Starting phenix.real_space_refine on Wed Oct 28 06:33:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30ie_57794/10_2026/30ie_57794.cif Found real_map, /net/cci-nas-00/data/ceres_data/30ie_57794/10_2026/30ie_57794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30ie_57794/10_2026/30ie_57794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30ie_57794/10_2026/30ie_57794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30ie_57794/10_2026/30ie_57794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30ie_57794/10_2026/30ie_57794.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 17391 2.51 5 N 4485 2.21 5 O 4993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27005 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Chain: "H" Number of atoms: 3381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 bond proxies already assigned to first conformer: 3436 Chain: "C" Number of atoms: 3381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 bond proxies already assigned to first conformer: 3436 Chain: "A" Number of atoms: 3374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 415, 3365 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3440 Chain: "F" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Chain: "D" Number of atoms: 3381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 bond proxies already assigned to first conformer: 3436 Chain: "G" Number of atoms: 3381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 bond proxies already assigned to first conformer: 3436 Chain: "E" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3369 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 396} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ATYR H 24 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR H 24 " occ=0.50 residue: pdb=" N ATYR C 24 " occ=0.54 ... (22 atoms not shown) pdb=" OH BTYR C 24 " occ=0.46 residue: pdb=" N ATYR D 24 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR D 24 " occ=0.49 residue: pdb=" N ATYR G 24 " occ=0.53 ... (22 atoms not shown) pdb=" OH BTYR G 24 " occ=0.47 Time building chain proxies: 7.71, per 1000 atoms: 0.29 Number of scatterers: 27005 At special positions: 0 Unit cell: (140.835, 188.925, 108.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 4993 8.00 N 4485 7.00 C 17391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS H 279 " - pdb=" SG CYS H 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS F 279 " - pdb=" SG CYS F 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS G 279 " - pdb=" SG CYS G 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 394 " distance=2.03 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: 2.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6378 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 32 sheets defined 34.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'B' and resid 26 through 38 Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 88 through 97 Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 151 through 171 removed outlier: 4.065A pdb=" N VAL B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 229 Processing helix chain 'B' and resid 257 through 269 Processing helix chain 'B' and resid 284 through 297 removed outlier: 4.153A pdb=" N LEU B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 363 through 378 removed outlier: 3.598A pdb=" N ASN B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 51 through 54 removed outlier: 3.837A pdb=" N GLU H 54 " --> pdb=" O LEU H 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 51 through 54' Processing helix chain 'H' and resid 58 through 73 removed outlier: 3.660A pdb=" N LEU H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) Proline residue: H 71 - end of helix Processing helix chain 'H' and resid 88 through 97 Processing helix chain 'H' and resid 105 through 110 Processing helix chain 'H' and resid 135 through 140 Processing helix chain 'H' and resid 151 through 171 removed outlier: 3.905A pdb=" N VAL H 170 " --> pdb=" O TRP H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 218 through 229 Processing helix chain 'H' and resid 257 through 269 Processing helix chain 'H' and resid 284 through 296 Processing helix chain 'H' and resid 344 through 349 Processing helix chain 'H' and resid 363 through 378 removed outlier: 3.576A pdb=" N ASN H 378 " --> pdb=" O MET H 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 417 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 51 through 54 removed outlier: 3.933A pdb=" N GLU C 54 " --> pdb=" O LEU C 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 54' Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 88 through 97 Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 151 through 171 removed outlier: 3.978A pdb=" N VAL C 170 " --> pdb=" O TRP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 257 through 269 Processing helix chain 'C' and resid 284 through 297 removed outlier: 3.501A pdb=" N ARG C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 363 through 378 removed outlier: 3.510A pdb=" N ASN C 378 " --> pdb=" O MET C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 51 through 54 removed outlier: 3.873A pdb=" N GLU A 54 " --> pdb=" O LEU A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.698A pdb=" N LEU A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 151 through 171 removed outlier: 3.830A pdb=" N VAL A 170 " --> pdb=" O TRP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.658A pdb=" N ALA A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 284 through 297 removed outlier: 4.041A pdb=" N LEU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 363 through 378 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'F' and resid 26 through 38 Processing helix chain 'F' and resid 58 through 69 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 88 through 97 Processing helix chain 'F' and resid 105 through 110 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 151 through 171 removed outlier: 4.066A pdb=" N VAL F 170 " --> pdb=" O TRP F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 229 Processing helix chain 'F' and resid 257 through 269 Processing helix chain 'F' and resid 284 through 297 removed outlier: 4.153A pdb=" N LEU F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 349 Processing helix chain 'F' and resid 363 through 378 removed outlier: 3.599A pdb=" N ASN F 378 " --> pdb=" O MET F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 417 Processing helix chain 'D' and resid 26 through 38 Processing helix chain 'D' and resid 51 through 54 removed outlier: 3.837A pdb=" N GLU D 54 " --> pdb=" O LEU D 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 54' Processing helix chain 'D' and resid 58 through 73 removed outlier: 3.660A pdb=" N LEU D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 88 through 97 Processing helix chain 'D' and resid 105 through 110 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 151 through 171 removed outlier: 3.907A pdb=" N VAL D 170 " --> pdb=" O TRP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 257 through 269 Processing helix chain 'D' and resid 284 through 296 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.575A pdb=" N ASN D 378 " --> pdb=" O MET D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'G' and resid 26 through 38 Processing helix chain 'G' and resid 51 through 54 removed outlier: 3.933A pdb=" N GLU G 54 " --> pdb=" O LEU G 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 51 through 54' Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 88 through 97 Processing helix chain 'G' and resid 105 through 110 Processing helix chain 'G' and resid 135 through 140 Processing helix chain 'G' and resid 151 through 171 removed outlier: 3.978A pdb=" N VAL G 170 " --> pdb=" O TRP G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 218 through 229 Processing helix chain 'G' and resid 257 through 269 Processing helix chain 'G' and resid 284 through 297 removed outlier: 3.501A pdb=" N ARG G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 363 through 378 removed outlier: 3.510A pdb=" N ASN G 378 " --> pdb=" O MET G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 417 Processing helix chain 'E' and resid 26 through 38 Processing helix chain 'E' and resid 51 through 54 removed outlier: 3.873A pdb=" N GLU E 54 " --> pdb=" O LEU E 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 51 through 54' Processing helix chain 'E' and resid 58 through 74 removed outlier: 3.698A pdb=" N LEU E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Proline residue: E 71 - end of helix Processing helix chain 'E' and resid 88 through 96 Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 151 through 171 removed outlier: 3.829A pdb=" N VAL E 170 " --> pdb=" O TRP E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 218 through 230 removed outlier: 3.657A pdb=" N ALA E 230 " --> pdb=" O CYS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 269 Processing helix chain 'E' and resid 284 through 297 removed outlier: 4.042A pdb=" N LEU E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 349 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 413 through 417 Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 13 removed outlier: 6.354A pdb=" N VAL B 77 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ARG B 102 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 79 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 104 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 81 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA3, first strand: chain 'B' and resid 191 through 195 removed outlier: 6.689A pdb=" N VAL B 234 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU B 276 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 236 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER B 278 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 238 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 273 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LYS B 307 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 275 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE B 309 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 277 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'H' and resid 7 through 13 removed outlier: 6.209A pdb=" N LEU H 42 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA H 80 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE H 44 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN H 82 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL H 77 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG H 102 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL H 79 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE H 104 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL H 81 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 50 Processing sheet with id=AA7, first strand: chain 'H' and resid 191 through 195 removed outlier: 6.668A pdb=" N VAL H 234 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU H 276 " --> pdb=" O VAL H 234 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL H 236 " --> pdb=" O LEU H 276 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER H 278 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL H 238 " --> pdb=" O SER H 278 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL H 273 " --> pdb=" O GLU H 305 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LYS H 307 " --> pdb=" O VAL H 273 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU H 275 " --> pdb=" O LYS H 307 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE H 309 " --> pdb=" O LEU H 275 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE H 277 " --> pdb=" O PHE H 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.464A pdb=" N VAL C 77 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ARG C 102 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL C 79 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE C 104 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 81 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AB2, first strand: chain 'C' and resid 191 through 195 removed outlier: 6.576A pdb=" N VAL C 234 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU C 276 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 236 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N SER C 278 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL C 238 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 273 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LYS C 307 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU C 275 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE C 309 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 277 " --> pdb=" O PHE C 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AB4, first strand: chain 'A' and resid 7 through 13 removed outlier: 6.099A pdb=" N LEU A 42 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA A 80 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 44 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ASN A 82 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N SER A 46 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 77 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ARG A 102 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 79 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 104 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 81 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AB6, first strand: chain 'A' and resid 191 through 195 removed outlier: 3.541A pdb=" N VAL A 238 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AB8, first strand: chain 'F' and resid 7 through 13 removed outlier: 6.354A pdb=" N VAL F 77 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ARG F 102 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL F 79 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE F 104 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL F 81 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=AC1, first strand: chain 'F' and resid 191 through 195 removed outlier: 6.689A pdb=" N VAL F 234 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU F 276 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL F 236 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER F 278 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL F 238 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL F 273 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LYS F 307 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU F 275 " --> pdb=" O LYS F 307 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE F 309 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE F 277 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 244 through 246 Processing sheet with id=AC3, first strand: chain 'D' and resid 7 through 13 removed outlier: 6.210A pdb=" N LEU D 42 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA D 80 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 44 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASN D 82 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 77 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG D 102 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 79 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE D 104 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL D 81 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'D' and resid 191 through 195 removed outlier: 6.667A pdb=" N VAL D 234 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU D 276 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 236 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER D 278 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL D 238 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL D 273 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LYS D 307 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 275 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE D 309 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE D 277 " --> pdb=" O PHE D 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AC7, first strand: chain 'G' and resid 7 through 13 removed outlier: 6.465A pdb=" N VAL G 77 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ARG G 102 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL G 79 " --> pdb=" O ARG G 102 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE G 104 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL G 81 " --> pdb=" O ILE G 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 49 through 50 Processing sheet with id=AC9, first strand: chain 'G' and resid 191 through 195 removed outlier: 6.576A pdb=" N VAL G 234 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU G 276 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL G 236 " --> pdb=" O LEU G 276 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER G 278 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL G 238 " --> pdb=" O SER G 278 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL G 273 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS G 307 " --> pdb=" O VAL G 273 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU G 275 " --> pdb=" O LYS G 307 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE G 309 " --> pdb=" O LEU G 275 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE G 277 " --> pdb=" O PHE G 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 244 through 246 Processing sheet with id=AD2, first strand: chain 'E' and resid 7 through 13 removed outlier: 6.098A pdb=" N LEU E 42 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA E 80 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE E 44 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ASN E 82 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N SER E 46 " --> pdb=" O ASN E 82 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL E 77 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ARG E 102 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL E 79 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE E 104 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL E 81 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AD4, first strand: chain 'E' and resid 191 through 195 removed outlier: 3.541A pdb=" N VAL E 238 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 244 through 246 1128 hydrogen bonds defined for protein. 3048 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: 5.40 Time building geometry restraints manager: 2.92 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: 8517 1.34 - 1.46: 6310 1.46 - 1.58: 12611 1.58 - 1.70: 0 1.70 - 1.82: 224 Bond restraints: 27662 Sorted by residual: bond pdb=" SD MET B 214 " pdb=" CE MET B 214 " ideal model delta sigma weight residual 1.791 1.824 -0.033 2.50e-02 1.60e+03 1.72e+00 bond pdb=" CB TYR F 181 " pdb=" CG TYR F 181 " ideal model delta sigma weight residual 1.512 1.540 -0.028 2.20e-02 2.07e+03 1.65e+00 bond pdb=" CE1 TYR B 24 " pdb=" CZ TYR B 24 " ideal model delta sigma weight residual 1.378 1.347 0.031 2.40e-02 1.74e+03 1.64e+00 bond pdb=" CE1 TYR F 24 " pdb=" CZ TYR F 24 " ideal model delta sigma weight residual 1.378 1.347 0.031 2.40e-02 1.74e+03 1.63e+00 bond pdb=" SD MET F 214 " pdb=" CE MET F 214 " ideal model delta sigma weight residual 1.791 1.823 -0.032 2.50e-02 1.60e+03 1.62e+00 ... (remaining 27657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 37094 2.49 - 4.98: 438 4.98 - 7.47: 62 7.47 - 9.97: 12 9.97 - 12.46: 8 Bond angle restraints: 37614 Sorted by residual: angle pdb=" C LYS D 178 " pdb=" CA LYS D 178 " pdb=" CB LYS D 178 " ideal model delta sigma weight residual 117.23 110.36 6.87 1.36e+00 5.41e-01 2.55e+01 angle pdb=" C LYS H 178 " pdb=" CA LYS H 178 " pdb=" CB LYS H 178 " ideal model delta sigma weight residual 117.23 110.37 6.86 1.36e+00 5.41e-01 2.55e+01 angle pdb=" CA GLU B 261 " pdb=" CB GLU B 261 " pdb=" CG GLU B 261 " ideal model delta sigma weight residual 114.10 105.11 8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CA GLU F 261 " pdb=" CB GLU F 261 " pdb=" CG GLU F 261 " ideal model delta sigma weight residual 114.10 105.19 8.91 2.00e+00 2.50e-01 1.98e+01 angle pdb=" N TYR F 24 " pdb=" CA TYR F 24 " pdb=" C TYR F 24 " ideal model delta sigma weight residual 109.52 116.31 -6.79 1.55e+00 4.16e-01 1.92e+01 ... (remaining 37609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 14254 17.81 - 35.61: 1728 35.61 - 53.42: 526 53.42 - 71.22: 42 71.22 - 89.03: 18 Dihedral angle restraints: 16568 sinusoidal: 6696 harmonic: 9872 Sorted by residual: dihedral pdb=" CA ASN G 176 " pdb=" C ASN G 176 " pdb=" N TRP G 177 " pdb=" CA TRP G 177 " ideal model delta harmonic sigma weight residual -180.00 -155.71 -24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ASN C 176 " pdb=" C ASN C 176 " pdb=" N TRP C 177 " pdb=" CA TRP C 177 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA THR F 391 " pdb=" C THR F 391 " pdb=" N LYS F 392 " pdb=" CA LYS F 392 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 16565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3907 0.095 - 0.190: 311 0.190 - 0.286: 9 0.286 - 0.381: 0 0.381 - 0.476: 2 Chirality restraints: 4229 Sorted by residual: chirality pdb=" CG LEU F 297 " pdb=" CB LEU F 297 " pdb=" CD1 LEU F 297 " pdb=" CD2 LEU F 297 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CG LEU B 297 " pdb=" CB LEU B 297 " pdb=" CD1 LEU B 297 " pdb=" CD2 LEU B 297 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CB ILE B 252 " pdb=" CA ILE B 252 " pdb=" CG1 ILE B 252 " pdb=" CG2 ILE B 252 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 4226 not shown) Planarity restraints: 4726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 24 " -0.019 2.00e-02 2.50e+03 4.99e-02 4.98e+01 pdb=" CG TYR F 24 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR F 24 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR F 24 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 24 " 0.084 2.00e-02 2.50e+03 pdb=" CE2 TYR F 24 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR F 24 " -0.092 2.00e-02 2.50e+03 pdb=" OH TYR F 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 24 " 0.019 2.00e-02 2.50e+03 4.99e-02 4.97e+01 pdb=" CG TYR B 24 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 24 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR B 24 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 24 " -0.084 2.00e-02 2.50e+03 pdb=" CE2 TYR B 24 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR B 24 " 0.091 2.00e-02 2.50e+03 pdb=" OH TYR B 24 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 175 " 0.018 2.00e-02 2.50e+03 3.35e-02 2.24e+01 pdb=" CG TYR F 175 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR F 175 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 175 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR F 175 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR F 175 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR F 175 " 0.065 2.00e-02 2.50e+03 pdb=" OH TYR F 175 " 0.005 2.00e-02 2.50e+03 ... (remaining 4723 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 12871 2.96 - 3.45: 26852 3.45 - 3.93: 46744 3.93 - 4.42: 56090 4.42 - 4.90: 89829 Nonbonded interactions: 232386 Sorted by model distance: nonbonded pdb=" N THR F 213 " pdb=" OG1 THR F 213 " model vdw 2.477 2.496 nonbonded pdb=" N THR B 213 " pdb=" OG1 THR B 213 " model vdw 2.477 2.496 nonbonded pdb=" C ASP F 376 " pdb=" OD1 ASP F 376 " model vdw 2.594 3.270 nonbonded pdb=" C ASP B 376 " pdb=" OD1 ASP B 376 " model vdw 2.594 3.270 nonbonded pdb=" C ASP G 376 " pdb=" OD1 ASP G 376 " model vdw 2.595 3.270 ... (remaining 232381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 23 or resid 25 through 391 or resid 393 through \ 423)) selection = (chain 'B' and (resid 3 through 23 or resid 25 through 391 or resid 393 through \ 423)) selection = (chain 'C' and (resid 3 through 23 or resid 25 through 391 or resid 393 through \ 423)) selection = (chain 'D' and (resid 3 through 23 or resid 25 through 391 or resid 393 through \ 423)) selection = (chain 'E' and (resid 3 through 23 or resid 25 through 391 or resid 393 through \ 423)) selection = (chain 'F' and (resid 3 through 23 or resid 25 through 391 or resid 393 through \ 423)) selection = (chain 'G' and (resid 3 through 23 or resid 25 through 391 or resid 393 through \ 423)) selection = (chain 'H' and (resid 3 through 23 or resid 25 through 391 or resid 393 through \ 423)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.330 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 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 : 0.004 0.060 27670 Z= 0.172 Angle : 0.678 12.458 37630 Z= 0.352 Chirality : 0.050 0.476 4229 Planarity : 0.005 0.149 4726 Dihedral : 16.578 89.031 10166 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 2.69 % Allowed : 24.53 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3303 helix: 0.64 (0.18), residues: 904 sheet: 0.08 (0.18), residues: 792 loop : -1.37 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG F 93 TYR 0.092 0.003 TYR F 24 PHE 0.018 0.001 PHE F 373 TRP 0.071 0.002 TRP B 177 HIS 0.017 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (27662) covalent geometry : angle 0.67770 / 0.35 (37614) SS BOND : bond 0.00087 / 0.05 ( 8) SS BOND : angle 0.44018 / 0.25 ( 16) hydrogen bonds : bond 0.13316 / 8.84 ( 1128) hydrogen bonds : angle 6.10938 / 4.35 ( 3048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 181 time to evaluate : 1.063 Fit side-chains REVERT: B 143 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 398 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7818 (tmmt) REVERT: B 420 GLU cc_start: 0.8417 (pm20) cc_final: 0.8068 (pm20) REVERT: H 53 ASP cc_start: 0.8231 (t0) cc_final: 0.7428 (t0) REVERT: H 81 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9101 (p) REVERT: H 398 LYS cc_start: 0.9102 (tmmt) cc_final: 0.8592 (tmmt) REVERT: C 117 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8309 (pmtt) REVERT: C 232 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8645 (mptm) REVERT: C 296 MET cc_start: 0.9176 (tpp) cc_final: 0.8922 (mmt) REVERT: C 398 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8145 (tmmt) REVERT: A 30 MET cc_start: 0.9088 (mmm) cc_final: 0.8819 (mmp) REVERT: A 93 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8866 (mmm160) REVERT: A 201 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8799 (t) REVERT: A 215 GLU cc_start: 0.9216 (pt0) cc_final: 0.8487 (pp20) REVERT: F 143 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7767 (mt-10) REVERT: F 398 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7809 (tmmt) REVERT: F 420 GLU cc_start: 0.8460 (pm20) cc_final: 0.8096 (pm20) REVERT: D 53 ASP cc_start: 0.8258 (t0) cc_final: 0.7448 (t0) REVERT: D 81 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9114 (p) REVERT: D 398 LYS cc_start: 0.9102 (tmmt) cc_final: 0.8577 (tmmt) REVERT: G 117 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8296 (pmtt) REVERT: G 232 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8681 (mptm) REVERT: G 398 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8147 (tmmt) REVERT: E 30 MET cc_start: 0.9078 (mmm) cc_final: 0.8806 (mmp) REVERT: E 93 ARG cc_start: 0.9172 (mmm-85) cc_final: 0.8868 (mmm160) REVERT: E 201 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8791 (t) REVERT: E 215 GLU cc_start: 0.9168 (pt0) cc_final: 0.8435 (pp20) outliers start: 82 outliers final: 49 residues processed: 249 average time/residue: 0.5643 time to fit residues: 167.5910 Evaluate side-chains 235 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 325 HIS Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 378 ASN Chi-restraints excluded: chain F residue 398 LYS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 325 HIS Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 232 LYS Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 398 LYS Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 GLN C 171 ASN A 115 HIS A 125 HIS F 69 GLN G 171 ASN E 115 HIS E 125 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.059616 restraints weight = 54930.599| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.78 r_work: 0.2542 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27670 Z= 0.148 Angle : 0.530 11.092 37630 Z= 0.277 Chirality : 0.046 0.147 4229 Planarity : 0.003 0.035 4726 Dihedral : 5.423 51.013 3766 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.63 % Allowed : 23.71 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3303 helix: 1.25 (0.18), residues: 920 sheet: 0.16 (0.17), residues: 864 loop : -1.06 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 263 TYR 0.013 0.001 TYR H 336 PHE 0.012 0.001 PHE D 118 TRP 0.015 0.001 TRP F 119 HIS 0.003 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (27662) covalent geometry : angle 0.53018 / 0.28 (37614) SS BOND : bond 0.00120 / 0.08 ( 8) SS BOND : angle 0.26336 / 0.15 ( 16) hydrogen bonds : bond 0.04612 / 3.13 ( 1128) hydrogen bonds : angle 5.30545 / 3.77 ( 3048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 188 time to evaluate : 1.150 Fit side-chains REVERT: B 53 ASP cc_start: 0.7920 (t0) cc_final: 0.7586 (p0) REVERT: B 398 LYS cc_start: 0.8627 (tmmt) cc_final: 0.8014 (tmmt) REVERT: H 53 ASP cc_start: 0.8334 (t0) cc_final: 0.7471 (t0) REVERT: H 398 LYS cc_start: 0.9091 (tmmt) cc_final: 0.8544 (tmmt) REVERT: C 117 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8328 (pmtt) REVERT: C 296 MET cc_start: 0.9165 (tpp) cc_final: 0.8922 (tpp) REVERT: C 398 LYS cc_start: 0.8491 (tmtp) cc_final: 0.8067 (tmmt) REVERT: A 93 ARG cc_start: 0.8982 (mmm-85) cc_final: 0.8539 (mmm160) REVERT: A 215 GLU cc_start: 0.9163 (pt0) cc_final: 0.8274 (pp20) REVERT: A 376 ASP cc_start: 0.8515 (p0) cc_final: 0.8291 (p0) REVERT: F 53 ASP cc_start: 0.7924 (t0) cc_final: 0.7595 (p0) REVERT: F 398 LYS cc_start: 0.8633 (tmmt) cc_final: 0.8236 (tmmt) REVERT: D 53 ASP cc_start: 0.8348 (t0) cc_final: 0.7482 (t0) REVERT: D 398 LYS cc_start: 0.9090 (tmmt) cc_final: 0.8522 (tmmt) REVERT: G 117 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8327 (pmtt) REVERT: G 398 LYS cc_start: 0.8501 (tmtp) cc_final: 0.8091 (tmmt) REVERT: E 93 ARG cc_start: 0.8992 (mmm-85) cc_final: 0.8507 (mmm160) REVERT: E 215 GLU cc_start: 0.9156 (pt0) cc_final: 0.8282 (pp20) REVERT: E 376 ASP cc_start: 0.8484 (p0) cc_final: 0.8284 (p0) outliers start: 80 outliers final: 42 residues processed: 252 average time/residue: 0.5815 time to fit residues: 174.2313 Evaluate side-chains 223 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [247, 137, 23, 44, 219, 214, 94, 191, 217, 142, 324] chunk 247 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.056215 restraints weight = 71169.120| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 3.13 r_work: 0.2463 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27670 Z= 0.202 Angle : 0.558 9.300 37630 Z= 0.292 Chirality : 0.048 0.156 4229 Planarity : 0.003 0.033 4726 Dihedral : 4.669 42.447 3693 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.12 % Allowed : 23.42 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3303 helix: 1.39 (0.18), residues: 920 sheet: 0.35 (0.18), residues: 792 loop : -0.88 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 73 TYR 0.015 0.001 TYR A 336 PHE 0.014 0.001 PHE D 118 TRP 0.012 0.001 TRP A 377 HIS 0.005 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (27662) covalent geometry : angle 0.55810 / 0.29 (37614) SS BOND : bond 0.00125 / 0.08 ( 8) SS BOND : angle 0.51302 / 0.28 ( 16) hydrogen bonds : bond 0.05103 / 3.45 ( 1128) hydrogen bonds : angle 5.26028 / 3.74 ( 3048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 184 time to evaluate : 0.862 Fit side-chains REVERT: B 53 ASP cc_start: 0.7951 (t0) cc_final: 0.7713 (p0) REVERT: B 287 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8522 (ttt) REVERT: B 398 LYS cc_start: 0.8694 (tmmt) cc_final: 0.8091 (tmmt) REVERT: H 398 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8526 (tmmt) REVERT: C 152 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7857 (mmm160) REVERT: C 398 LYS cc_start: 0.8612 (tmtp) cc_final: 0.8185 (tmmt) REVERT: A 24 TYR cc_start: 0.7717 (p90) cc_final: 0.7417 (p90) REVERT: A 37 ASN cc_start: 0.9021 (m-40) cc_final: 0.8664 (t0) REVERT: A 93 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8421 (mmm160) REVERT: A 376 ASP cc_start: 0.8567 (p0) cc_final: 0.8332 (p0) REVERT: F 53 ASP cc_start: 0.7954 (t0) cc_final: 0.7706 (p0) REVERT: F 287 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8500 (ttt) REVERT: F 398 LYS cc_start: 0.8635 (tmmt) cc_final: 0.8045 (tmmt) REVERT: D 398 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8522 (tmmt) REVERT: G 152 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7857 (mmm160) REVERT: G 398 LYS cc_start: 0.8635 (tmtp) cc_final: 0.8189 (tmmt) REVERT: E 24 TYR cc_start: 0.7700 (p90) cc_final: 0.7400 (p90) REVERT: E 37 ASN cc_start: 0.9006 (m-40) cc_final: 0.8684 (t0) REVERT: E 93 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.8490 (mmm160) REVERT: E 376 ASP cc_start: 0.8537 (p0) cc_final: 0.8276 (p0) REVERT: E 413 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7718 (mt0) outliers start: 95 outliers final: 59 residues processed: 260 average time/residue: 0.5539 time to fit residues: 171.8934 Evaluate side-chains 240 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 287 MET Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [172, 122, 7, 285, 112, 20, 255, 316, 165, 173, 273] chunk 172 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 316 optimal weight: 0.0670 chunk 165 optimal weight: 0.0570 chunk 173 optimal weight: 0.9980 chunk 273 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.059633 restraints weight = 80907.040| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.33 r_work: 0.2537 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27670 Z= 0.104 Angle : 0.503 8.920 37630 Z= 0.261 Chirality : 0.045 0.149 4229 Planarity : 0.003 0.035 4726 Dihedral : 4.299 38.750 3685 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.05 % Allowed : 23.25 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3303 helix: 1.50 (0.18), residues: 920 sheet: 0.31 (0.17), residues: 864 loop : -0.84 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.011 0.001 TYR H 336 PHE 0.018 0.001 PHE B 118 TRP 0.010 0.001 TRP C 177 HIS 0.007 0.001 HIS F 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (27662) covalent geometry : angle 0.50313 / 0.26 (37614) SS BOND : bond 0.00063 / 0.04 ( 8) SS BOND : angle 0.35602 / 0.20 ( 16) hydrogen bonds : bond 0.04057 / 2.77 ( 1128) hydrogen bonds : angle 5.09666 / 3.63 ( 3048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 191 time to evaluate : 1.291 Fit side-chains REVERT: B 287 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8518 (ttt) REVERT: B 398 LYS cc_start: 0.8615 (tmmt) cc_final: 0.7975 (tmmt) REVERT: H 53 ASP cc_start: 0.8208 (t0) cc_final: 0.7363 (t0) REVERT: H 398 LYS cc_start: 0.9132 (tmmt) cc_final: 0.8582 (tmmt) REVERT: C 398 LYS cc_start: 0.8545 (tmtp) cc_final: 0.8102 (tmmt) REVERT: A 37 ASN cc_start: 0.8997 (m-40) cc_final: 0.8656 (t0) REVERT: A 93 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8419 (mmm160) REVERT: A 376 ASP cc_start: 0.8462 (p0) cc_final: 0.8210 (p0) REVERT: A 413 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: F 287 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8489 (ttt) REVERT: F 398 LYS cc_start: 0.8659 (tmmt) cc_final: 0.8045 (tmmt) REVERT: D 53 ASP cc_start: 0.8208 (t0) cc_final: 0.7362 (t0) REVERT: D 398 LYS cc_start: 0.9126 (tmmt) cc_final: 0.8578 (tmmt) REVERT: G 296 MET cc_start: 0.8582 (tpp) cc_final: 0.8336 (mmm) REVERT: G 398 LYS cc_start: 0.8546 (tmtp) cc_final: 0.8108 (tmmt) REVERT: E 24 TYR cc_start: 0.7643 (p90) cc_final: 0.7393 (p90) REVERT: E 37 ASN cc_start: 0.8981 (m-40) cc_final: 0.8673 (t0) REVERT: E 93 ARG cc_start: 0.8918 (mmm-85) cc_final: 0.8374 (mmm160) REVERT: E 117 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8077 (pttm) REVERT: E 376 ASP cc_start: 0.8483 (p0) cc_final: 0.8237 (p0) REVERT: E 413 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7641 (mt0) outliers start: 93 outliers final: 33 residues processed: 268 average time/residue: 0.5195 time to fit residues: 168.0159 Evaluate side-chains 211 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [161, 27, 25, 166, 240, 196, 271, 288, 133, 14, 224] chunk 161 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 240 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 271 optimal weight: 0.4980 chunk 288 optimal weight: 4.9990 chunk 133 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.084688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.059895 restraints weight = 79630.912| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.32 r_work: 0.2543 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27670 Z= 0.106 Angle : 0.504 8.932 37630 Z= 0.261 Chirality : 0.045 0.148 4229 Planarity : 0.003 0.033 4726 Dihedral : 4.197 38.737 3681 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.33 % Allowed : 24.04 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3303 helix: 1.52 (0.18), residues: 920 sheet: 0.40 (0.17), residues: 864 loop : -0.78 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.011 0.001 TYR E 336 PHE 0.015 0.001 PHE B 118 TRP 0.009 0.001 TRP G 177 HIS 0.007 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (27662) covalent geometry : angle 0.50441 / 0.26 (37614) SS BOND : bond 0.00062 / 0.04 ( 8) SS BOND : angle 0.37037 / 0.19 ( 16) hydrogen bonds : bond 0.04043 / 2.75 ( 1128) hydrogen bonds : angle 5.00651 / 3.57 ( 3048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 1.156 Fit side-chains REVERT: B 325 HIS cc_start: 0.8947 (t-90) cc_final: 0.8698 (t70) REVERT: B 398 LYS cc_start: 0.8622 (tmmt) cc_final: 0.7983 (tmmt) REVERT: H 53 ASP cc_start: 0.8199 (t0) cc_final: 0.7351 (t0) REVERT: H 81 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.8875 (p) REVERT: H 398 LYS cc_start: 0.9117 (tmmt) cc_final: 0.8557 (tmmt) REVERT: C 296 MET cc_start: 0.8690 (tpp) cc_final: 0.8341 (mmm) REVERT: C 398 LYS cc_start: 0.8565 (tmtp) cc_final: 0.8133 (tmmt) REVERT: A 37 ASN cc_start: 0.9010 (m-40) cc_final: 0.8667 (t0) REVERT: A 93 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8454 (mmm160) REVERT: A 376 ASP cc_start: 0.8476 (p0) cc_final: 0.8237 (p0) REVERT: A 413 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: F 287 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8468 (ttt) REVERT: F 325 HIS cc_start: 0.8944 (t-90) cc_final: 0.8676 (t70) REVERT: F 398 LYS cc_start: 0.8665 (tmmt) cc_final: 0.8051 (tmmt) REVERT: D 53 ASP cc_start: 0.8207 (t0) cc_final: 0.7359 (t0) REVERT: D 81 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.8876 (p) REVERT: D 398 LYS cc_start: 0.9134 (tmmt) cc_final: 0.8568 (tmmt) REVERT: G 398 LYS cc_start: 0.8568 (tmtp) cc_final: 0.8139 (tmmt) REVERT: E 24 TYR cc_start: 0.7708 (p90) cc_final: 0.7453 (p90) REVERT: E 37 ASN cc_start: 0.8990 (m-40) cc_final: 0.8667 (t0) REVERT: E 93 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8448 (mmm160) REVERT: E 117 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7995 (pttm) REVERT: E 376 ASP cc_start: 0.8469 (p0) cc_final: 0.8205 (p0) REVERT: E 413 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7596 (mt0) outliers start: 71 outliers final: 40 residues processed: 243 average time/residue: 0.5622 time to fit residues: 162.6907 Evaluate side-chains 222 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [117, 252, 285, 186, 303, 255, 1, 205, 254, 313, 77] chunk 117 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.056678 restraints weight = 78809.074| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 3.27 r_work: 0.2461 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27670 Z= 0.204 Angle : 0.571 12.654 37630 Z= 0.295 Chirality : 0.048 0.162 4229 Planarity : 0.003 0.031 4726 Dihedral : 4.525 42.917 3681 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.56 % Allowed : 23.68 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3303 helix: 1.50 (0.18), residues: 920 sheet: 0.38 (0.17), residues: 864 loop : -0.80 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 322 TYR 0.015 0.001 TYR C 336 PHE 0.017 0.001 PHE B 118 TRP 0.011 0.001 TRP C 377 HIS 0.007 0.001 HIS F 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (27662) covalent geometry : angle 0.57091 / 0.30 (37614) SS BOND : bond 0.00098 / 0.06 ( 8) SS BOND : angle 0.51496 / 0.27 ( 16) hydrogen bonds : bond 0.04926 / 3.32 ( 1128) hydrogen bonds : angle 5.09953 / 3.63 ( 3048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 179 time to evaluate : 1.090 Fit side-chains REVERT: B 287 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8569 (ttt) REVERT: B 398 LYS cc_start: 0.8636 (tmmt) cc_final: 0.7971 (tmmt) REVERT: H 53 ASP cc_start: 0.8355 (t0) cc_final: 0.8042 (t0) REVERT: H 398 LYS cc_start: 0.9112 (tmmt) cc_final: 0.8567 (tmmt) REVERT: C 296 MET cc_start: 0.8824 (tpp) cc_final: 0.8520 (mmm) REVERT: C 398 LYS cc_start: 0.8638 (tmtp) cc_final: 0.8187 (tmmt) REVERT: A 24 TYR cc_start: 0.7666 (p90) cc_final: 0.7410 (p90) REVERT: A 37 ASN cc_start: 0.9019 (m-40) cc_final: 0.8618 (t0) REVERT: A 93 ARG cc_start: 0.8942 (mmm-85) cc_final: 0.8472 (mmm160) REVERT: A 376 ASP cc_start: 0.8587 (p0) cc_final: 0.8339 (p0) REVERT: F 287 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8448 (ttt) REVERT: F 398 LYS cc_start: 0.8673 (tmmt) cc_final: 0.8033 (tmmt) REVERT: D 53 ASP cc_start: 0.8304 (t0) cc_final: 0.7984 (t0) REVERT: D 398 LYS cc_start: 0.9109 (tmmt) cc_final: 0.8566 (tmmt) REVERT: G 296 MET cc_start: 0.8670 (tpp) cc_final: 0.8344 (mmm) REVERT: G 398 LYS cc_start: 0.8638 (tmtp) cc_final: 0.8190 (tmmt) REVERT: E 24 TYR cc_start: 0.7628 (p90) cc_final: 0.7426 (p90) REVERT: E 37 ASN cc_start: 0.9019 (m-40) cc_final: 0.8619 (t0) REVERT: E 376 ASP cc_start: 0.8577 (p0) cc_final: 0.8326 (p0) REVERT: E 413 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7690 (mt0) outliers start: 78 outliers final: 54 residues processed: 252 average time/residue: 0.5429 time to fit residues: 164.9301 Evaluate side-chains 224 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [116, 86, 99, 167, 2, 187, 152, 49, 118, 314, 197] chunk 116 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 314 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.058642 restraints weight = 67960.352| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.07 r_work: 0.2515 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27670 Z= 0.126 Angle : 0.528 11.920 37630 Z= 0.272 Chirality : 0.046 0.150 4229 Planarity : 0.003 0.032 4726 Dihedral : 4.359 40.081 3681 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.36 % Allowed : 24.37 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3303 helix: 1.51 (0.18), residues: 920 sheet: 0.37 (0.17), residues: 864 loop : -0.76 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.012 0.001 TYR A 336 PHE 0.016 0.001 PHE F 118 TRP 0.010 0.001 TRP G 177 HIS 0.008 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (27662) covalent geometry : angle 0.52844 / 0.27 (37614) SS BOND : bond 0.00076 / 0.05 ( 8) SS BOND : angle 0.37908 / 0.20 ( 16) hydrogen bonds : bond 0.04316 / 2.93 ( 1128) hydrogen bonds : angle 5.03237 / 3.59 ( 3048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 1.121 Fit side-chains REVERT: B 287 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8499 (ttt) REVERT: B 325 HIS cc_start: 0.8931 (t-90) cc_final: 0.8613 (t70) REVERT: B 398 LYS cc_start: 0.8646 (tmmt) cc_final: 0.7905 (tmmt) REVERT: H 53 ASP cc_start: 0.8287 (t0) cc_final: 0.7466 (t0) REVERT: H 398 LYS cc_start: 0.9109 (tmmt) cc_final: 0.8574 (tmmt) REVERT: C 398 LYS cc_start: 0.8630 (tmtp) cc_final: 0.8200 (tmmt) REVERT: A 24 TYR cc_start: 0.7632 (p90) cc_final: 0.7373 (p90) REVERT: A 37 ASN cc_start: 0.8990 (m-40) cc_final: 0.8572 (t0) REVERT: A 93 ARG cc_start: 0.8929 (mmm-85) cc_final: 0.8498 (mmm160) REVERT: A 376 ASP cc_start: 0.8501 (p0) cc_final: 0.8239 (p0) REVERT: F 287 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8522 (ttt) REVERT: F 325 HIS cc_start: 0.8945 (t-90) cc_final: 0.8676 (t70) REVERT: F 398 LYS cc_start: 0.8638 (tmmt) cc_final: 0.7957 (tmmt) REVERT: D 53 ASP cc_start: 0.8328 (t0) cc_final: 0.7528 (t0) REVERT: D 398 LYS cc_start: 0.9103 (tmmt) cc_final: 0.8571 (tmmt) REVERT: G 296 MET cc_start: 0.8567 (tpp) cc_final: 0.8262 (mmm) REVERT: G 398 LYS cc_start: 0.8633 (tmtp) cc_final: 0.8205 (tmmt) REVERT: E 24 TYR cc_start: 0.7616 (p90) cc_final: 0.7347 (p90) REVERT: E 37 ASN cc_start: 0.9008 (m-40) cc_final: 0.8613 (t0) REVERT: E 376 ASP cc_start: 0.8496 (p0) cc_final: 0.8263 (p0) REVERT: E 413 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7584 (mt0) outliers start: 72 outliers final: 47 residues processed: 237 average time/residue: 0.5451 time to fit residues: 155.2951 Evaluate side-chains 220 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [65, 300, 67, 2, 214, 84, 108, 24, 260, 165, 50] chunk 65 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 260 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.057434 restraints weight = 93037.095| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 3.50 r_work: 0.2471 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27670 Z= 0.157 Angle : 0.550 11.579 37630 Z= 0.284 Chirality : 0.047 0.161 4229 Planarity : 0.003 0.031 4726 Dihedral : 4.429 41.837 3681 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.43 % Allowed : 24.53 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3303 helix: 1.51 (0.18), residues: 920 sheet: 0.38 (0.17), residues: 864 loop : -0.77 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 102 TYR 0.013 0.001 TYR A 336 PHE 0.015 0.001 PHE B 118 TRP 0.009 0.001 TRP C 177 HIS 0.008 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (27662) covalent geometry : angle 0.54974 / 0.28 (37614) SS BOND : bond 0.00087 / 0.05 ( 8) SS BOND : angle 0.42196 / 0.22 ( 16) hydrogen bonds : bond 0.04575 / 3.10 ( 1128) hydrogen bonds : angle 5.03591 / 3.59 ( 3048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 176 time to evaluate : 1.041 Fit side-chains REVERT: B 287 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8570 (ttt) REVERT: B 325 HIS cc_start: 0.8940 (t-90) cc_final: 0.8623 (t70) REVERT: B 398 LYS cc_start: 0.8657 (tmmt) cc_final: 0.7913 (tmmt) REVERT: H 53 ASP cc_start: 0.8246 (t0) cc_final: 0.7453 (t0) REVERT: H 398 LYS cc_start: 0.9113 (tmmt) cc_final: 0.8598 (tmmt) REVERT: C 398 LYS cc_start: 0.8643 (tmtp) cc_final: 0.8207 (tmmt) REVERT: A 24 TYR cc_start: 0.7650 (p90) cc_final: 0.7385 (p90) REVERT: A 30 MET cc_start: 0.8702 (mmp) cc_final: 0.8457 (mmm) REVERT: A 37 ASN cc_start: 0.9006 (m-40) cc_final: 0.8574 (t0) REVERT: A 376 ASP cc_start: 0.8556 (p0) cc_final: 0.8298 (p0) REVERT: F 287 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8401 (ttt) REVERT: F 325 HIS cc_start: 0.8973 (t-90) cc_final: 0.8708 (t70) REVERT: F 398 LYS cc_start: 0.8654 (tmmt) cc_final: 0.7908 (tmmt) REVERT: D 53 ASP cc_start: 0.8252 (t0) cc_final: 0.7458 (t0) REVERT: D 398 LYS cc_start: 0.9108 (tmmt) cc_final: 0.8594 (tmmt) REVERT: G 296 MET cc_start: 0.8654 (tpp) cc_final: 0.8352 (mmm) REVERT: G 398 LYS cc_start: 0.8644 (tmtp) cc_final: 0.8210 (tmmt) REVERT: E 37 ASN cc_start: 0.9006 (m-40) cc_final: 0.8626 (t0) REVERT: E 104 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8927 (mm) REVERT: E 232 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8730 (tppt) REVERT: E 376 ASP cc_start: 0.8537 (p0) cc_final: 0.8271 (p0) REVERT: E 413 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7596 (mt0) outliers start: 74 outliers final: 55 residues processed: 243 average time/residue: 0.5450 time to fit residues: 159.5476 Evaluate side-chains 227 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [146, 25, 29, 227, 180, 172, 113, 174, 186, 283, 290] chunk 146 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 227 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 113 optimal weight: 0.0970 chunk 174 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.058358 restraints weight = 76488.957| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.24 r_work: 0.2500 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27670 Z= 0.144 Angle : 0.560 14.592 37630 Z= 0.284 Chirality : 0.047 0.155 4229 Planarity : 0.003 0.031 4726 Dihedral : 4.396 41.077 3681 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.17 % Allowed : 24.86 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3303 helix: 1.51 (0.18), residues: 920 sheet: 0.37 (0.17), residues: 864 loop : -0.76 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.012 0.001 TYR E 336 PHE 0.015 0.001 PHE B 118 TRP 0.010 0.001 TRP C 177 HIS 0.008 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (27662) covalent geometry : angle 0.55981 / 0.28 (37614) SS BOND : bond 0.00078 / 0.05 ( 8) SS BOND : angle 0.38430 / 0.20 ( 16) hydrogen bonds : bond 0.04434 / 3.01 ( 1128) hydrogen bonds : angle 5.02265 / 3.58 ( 3048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 1.243 Fit side-chains REVERT: B 287 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8542 (ttt) REVERT: B 325 HIS cc_start: 0.8900 (t-90) cc_final: 0.8564 (t70) REVERT: B 398 LYS cc_start: 0.8649 (tmmt) cc_final: 0.7939 (tmmt) REVERT: H 53 ASP cc_start: 0.8212 (t0) cc_final: 0.7437 (t0) REVERT: H 398 LYS cc_start: 0.9106 (tmmt) cc_final: 0.8597 (tmmt) REVERT: C 398 LYS cc_start: 0.8649 (tmtp) cc_final: 0.8216 (tmmt) REVERT: A 24 TYR cc_start: 0.7659 (p90) cc_final: 0.7455 (p90) REVERT: A 30 MET cc_start: 0.8730 (mmp) cc_final: 0.8469 (mmm) REVERT: A 37 ASN cc_start: 0.9001 (m-40) cc_final: 0.8581 (t0) REVERT: A 376 ASP cc_start: 0.8527 (p0) cc_final: 0.8308 (p0) REVERT: F 287 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8589 (ttt) REVERT: F 325 HIS cc_start: 0.8936 (t-90) cc_final: 0.8661 (t70) REVERT: F 398 LYS cc_start: 0.8640 (tmmt) cc_final: 0.7946 (tmmt) REVERT: D 53 ASP cc_start: 0.8218 (t0) cc_final: 0.7440 (t0) REVERT: D 398 LYS cc_start: 0.9110 (tmmt) cc_final: 0.8603 (tmmt) REVERT: G 296 MET cc_start: 0.8633 (tpp) cc_final: 0.8336 (mmm) REVERT: G 398 LYS cc_start: 0.8646 (tmtp) cc_final: 0.8215 (tmmt) REVERT: E 30 MET cc_start: 0.8807 (mmp) cc_final: 0.8557 (mmm) REVERT: E 37 ASN cc_start: 0.9153 (m-40) cc_final: 0.8613 (t0) REVERT: E 104 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8911 (mm) REVERT: E 232 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8745 (tppt) REVERT: E 376 ASP cc_start: 0.8518 (p0) cc_final: 0.8275 (p0) REVERT: E 398 LYS cc_start: 0.8824 (tmmt) cc_final: 0.8521 (tmmt) REVERT: E 413 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7583 (mt0) outliers start: 66 outliers final: 54 residues processed: 241 average time/residue: 0.5433 time to fit residues: 156.4644 Evaluate side-chains 234 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [246, 270, 214, 206, 79, 130, 261, 265, 90, 127, 267] chunk 246 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.057918 restraints weight = 71732.131| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 3.12 r_work: 0.2491 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27670 Z= 0.162 Angle : 0.575 17.158 37630 Z= 0.291 Chirality : 0.047 0.158 4229 Planarity : 0.003 0.030 4726 Dihedral : 4.452 41.957 3681 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.10 % Allowed : 25.02 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3303 helix: 1.51 (0.18), residues: 920 sheet: 0.38 (0.17), residues: 864 loop : -0.76 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.013 0.001 TYR A 336 PHE 0.015 0.001 PHE B 118 TRP 0.009 0.001 TRP C 177 HIS 0.008 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (27662) covalent geometry : angle 0.57514 / 0.29 (37614) SS BOND : bond 0.00093 / 0.06 ( 8) SS BOND : angle 0.42483 / 0.22 ( 16) hydrogen bonds : bond 0.04609 / 3.12 ( 1128) hydrogen bonds : angle 5.03233 / 3.58 ( 3048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 181 time to evaluate : 1.073 Fit side-chains REVERT: B 287 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8613 (ttt) REVERT: B 325 HIS cc_start: 0.8900 (t-90) cc_final: 0.8559 (t70) REVERT: B 398 LYS cc_start: 0.8615 (tmmt) cc_final: 0.7909 (tmmt) REVERT: H 53 ASP cc_start: 0.8257 (t0) cc_final: 0.7468 (t0) REVERT: H 398 LYS cc_start: 0.9111 (tmmt) cc_final: 0.8609 (tmmt) REVERT: C 398 LYS cc_start: 0.8663 (tmtp) cc_final: 0.8237 (tmmt) REVERT: A 24 TYR cc_start: 0.7680 (p90) cc_final: 0.7474 (p90) REVERT: A 30 MET cc_start: 0.8734 (mmp) cc_final: 0.8518 (mmm) REVERT: A 37 ASN cc_start: 0.8974 (m-40) cc_final: 0.8566 (t0) REVERT: A 376 ASP cc_start: 0.8537 (p0) cc_final: 0.8273 (p0) REVERT: F 287 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8595 (ttt) REVERT: F 325 HIS cc_start: 0.8924 (t-90) cc_final: 0.8648 (t70) REVERT: F 398 LYS cc_start: 0.8641 (tmmt) cc_final: 0.7947 (tmmt) REVERT: D 53 ASP cc_start: 0.8265 (t0) cc_final: 0.7476 (t0) REVERT: D 398 LYS cc_start: 0.9109 (tmmt) cc_final: 0.8608 (tmmt) REVERT: G 296 MET cc_start: 0.8610 (tpp) cc_final: 0.8318 (mmm) REVERT: G 398 LYS cc_start: 0.8707 (tmtp) cc_final: 0.8289 (tmmt) REVERT: E 30 MET cc_start: 0.8844 (mmp) cc_final: 0.8582 (mmm) REVERT: E 37 ASN cc_start: 0.9158 (m-40) cc_final: 0.8622 (t0) REVERT: E 104 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8913 (mm) REVERT: E 232 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8741 (tppt) REVERT: E 376 ASP cc_start: 0.8534 (p0) cc_final: 0.8258 (p0) REVERT: E 398 LYS cc_start: 0.8837 (tmmt) cc_final: 0.8508 (tmmt) outliers start: 64 outliers final: 56 residues processed: 240 average time/residue: 0.5801 time to fit residues: 167.0944 Evaluate side-chains 231 residues out of total 3035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 418 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: [0, 22, 37, 256, 23, 164, 306, 106, 167, 102, 68] chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 306 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.057950 restraints weight = 74302.697| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.20 r_work: 0.2501 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27670 Z= 0.144 Angle : 0.567 16.503 37630 Z= 0.287 Chirality : 0.047 0.157 4229 Planarity : 0.003 0.030 4726 Dihedral : 4.408 41.095 3681 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.23 % Allowed : 24.86 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3303 helix: 1.51 (0.18), residues: 920 sheet: 0.37 (0.17), residues: 864 loop : -0.75 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.013 0.001 TYR A 336 PHE 0.015 0.001 PHE B 118 TRP 0.010 0.001 TRP C 177 HIS 0.008 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (27662) covalent geometry : angle 0.56692 / 0.29 (37614) SS BOND : bond 0.00078 / 0.05 ( 8) SS BOND : angle 0.38580 / 0.20 ( 16) hydrogen bonds : bond 0.04426 / 3.00 ( 1128) hydrogen bonds : angle 5.01967 / 3.57 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9508.88 seconds wall clock time: 162 minutes 42.88 seconds (9762.88 seconds total)