328 ( 1776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.809 Fit side-chains REVERT: A 304 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8049 (p) REVERT: A 358 ASN cc_start: 0.7908 (m110) cc_final: 0.7589 (t0) REVERT: A 430 GLN cc_start: 0.8294 (mm110) cc_final: 0.8052 (mt0) REVERT: H 3 GLN cc_start: 0.8024 (mt0) cc_final: 0.7768 (mm110) REVERT: H 48 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7762 (pt) REVERT: B 304 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8040 (p) REVERT: B 358 ASN cc_start: 0.7891 (m110) cc_final: 0.7579 (t0) REVERT: B 430 GLN cc_start: 0.8291 (mm110) cc_final: 0.8048 (mt0) REVERT: E 3 GLN cc_start: 0.8028 (mt0) cc_final: 0.7775 (mm110) REVERT: E 48 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7762 (pt) REVERT: C 304 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.8038 (p) REVERT: C 358 ASN cc_start: 0.7898 (m110) cc_final: 0.7585 (t0) REVERT: C 430 GLN cc_start: 0.8275 (mm110) cc_final: 0.8035 (mt0) REVERT: F 3 GLN cc_start: 0.8029 (mt0) cc_final: 0.7779 (mm110) REVERT: F 48 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7755 (pt) REVERT: D 304 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8047 (p) REVERT: D 358 ASN cc_start: 0.7902 (m110) cc_final: 0.7587 (t0) REVERT: D 430 GLN cc_start: 0.8295 (mm110) cc_final: 0.8054 (mt0) REVERT: G 3 GLN cc_start: 0.8035 (mt0) cc_final: 0.7782 (mm110) REVERT: G 48 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7759 (pt) outliers start: 51 outliers final: 27 residues processed: 224 average time/residue: 0.5217 time to fit residues: 135.9168 Evaluate side-chains 207 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain G residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 20 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 162 optimal weight: 0.1980 chunk 176 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 210 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS A 347 ASN L 89 GLN H 81 ASN B 226 GLN B 296 HIS B 347 ASN I 89 GLN E 81 ASN C 226 GLN C 296 HIS C 347 ASN J 89 GLN F 81 ASN D 226 GLN D 296 HIS D 347 ASN K 89 GLN G 81 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125206 restraints weight = 21825.228| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.41 r_work: 0.3302 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19544 Z= 0.117 Angle : 0.565 10.208 26612 Z= 0.299 Chirality : 0.046 0.162 2860 Planarity : 0.004 0.035 3408 Dihedral : 5.036 32.485 2664 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.62 % Favored : 97.22 % Rotamer: Outliers : 2.43 % Allowed : 14.42 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2444 helix: -0.66 (0.80), residues: 24 sheet: 0.57 (0.16), residues: 976 loop : 0.02 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 364 TYR 0.012 0.001 TYR K 49 PHE 0.014 0.002 PHE B 121 TRP 0.013 0.001 TRP D 178 HIS 0.002 0.001 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00267 (19504) covalent geometry : angle 0.55670 (26532) SS BOND : bond 0.00409 ( 40) SS BOND : angle 1.87285 ( 80) hydrogen bonds : bond 0.03300 ( 672) hydrogen bonds : angle 5.87053 ( 1776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.826 Fit side-chains REVERT: A 304 SER cc_start: 0.8348 (p) cc_final: 0.7960 (p) REVERT: A 358 ASN cc_start: 0.7889 (m110) cc_final: 0.7587 (t0) REVERT: A 430 GLN cc_start: 0.8291 (mm110) cc_final: 0.8030 (mt0) REVERT: H 3 GLN cc_start: 0.8011 (mt0) cc_final: 0.7755 (mm110) REVERT: H 48 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7779 (pt) REVERT: B 304 SER cc_start: 0.8334 (p) cc_final: 0.7946 (p) REVERT: B 358 ASN cc_start: 0.7877 (m110) cc_final: 0.7576 (t0) REVERT: B 430 GLN cc_start: 0.8290 (mm110) cc_final: 0.8032 (mt0) REVERT: E 3 GLN cc_start: 0.8003 (mt0) cc_final: 0.7752 (mm110) REVERT: E 48 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7774 (pt) REVERT: C 304 SER cc_start: 0.8332 (p) cc_final: 0.7945 (p) REVERT: C 358 ASN cc_start: 0.7880 (m110) cc_final: 0.7578 (t0) REVERT: C 430 GLN cc_start: 0.8291 (mm110) cc_final: 0.8028 (mt0) REVERT: F 3 GLN cc_start: 0.8008 (mt0) cc_final: 0.7764 (mm110) REVERT: F 48 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7774 (pt) REVERT: D 304 SER cc_start: 0.8345 (p) cc_final: 0.7955 (p) REVERT: D 358 ASN cc_start: 0.7879 (m110) cc_final: 0.7587 (t0) REVERT: D 430 GLN cc_start: 0.8292 (mm110) cc_final: 0.8034 (mt0) REVERT: G 3 GLN cc_start: 0.8010 (mt0) cc_final: 0.7767 (mm110) REVERT: G 48 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7773 (pt) outliers start: 52 outliers final: 36 residues processed: 228 average time/residue: 0.4936 time to fit residues: 131.9072 Evaluate side-chains 216 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 198 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 3 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS A 347 ASN L 89 GLN H 81 ASN B 226 GLN B 296 HIS B 347 ASN I 89 GLN E 81 ASN C 226 GLN C 296 HIS C 347 ASN J 89 GLN F 81 ASN D 226 GLN D 296 HIS D 347 ASN K 89 GLN G 81 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.162784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125687 restraints weight = 21941.372| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.44 r_work: 0.3308 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19544 Z= 0.112 Angle : 0.550 9.416 26612 Z= 0.290 Chirality : 0.046 0.157 2860 Planarity : 0.004 0.033 3408 Dihedral : 4.951 30.705 2664 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 2.62 % Allowed : 14.42 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.17), residues: 2444 helix: -0.66 (0.84), residues: 24 sheet: 0.64 (0.16), residues: 976 loop : 0.04 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 327 TYR 0.017 0.001 TYR K 49 PHE 0.015 0.002 PHE A 121 TRP 0.011 0.001 TRP D 178 HIS 0.003 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00257 (19504) covalent geometry : angle 0.54212 (26532) SS BOND : bond 0.00392 ( 40) SS BOND : angle 1.73532 ( 80) hydrogen bonds : bond 0.03227 ( 672) hydrogen bonds : angle 5.76658 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6190.33 seconds wall clock time: 106 minutes 34.31 seconds (6394.31 seconds total)