Starting phenix.real_space_refine on Mon Jun 16 17:33:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6j_27920/06_2025/8e6j_27920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6j_27920/06_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_27920/06_2025/8e6j_27920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6j_27920/06_2025/8e6j_27920.map" model { file = "/net/cci-nas-00/data/ceres_data/8e6j_27920/06_2025/8e6j_27920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6j_27920/06_2025/8e6j_27920.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: "I" 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: "E" 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: C, B, D, G, F, H, K, J, L Time building chain proxies: 9.45, per 1000 atoms: 0.50 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=34, 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 C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.04 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.04 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " 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: 4.45 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 3.06 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: 6.89 Time building geometry restraints manager: 5.31 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: 472 35.08 - 52.63: 146 52.63 - 70.17: 48 70.17 - 87.71: 20 Dihedral angle restraints: 11442 sinusoidal: 4426 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 11439 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: 2.04 - 2.61: 202 2.61 - 3.18: 15944 3.18 - 3.75: 30632 3.75 - 4.33: 46744 4.33 - 4.90: 76624 Nonbonded interactions: 170146 Sorted by model distance: nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " model vdw 2.044 3.760 nonbonded pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " model vdw 2.044 3.760 ... (remaining 170141 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 42.930 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.430 ------------------------------------------------------------------------------- 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 19538 Z= 0.310 Angle : 1.181 7.899 26600 Z= 0.689 Chirality : 0.064 0.243 2860 Planarity : 0.006 0.039 3408 Dihedral : 12.050 87.709 6884 Min Nonbonded Distance : 2.035 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.028 0.004 TRP I 35 HIS 0.012 0.003 HIS D 412A PHE 0.022 0.004 PHE B 446 TYR 0.043 0.004 TYR E 34 ARG 0.009 0.001 ARG G 66 Details of bonding type rmsd hydrogen bonds : bond 0.13507 ( 672) hydrogen bonds : angle 7.89538 ( 1776) SS BOND : bond 0.00826 ( 34) SS BOND : angle 3.23532 ( 68) covalent geometry : bond 0.00679 (19504) covalent geometry : angle 1.17136 (26532) *********************** 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 : 2.074 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: 0.8664 time to fit residues: 255.8526 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 : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.161059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123503 restraints weight = 22107.786| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.50 r_work: 0.3292 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19538 Z= 0.214 Angle : 0.668 9.107 26600 Z= 0.366 Chirality : 0.050 0.174 2860 Planarity : 0.004 0.033 3408 Dihedral : 5.502 21.366 2664 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 8.85 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2444 helix: -0.25 (0.71), residues: 28 sheet: 0.60 (0.16), residues: 968 loop : 0.20 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 97 HIS 0.009 0.003 HIS D 412A PHE 0.020 0.003 PHE D 115 TYR 0.017 0.002 TYR A 169A ARG 0.004 0.001 ARG J 61 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 672) hydrogen bonds : angle 6.77286 ( 1776) SS BOND : bond 0.00536 ( 34) SS BOND : angle 1.46988 ( 68) covalent geometry : bond 0.00491 (19504) covalent geometry : angle 0.66456 (26532) *********************** 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 273 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 1.979 Fit side-chains REVERT: A 172 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7351 (ttm170) REVERT: A 358 ASN cc_start: 0.7761 (m110) cc_final: 0.7466 (t0) REVERT: B 172 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7333 (ttm170) REVERT: B 358 ASN cc_start: 0.7771 (m110) cc_final: 0.7470 (t0) REVERT: C 172 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7345 (ttm170) REVERT: C 358 ASN cc_start: 0.7766 (m110) cc_final: 0.7462 (t0) REVERT: D 172 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7343 (ttm170) REVERT: D 358 ASN cc_start: 0.7766 (m110) cc_final: 0.7466 (t0) outliers start: 55 outliers final: 12 residues processed: 253 average time/residue: 1.0399 time to fit residues: 303.9057 Evaluate side-chains 208 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 86 THR 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 I residue 28 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 86 THR 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 K residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 43 optimal weight: 0.0570 chunk 233 optimal weight: 3.9990 chunk 219 optimal weight: 40.0000 chunk 95 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.161653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124723 restraints weight = 21776.386| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.39 r_work: 0.3295 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19538 Z= 0.159 Angle : 0.618 8.038 26600 Z= 0.331 Chirality : 0.048 0.270 2860 Planarity : 0.004 0.041 3408 Dihedral : 5.466 42.067 2664 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.41 % Favored : 97.42 % Rotamer: Outliers : 2.25 % Allowed : 10.16 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2444 helix: -0.58 (0.72), residues: 28 sheet: 0.44 (0.15), residues: 992 loop : 0.25 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 47 HIS 0.005 0.001 HIS C 296 PHE 0.015 0.002 PHE G 78 TYR 0.012 0.002 TYR H 34 ARG 0.002 0.000 ARG A 224 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 672) hydrogen bonds : angle 6.55124 ( 1776) SS BOND : bond 0.00550 ( 34) SS BOND : angle 2.06729 ( 68) covalent geometry : bond 0.00362 (19504) covalent geometry : angle 0.60976 (26532) *********************** 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 266 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 1.909 Fit side-chains REVERT: A 172 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.7315 (ttm170) REVERT: A 358 ASN cc_start: 0.7746 (m110) cc_final: 0.7472 (t0) REVERT: A 396 ASP cc_start: 0.8777 (m-30) cc_final: 0.8565 (m-30) REVERT: B 172 ARG cc_start: 0.7613 (ttp-170) cc_final: 0.7314 (ttm170) REVERT: B 358 ASN cc_start: 0.7741 (m110) cc_final: 0.7468 (t0) REVERT: B 396 ASP cc_start: 0.8774 (m-30) cc_final: 0.8561 (m-30) REVERT: C 172 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7334 (ttm170) REVERT: C 358 ASN cc_start: 0.7741 (m110) cc_final: 0.7463 (t0) REVERT: C 396 ASP cc_start: 0.8769 (m-30) cc_final: 0.8554 (m-30) REVERT: D 172 ARG cc_start: 0.7628 (ttp-170) cc_final: 0.7331 (ttm170) REVERT: D 358 ASN cc_start: 0.7753 (m110) cc_final: 0.7475 (t0) REVERT: D 396 ASP cc_start: 0.8774 (m-30) cc_final: 0.8562 (m-30) outliers start: 48 outliers final: 33 residues processed: 246 average time/residue: 1.1129 time to fit residues: 315.4284 Evaluate side-chains 228 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 2.164 ------------------------------------------------------------------------------- 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 304 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 37 GLN 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 284 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 28 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 284 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 28 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 284 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 225 optimal weight: 0.0000 chunk 150 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 313 GLN L 89 GLN H 81 ASN B 226 GLN B 313 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN C 226 GLN C 313 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN D 226 GLN D 313 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127401 restraints weight = 21847.977| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.39 r_work: 0.3330 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19538 Z= 0.112 Angle : 0.535 7.780 26600 Z= 0.287 Chirality : 0.046 0.162 2860 Planarity : 0.004 0.036 3408 Dihedral : 5.048 35.795 2664 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.38 % Rotamer: Outliers : 2.53 % Allowed : 10.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2444 helix: -0.32 (0.75), residues: 28 sheet: 0.50 (0.16), residues: 968 loop : 0.22 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS A 296 PHE 0.016 0.002 PHE F 78 TYR 0.011 0.001 TYR H 34 ARG 0.002 0.000 ARG D 364 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 672) hydrogen bonds : angle 6.21366 ( 1776) SS BOND : bond 0.00304 ( 34) SS BOND : angle 1.36738 ( 68) covalent geometry : bond 0.00254 (19504) covalent geometry : angle 0.53077 (26532) *********************** 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 293 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 2.137 Fit side-chains REVERT: A 358 ASN cc_start: 0.7736 (m110) cc_final: 0.7494 (t0) REVERT: L 37 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: B 358 ASN cc_start: 0.7738 (m110) cc_final: 0.7492 (t0) REVERT: C 358 ASN cc_start: 0.7739 (m110) cc_final: 0.7494 (t0) REVERT: D 358 ASN cc_start: 0.7750 (m110) cc_final: 0.7502 (t0) outliers start: 54 outliers final: 21 residues processed: 277 average time/residue: 1.1263 time to fit residues: 359.8981 Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 2.245 ------------------------------------------------------------------------------- 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 467 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 284 THR 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 89 SER Chi-restraints excluded: chain C residue 284 THR 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 89 SER Chi-restraints excluded: chain D residue 284 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 47 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 198 optimal weight: 0.0010 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 221 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- 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 A 347 ASN L 89 GLN H 81 ASN B 226 GLN B 294 ASN B 296 HIS B 313 GLN B 347 ASN I 89 GLN E 81 ASN C 226 GLN C 294 ASN C 296 HIS C 313 GLN C 347 ASN J 89 GLN F 81 ASN D 226 GLN D 294 ASN D 296 HIS D 313 GLN D 347 ASN 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 = 0.3880 r_free = 0.3880 target = 0.162208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125882 restraints weight = 21911.732| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.39 r_work: 0.3313 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 19538 Z= 0.143 Angle : 0.573 7.712 26600 Z= 0.306 Chirality : 0.046 0.164 2860 Planarity : 0.004 0.038 3408 Dihedral : 5.154 33.784 2664 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 2.48 % Allowed : 12.78 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2444 helix: -0.63 (0.73), residues: 28 sheet: 0.47 (0.16), residues: 968 loop : 0.15 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS G 95 PHE 0.015 0.002 PHE B 121 TYR 0.011 0.001 TYR K 49 ARG 0.003 0.000 ARG F 100D Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 672) hydrogen bonds : angle 6.25051 ( 1776) SS BOND : bond 0.00316 ( 34) SS BOND : angle 2.16768 ( 68) covalent geometry : bond 0.00333 (19504) covalent geometry : angle 0.56333 (26532) *********************** 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 259 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 2.079 Fit side-chains REVERT: A 358 ASN cc_start: 0.7848 (m110) cc_final: 0.7599 (t0) REVERT: L 37 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: B 358 ASN cc_start: 0.7856 (m110) cc_final: 0.7599 (t0) REVERT: C 358 ASN cc_start: 0.7850 (m110) cc_final: 0.7592 (t0) REVERT: D 358 ASN cc_start: 0.7856 (m110) cc_final: 0.7599 (t0) outliers start: 53 outliers final: 31 residues processed: 247 average time/residue: 0.9030 time to fit residues: 264.5480 Evaluate side-chains 223 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 467 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 37 GLN 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 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 110 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 51 optimal weight: 0.0270 overall best weight: 2.2046 ------------------------------------------------------------------------------- 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 294 ASN A 296 HIS A 347 ASN L 89 GLN H 81 ASN B 136 GLN B 226 GLN B 294 ASN B 296 HIS B 347 ASN I 89 GLN E 81 ASN C 136 GLN C 226 GLN C 294 ASN C 296 HIS C 347 ASN J 89 GLN F 81 ASN D 136 GLN D 226 GLN D 294 ASN D 296 HIS D 347 ASN 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 = 0.3835 r_free = 0.3835 target = 0.158112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120873 restraints weight = 22098.698| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.40 r_work: 0.3250 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 19538 Z= 0.230 Angle : 0.660 9.018 26600 Z= 0.354 Chirality : 0.049 0.170 2860 Planarity : 0.005 0.044 3408 Dihedral : 5.525 33.811 2664 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.05 % Rotamer: Outliers : 3.00 % Allowed : 12.13 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2444 helix: -0.83 (0.89), residues: 24 sheet: 0.41 (0.16), residues: 976 loop : 0.05 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 97 HIS 0.006 0.002 HIS H 95 PHE 0.022 0.002 PHE A 410 TYR 0.013 0.002 TYR H 100G ARG 0.004 0.000 ARG E 100D Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 672) hydrogen bonds : angle 6.33481 ( 1776) SS BOND : bond 0.00340 ( 34) SS BOND : angle 2.69797 ( 68) covalent geometry : bond 0.00537 (19504) covalent geometry : angle 0.64650 (26532) *********************** 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 241 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 2.138 Fit side-chains REVERT: A 358 ASN cc_start: 0.7858 (m110) cc_final: 0.7593 (t0) REVERT: L 37 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: B 358 ASN cc_start: 0.7874 (m110) cc_final: 0.7606 (t0) REVERT: C 358 ASN cc_start: 0.7872 (m110) cc_final: 0.7605 (t0) REVERT: D 358 ASN cc_start: 0.7885 (m110) cc_final: 0.7612 (t0) outliers start: 64 outliers final: 42 residues processed: 222 average time/residue: 0.9774 time to fit residues: 254.9208 Evaluate side-chains 213 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 407 SER Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 37 GLN 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 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 22 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 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 22 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 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 22 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 313 GLN A 347 ASN L 89 GLN H 81 ASN B 226 GLN B 296 HIS B 313 GLN B 347 ASN I 89 GLN E 81 ASN C 226 GLN C 296 HIS C 313 GLN C 347 ASN J 89 GLN F 81 ASN D 226 GLN D 296 HIS 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 = 0.3810 r_free = 0.3810 target = 0.156062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118582 restraints weight = 21921.851| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.37 r_work: 0.3225 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 19538 Z= 0.292 Angle : 0.710 9.157 26600 Z= 0.381 Chirality : 0.051 0.215 2860 Planarity : 0.005 0.047 3408 Dihedral : 5.853 40.865 2664 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.56 % Rotamer: Outliers : 4.03 % Allowed : 12.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2444 helix: -1.23 (0.84), residues: 24 sheet: 0.25 (0.16), residues: 996 loop : -0.16 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 97 HIS 0.007 0.002 HIS H 95 PHE 0.024 0.003 PHE D 121 TYR 0.014 0.002 TYR E 100G ARG 0.003 0.001 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 672) hydrogen bonds : angle 6.56634 ( 1776) SS BOND : bond 0.00444 ( 34) SS BOND : angle 3.16875 ( 68) covalent geometry : bond 0.00681 (19504) covalent geometry : angle 0.69208 (26532) *********************** 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 257 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 171 time to evaluate : 1.997 Fit side-chains REVERT: L 37 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7693 (pt0) outliers start: 86 outliers final: 53 residues processed: 242 average time/residue: 0.9433 time to fit residues: 272.5091 Evaluate side-chains 215 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 149 VAL 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 28 THR Chi-restraints excluded: chain L residue 37 GLN 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 149 VAL 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 22 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 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 149 VAL 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 22 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 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 149 VAL 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 22 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 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 A 347 ASN L 89 GLN H 81 ASN B 136 GLN B 170 ASN B 226 GLN B 296 HIS B 313 GLN B 347 ASN I 89 GLN E 81 ASN C 136 GLN C 170 ASN C 226 GLN C 296 HIS C 313 GLN C 347 ASN J 89 GLN F 81 ASN D 136 GLN D 170 ASN D 226 GLN D 296 HIS D 313 GLN D 347 ASN K 89 GLN G 81 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124300 restraints weight = 21805.403| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.44 r_work: 0.3294 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19538 Z= 0.140 Angle : 0.583 8.420 26600 Z= 0.314 Chirality : 0.047 0.164 2860 Planarity : 0.004 0.038 3408 Dihedral : 5.326 37.406 2664 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.38 % Rotamer: Outliers : 3.51 % Allowed : 12.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2444 helix: -0.97 (0.76), residues: 24 sheet: 0.46 (0.16), residues: 976 loop : -0.06 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 178 HIS 0.003 0.001 HIS H 95 PHE 0.017 0.002 PHE C 410 TYR 0.011 0.001 TYR H 34 ARG 0.003 0.000 ARG C 364 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 672) hydrogen bonds : angle 6.18703 ( 1776) SS BOND : bond 0.00184 ( 34) SS BOND : angle 2.04809 ( 68) covalent geometry : bond 0.00323 (19504) covalent geometry : angle 0.57447 (26532) *********************** 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 247 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 172 time to evaluate : 1.972 Fit side-chains REVERT: A 418 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7401 (mpp) REVERT: L 37 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: H 3 GLN cc_start: 0.8029 (mt0) cc_final: 0.7775 (mm110) REVERT: B 418 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7387 (mpp) REVERT: E 3 GLN cc_start: 0.8012 (mt0) cc_final: 0.7785 (mm110) REVERT: C 418 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7422 (mpp) REVERT: F 3 GLN cc_start: 0.7996 (mt0) cc_final: 0.7768 (mm110) REVERT: D 418 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7416 (mpp) REVERT: G 3 GLN cc_start: 0.8011 (mt0) cc_final: 0.7786 (mm110) outliers start: 75 outliers final: 42 residues processed: 228 average time/residue: 0.9625 time to fit residues: 258.7046 Evaluate side-chains 211 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 2.156 ------------------------------------------------------------------------------- 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 303 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 37 GLN 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 303 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 22 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 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 303 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 22 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 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 303 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 22 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 0.0050 chunk 122 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 A 347 ASN L 89 GLN H 81 ASN B 136 GLN B 226 GLN B 296 HIS B 313 GLN B 347 ASN I 89 GLN E 81 ASN C 136 GLN C 226 GLN C 296 HIS C 313 GLN C 347 ASN J 89 GLN F 81 ASN D 136 GLN D 226 GLN D 296 HIS D 313 GLN D 347 ASN 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 = 0.3873 r_free = 0.3873 target = 0.161443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124800 restraints weight = 21941.412| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.40 r_work: 0.3311 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19538 Z= 0.126 Angle : 0.558 8.131 26600 Z= 0.299 Chirality : 0.046 0.167 2860 Planarity : 0.004 0.035 3408 Dihedral : 5.077 34.712 2664 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.05 % Rotamer: Outliers : 2.62 % Allowed : 14.09 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2444 helix: -0.82 (0.78), residues: 24 sheet: 0.56 (0.16), residues: 976 loop : -0.05 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 178 HIS 0.003 0.001 HIS G 95 PHE 0.016 0.002 PHE C 121 TYR 0.012 0.001 TYR J 49 ARG 0.002 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 672) hydrogen bonds : angle 5.94757 ( 1776) SS BOND : bond 0.00158 ( 34) SS BOND : angle 1.85952 ( 68) covalent geometry : bond 0.00293 (19504) covalent geometry : angle 0.55060 (26532) *********************** 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 247 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 1.977 Fit side-chains REVERT: A 304 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 418 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7399 (mpp) REVERT: L 37 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: H 3 GLN cc_start: 0.8027 (mt0) cc_final: 0.7785 (mm110) REVERT: B 304 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8065 (p) REVERT: B 418 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7406 (mpp) REVERT: C 304 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8067 (p) REVERT: C 418 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7406 (mpp) REVERT: D 304 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8072 (p) REVERT: D 418 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7413 (mpp) outliers start: 56 outliers final: 34 residues processed: 236 average time/residue: 0.8298 time to fit residues: 235.2183 Evaluate side-chains 227 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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 304 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 37 GLN 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 303 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 22 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 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 407 SER Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain J residue 22 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 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 407 SER Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain K residue 22 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 110 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 121 optimal weight: 0.0770 chunk 111 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.158045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120810 restraints weight = 21836.753| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.39 r_work: 0.3253 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19538 Z= 0.213 Angle : 0.631 8.555 26600 Z= 0.340 Chirality : 0.048 0.176 2860 Planarity : 0.004 0.042 3408 Dihedral : 5.463 36.967 2664 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.05 % Rotamer: Outliers : 2.57 % Allowed : 14.79 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2444 helix: -1.07 (0.82), residues: 24 sheet: 0.50 (0.16), residues: 976 loop : -0.12 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 97 HIS 0.005 0.002 HIS H 95 PHE 0.023 0.002 PHE C 121 TYR 0.019 0.002 TYR J 49 ARG 0.002 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 672) hydrogen bonds : angle 6.18622 ( 1776) SS BOND : bond 0.00278 ( 34) SS BOND : angle 2.40363 ( 68) covalent geometry : bond 0.00495 (19504) covalent geometry : angle 0.62003 (26532) ********************** 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 233 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 2.050 Fit side-chains REVERT: A 150 LYS cc_start: 0.7933 (pttm) cc_final: 0.7556 (pttp) REVERT: A 358 ASN cc_start: 0.8025 (m110) cc_final: 0.7632 (t0) REVERT: L 37 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: H 3 GLN cc_start: 0.8027 (mt0) cc_final: 0.7780 (mm110) REVERT: B 150 LYS cc_start: 0.7922 (pttm) cc_final: 0.7541 (pttp) REVERT: B 358 ASN cc_start: 0.7977 (m110) cc_final: 0.7606 (t0) REVERT: C 150 LYS cc_start: 0.7928 (pttm) cc_final: 0.7549 (pttp) REVERT: C 358 ASN cc_start: 0.7983 (m110) cc_final: 0.7608 (t0) REVERT: D 150 LYS cc_start: 0.7934 (pttm) cc_final: 0.7551 (pttp) REVERT: D 358 ASN cc_start: 0.7990 (m110) cc_final: 0.7611 (t0) outliers start: 55 outliers final: 42 residues processed: 226 average time/residue: 0.9103 time to fit residues: 247.4072 Evaluate side-chains 217 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 2.128 ------------------------------------------------------------------------------- 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 303 VAL 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 28 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 170 ASN 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 407 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain I residue 22 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 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 303 VAL 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 22 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 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 303 VAL 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 22 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 93 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 229 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 313 GLN L 89 GLN H 81 ASN B 226 GLN B 296 HIS B 313 GLN I 89 GLN E 81 ASN C 226 GLN C 296 HIS C 313 GLN J 89 GLN F 81 ASN D 226 GLN D 296 HIS D 313 GLN 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 = 0.3822 r_free = 0.3822 target = 0.157175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119772 restraints weight = 21924.398| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.38 r_work: 0.3234 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 19538 Z= 0.237 Angle : 0.653 8.754 26600 Z= 0.352 Chirality : 0.049 0.184 2860 Planarity : 0.005 0.045 3408 Dihedral : 5.591 38.024 2664 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Rotamer: Outliers : 3.04 % Allowed : 14.33 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2444 helix: -1.23 (0.80), residues: 24 sheet: 0.35 (0.16), residues: 976 loop : -0.19 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 97 HIS 0.006 0.002 HIS H 95 PHE 0.023 0.002 PHE A 121 TYR 0.020 0.002 TYR J 49 ARG 0.004 0.000 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 672) hydrogen bonds : angle 6.26056 ( 1776) SS BOND : bond 0.00313 ( 34) SS BOND : angle 2.49011 ( 68) covalent geometry : bond 0.00551 (19504) covalent geometry : angle 0.64160 (26532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13402.82 seconds wall clock time: 232 minutes 56.47 seconds (13976.47 seconds total)