Starting phenix.real_space_refine on Thu Feb 5 07:41:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hh9_52169/02_2026/9hh9_52169.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hh9_52169/02_2026/9hh9_52169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hh9_52169/02_2026/9hh9_52169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hh9_52169/02_2026/9hh9_52169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hh9_52169/02_2026/9hh9_52169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hh9_52169/02_2026/9hh9_52169.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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 87 5.16 5 C 9901 2.51 5 N 2605 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15613 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Conformer: "B" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} bond proxies already assigned to first conformer: 3419 Chain: "B" Number of atoms: 3379 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Conformer: "B" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} bond proxies already assigned to first conformer: 3449 Chain: "C" Number of atoms: 3388 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Conformer: "B" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} bond proxies already assigned to first conformer: 3439 Chain: "D" Number of atoms: 849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 827 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "H" Number of atoms: 849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 827 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" N AHIS A 8 " occ=0.66 ... (18 atoms not shown) pdb=" NE2BHIS A 8 " occ=0.34 residue: pdb=" N ALYS A 15 " occ=0.79 ... (16 atoms not shown) pdb=" NZ BLYS A 15 " occ=0.21 residue: pdb=" N AGLN A 112 " occ=0.20 ... (16 atoms not shown) pdb=" NE2BGLN A 112 " occ=0.80 residue: pdb=" N AGLU A 355 " occ=0.61 ... (16 atoms not shown) pdb=" OE2BGLU A 355 " occ=0.39 residue: pdb=" N AALA A 402 " occ=0.47 ... (8 atoms not shown) pdb=" CB BALA A 402 " occ=0.53 residue: pdb=" N AHIS B 8 " occ=0.57 ... (18 atoms not shown) pdb=" NE2BHIS B 8 " occ=0.43 residue: pdb=" N AALA B 402 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 402 " occ=0.50 residue: pdb=" N AHIS C 8 " occ=0.74 ... (18 atoms not shown) pdb=" NE2BHIS C 8 " occ=0.26 residue: pdb=" N AGLU C 355 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU C 355 " occ=0.50 residue: pdb=" N LYS C 401 " occ=0.94 ... (7 atoms not shown) pdb=" NZ LYS C 401 " occ=0.94 residue: pdb=" N AALA C 402 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA C 402 " occ=0.50 residue: pdb=" N AARG D 61 " occ=0.67 ... (20 atoms not shown) pdb=" NH2BARG D 61 " occ=0.33 ... (remaining 3 not shown) Time building chain proxies: 5.13, per 1000 atoms: 0.33 Number of scatterers: 15613 At special positions: 0 Unit cell: (133.965, 145.415, 147.705, 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 87 16.00 O 3020 8.00 N 2605 7.00 C 9901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 114 " distance=1.99 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 114 " distance=2.06 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 253 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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: 1.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 41 sheets defined 13.3% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.645A pdb=" N ALA A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 273 through 294 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.523A pdb=" N TYR A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 408 through 414 removed outlier: 4.468A pdb=" N ASP A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 removed outlier: 3.911A pdb=" N ALA B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 88 through 102 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.524A pdb=" N LEU B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.651A pdb=" N ARG B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 273 through 294 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 409 through 417 removed outlier: 3.518A pdb=" N SER B 415 " --> pdb=" O GLN B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.574A pdb=" N LYS C 50 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 88 through 98 Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.980A pdb=" N LYS C 152 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 218 removed outlier: 4.232A pdb=" N LYS C 217 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 273 through 293 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 383 through 386 Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 214 removed outlier: 5.238A pdb=" N ALA A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER A 207 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET A 239 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N TRP A 227 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 84 Processing sheet with id=AA6, first strand: chain 'A' and resid 82 through 84 Processing sheet with id=AA7, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA9, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AB1, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AB3, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.604A pdb=" N TYR B 325 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'B' and resid 213 through 214 removed outlier: 4.714A pdb=" N MET B 239 " --> pdb=" O TRP B 227 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TRP B 227 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'B' and resid 119 through 122 removed outlier: 4.167A pdb=" N THR B 120 " --> pdb=" O CYS B 68 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS B 68 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 66 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 125 through 131 removed outlier: 3.580A pdb=" N ASP B 69 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR B 77 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 424 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AC1, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 45 Processing sheet with id=AC4, first strand: chain 'C' and resid 125 through 130 Processing sheet with id=AC5, first strand: chain 'C' and resid 125 through 130 removed outlier: 3.947A pdb=" N ARG C 83 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N HIS C 80 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AC7, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AC8, first strand: chain 'C' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AD1, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AD3, first strand: chain 'E' and resid 16 through 19 removed outlier: 5.760A pdb=" N GLN E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.888A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AD6, first strand: chain 'F' and resid 21 through 22 Processing sheet with id=AD7, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.424A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE F 87 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.534A pdb=" N GLN G 3 " --> pdb=" O THR G 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 16 through 20 removed outlier: 6.023A pdb=" N GLN G 16 " --> pdb=" O SER G 85 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER G 85 " --> pdb=" O GLN G 16 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 58 through 60 removed outlier: 3.522A pdb=" N ASN G 59 " --> pdb=" O TYR G 51 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TRP G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG G 39 " --> pdb=" O TRP G 48 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA G 92 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 19 through 21 removed outlier: 4.593A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE H 75 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE H 21 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 73 " --> pdb=" O ILE H 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'H' and resid 46 through 48 removed outlier: 6.219A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN H 89 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 56 through 60 removed outlier: 4.221A pdb=" N THR I 58 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR I 51 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR I 60 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET I 49 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG I 39 " --> pdb=" O TRP I 48 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 71 through 72 435 hydrogen bonds defined for protein. 1062 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: 1.99 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4202 1.33 - 1.46: 4379 1.46 - 1.58: 7376 1.58 - 1.71: 0 1.71 - 1.84: 126 Bond restraints: 16083 Sorted by residual: bond pdb=" C ASP A 241 " pdb=" N LYS A 242 " ideal model delta sigma weight residual 1.335 1.534 -0.199 1.31e-02 5.83e+03 2.32e+02 bond pdb=" CA SER A 48 " pdb=" CB SER A 48 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.57e-02 4.06e+03 9.04e+00 bond pdb=" N PHE F 87 " pdb=" CA PHE F 87 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.79e+00 bond pdb=" CA SER D 93 " pdb=" CB SER D 93 " ideal model delta sigma weight residual 1.533 1.489 0.044 1.51e-02 4.39e+03 8.58e+00 bond pdb=" CA SER D 92 " pdb=" CB SER D 92 " ideal model delta sigma weight residual 1.532 1.486 0.045 1.57e-02 4.06e+03 8.33e+00 ... (remaining 16078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 21394 2.57 - 5.15: 445 5.15 - 7.72: 52 7.72 - 10.30: 12 10.30 - 12.87: 3 Bond angle restraints: 21906 Sorted by residual: angle pdb=" N TYR I 101 " pdb=" CA TYR I 101 " pdb=" C TYR I 101 " ideal model delta sigma weight residual 108.67 121.54 -12.87 1.55e+00 4.16e-01 6.90e+01 angle pdb=" CA ASP A 241 " pdb=" C ASP A 241 " pdb=" N LYS A 242 " ideal model delta sigma weight residual 115.10 105.28 9.82 1.26e+00 6.30e-01 6.07e+01 angle pdb=" O ASP A 241 " pdb=" C ASP A 241 " pdb=" N LYS A 242 " ideal model delta sigma weight residual 122.46 131.62 -9.16 1.19e+00 7.06e-01 5.93e+01 angle pdb=" C TYR E 106 " pdb=" CA TYR E 106 " pdb=" CB TYR E 106 " ideal model delta sigma weight residual 111.70 100.95 10.75 1.52e+00 4.33e-01 5.00e+01 angle pdb=" C GLN E 5 " pdb=" N GLU E 6 " pdb=" CA GLU E 6 " ideal model delta sigma weight residual 121.54 132.80 -11.26 1.91e+00 2.74e-01 3.48e+01 ... (remaining 21901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7869 17.95 - 35.90: 1113 35.90 - 53.85: 326 53.85 - 71.79: 78 71.79 - 89.74: 41 Dihedral angle restraints: 9427 sinusoidal: 3710 harmonic: 5717 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 -177.84 -89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS C 219 " pdb=" SG CYS C 219 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual 93.00 176.63 -83.63 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS C 68 " pdb=" SG CYS C 68 " pdb=" SG CYS C 114 " pdb=" CB CYS C 114 " ideal model delta sinusoidal sigma weight residual 93.00 13.05 79.95 1 1.00e+01 1.00e-02 7.92e+01 ... (remaining 9424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2241 0.112 - 0.224: 70 0.224 - 0.336: 5 0.336 - 0.449: 1 0.449 - 0.561: 1 Chirality restraints: 2318 Sorted by residual: chirality pdb=" CA TYR D 94 " pdb=" N TYR D 94 " pdb=" C TYR D 94 " pdb=" CB TYR D 94 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" CA CYS A 68 " pdb=" N CYS A 68 " pdb=" C CYS A 68 " pdb=" CB CYS A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA LYS A 220 " pdb=" N LYS A 220 " pdb=" C LYS A 220 " pdb=" CB LYS A 220 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2315 not shown) Planarity restraints: 2822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 85 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ASP F 85 " 0.070 2.00e-02 2.50e+03 pdb=" O ASP F 85 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR F 86 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 94 " 0.042 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR D 94 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR D 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 94 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 94 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 54 " -0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C TYR E 54 " 0.061 2.00e-02 2.50e+03 pdb=" O TYR E 54 " -0.024 2.00e-02 2.50e+03 pdb=" N SER E 55 " -0.021 2.00e-02 2.50e+03 ... (remaining 2819 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 66 2.43 - 3.04: 9735 3.04 - 3.66: 23348 3.66 - 4.28: 35068 4.28 - 4.90: 60413 Nonbonded interactions: 128630 Sorted by model distance: nonbonded pdb=" CG1 VAL G 12 " pdb=" OE1 GLN G 16 " model vdw 1.808 3.460 nonbonded pdb=" OG SER B 298 " pdb=" OD2 ASP B 301 " model vdw 2.163 3.040 nonbonded pdb=" OG SER F 76 " pdb=" OD1 ASP F 77 " model vdw 2.164 3.040 nonbonded pdb=" OG SER A 26 " pdb=" O GLN A 264 " model vdw 2.190 3.040 nonbonded pdb=" NE1 TRP C 357 " pdb=" O ASP C 359 " model vdw 2.211 3.120 ... (remaining 128625 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 1 through 7 or resid 9 through 14 or resid 16 through 111 \ or resid 113 through 354 or resid 356 through 401 or resid 403 through 426)) selection = (chain 'B' and (resid 1 through 7 or resid 9 through 14 or resid 16 through 111 \ or resid 113 through 354 or resid 356 through 401 or resid 403 through 426)) selection = (chain 'C' and (resid 1 through 7 or resid 9 through 14 or resid 16 through 111 \ or resid 113 through 354 or resid 356 through 401 or resid 403 through 426)) } ncs_group { reference = (chain 'D' and (resid 1 through 60 or resid 62 through 80 or resid 82 through 10 \ 6)) selection = (chain 'F' and (resid 1 through 60 or resid 62 through 80 or resid 82 through 10 \ 6)) selection = (chain 'H' and (resid 1 through 60 or resid 62 through 80 or resid 82 through 10 \ 6)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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=0.20 max=1.00 mean=0.99 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: 1.690 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.060 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 0.199 16107 Z= 0.248 Angle : 0.872 12.874 21954 Z= 0.495 Chirality : 0.052 0.561 2318 Planarity : 0.006 0.075 2822 Dihedral : 19.054 89.743 5715 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.93 % Allowed : 12.00 % Favored : 87.07 % Rotamer: Outliers : 6.17 % Allowed : 32.14 % Favored : 61.68 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % 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: -2.66 (0.18), residues: 1983 helix: 0.09 (0.38), residues: 189 sheet: -2.07 (0.25), residues: 393 loop : -2.06 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 54 TYR 0.060 0.002 TYR D 94 PHE 0.021 0.002 PHE C 188 TRP 0.017 0.002 TRP H 35 HIS 0.005 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00441 (16083) covalent geometry : angle 0.86484 (21906) SS BOND : bond 0.01222 ( 24) SS BOND : angle 2.49227 ( 48) hydrogen bonds : bond 0.18751 ( 427) hydrogen bonds : angle 8.68187 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 209 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7586 (ttpt) REVERT: B 83 ARG cc_start: 0.7357 (mtm110) cc_final: 0.7112 (mtt180) REVERT: C 417 LEU cc_start: 0.6940 (tp) cc_final: 0.6577 (tt) REVERT: D 50 TRP cc_start: 0.6866 (p-90) cc_final: 0.6604 (p-90) REVERT: E 105 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7904 (t70) REVERT: F 91 TYR cc_start: 0.8038 (p90) cc_final: 0.7810 (p90) outliers start: 95 outliers final: 76 residues processed: 295 average time/residue: 0.4053 time to fit residues: 136.4846 Evaluate side-chains 279 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 201 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 38 ASN Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.3980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 42 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 53 HIS ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.194336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132568 restraints weight = 81308.698| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 6.14 r_work: 0.3350 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16107 Z= 0.157 Angle : 0.742 9.818 21954 Z= 0.388 Chirality : 0.048 0.301 2318 Planarity : 0.006 0.065 2822 Dihedral : 8.915 59.339 2272 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.54 % Favored : 88.05 % Rotamer: Outliers : 6.92 % Allowed : 28.74 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.18), residues: 1983 helix: -0.01 (0.37), residues: 210 sheet: -1.93 (0.24), residues: 414 loop : -1.90 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 54 TYR 0.046 0.002 TYR D 94 PHE 0.017 0.002 PHE A 326 TRP 0.014 0.001 TRP B 236 HIS 0.005 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00359 (16083) covalent geometry : angle 0.73854 (21906) SS BOND : bond 0.00244 ( 24) SS BOND : angle 1.69889 ( 48) hydrogen bonds : bond 0.04249 ( 427) hydrogen bonds : angle 6.68591 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 207 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.6905 (pttt) REVERT: A 253 CYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6080 (m) REVERT: B 20 ASN cc_start: 0.8686 (t0) cc_final: 0.8377 (t160) REVERT: B 206 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7538 (ptt90) REVERT: B 346 MET cc_start: 0.7738 (tpp) cc_final: 0.7476 (mmm) REVERT: B 347 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 393 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8415 (t0) REVERT: C 58 MET cc_start: 0.8351 (tpp) cc_final: 0.7972 (mmt) REVERT: C 223 TYR cc_start: 0.6503 (t80) cc_final: 0.6146 (t80) REVERT: C 417 LEU cc_start: 0.6211 (tp) cc_final: 0.5848 (tt) REVERT: D 9 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6846 (mmtp) REVERT: D 50 TRP cc_start: 0.7013 (p-90) cc_final: 0.6812 (p-90) REVERT: E 47 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: E 57 LEU cc_start: 0.8709 (mt) cc_final: 0.8305 (mt) REVERT: F 24 LYS cc_start: 0.6595 (tptt) cc_final: 0.6076 (mtpt) REVERT: F 37 GLN cc_start: 0.6242 (tp-100) cc_final: 0.5988 (tp40) REVERT: G 28 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7370 (p) REVERT: G 82 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6156 (mm-40) REVERT: I 109 MET cc_start: 0.0794 (mpp) cc_final: -0.0240 (ttp) outliers start: 108 outliers final: 52 residues processed: 285 average time/residue: 0.4356 time to fit residues: 140.0619 Evaluate side-chains 259 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 128 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS D 38 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.194864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136249 restraints weight = 87985.392| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 6.20 r_work: 0.3392 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16107 Z= 0.166 Angle : 0.733 10.319 21954 Z= 0.380 Chirality : 0.048 0.283 2318 Planarity : 0.006 0.063 2822 Dihedral : 7.691 58.282 2186 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.80 % Favored : 87.89 % Rotamer: Outliers : 6.87 % Allowed : 28.39 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.34 (0.18), residues: 1983 helix: 0.28 (0.38), residues: 204 sheet: -1.81 (0.25), residues: 392 loop : -1.87 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 249 TYR 0.043 0.002 TYR D 94 PHE 0.017 0.002 PHE A 326 TRP 0.012 0.001 TRP B 236 HIS 0.005 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00387 (16083) covalent geometry : angle 0.72972 (21906) SS BOND : bond 0.00238 ( 24) SS BOND : angle 1.61196 ( 48) hydrogen bonds : bond 0.03993 ( 427) hydrogen bonds : angle 6.35693 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 200 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6994 (pttt) REVERT: A 253 CYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6371 (m) REVERT: B 20 ASN cc_start: 0.8661 (t0) cc_final: 0.8337 (t160) REVERT: B 78 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6823 (pt) REVERT: B 181 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8455 (mt) REVERT: B 206 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7594 (ptt90) REVERT: C 39 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6990 (p) REVERT: C 58 MET cc_start: 0.8310 (tpp) cc_final: 0.7880 (mmt) REVERT: C 184 MET cc_start: 0.8535 (ptm) cc_final: 0.8266 (ptm) REVERT: C 222 GLN cc_start: 0.7055 (mm-40) cc_final: 0.6799 (tp-100) REVERT: C 417 LEU cc_start: 0.6557 (tp) cc_final: 0.6171 (tt) REVERT: D 4 MET cc_start: 0.6994 (mtm) cc_final: 0.6734 (mtm) REVERT: D 9 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6907 (mmtp) REVERT: D 27 GLN cc_start: 0.6449 (tm130) cc_final: 0.6153 (tm-30) REVERT: E 47 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: E 57 LEU cc_start: 0.8785 (mt) cc_final: 0.8391 (mt) REVERT: F 24 LYS cc_start: 0.6383 (tptt) cc_final: 0.6104 (mtpt) REVERT: F 37 GLN cc_start: 0.6591 (tp-100) cc_final: 0.6385 (tp40) REVERT: F 38 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6393 (tp40) REVERT: G 28 SER cc_start: 0.7907 (OUTLIER) cc_final: 0.7452 (p) REVERT: G 36 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7861 (m-70) REVERT: G 47 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7171 (tm-30) REVERT: I 109 MET cc_start: 0.0960 (mpp) cc_final: -0.0313 (ttp) outliers start: 107 outliers final: 54 residues processed: 273 average time/residue: 0.4414 time to fit residues: 135.5195 Evaluate side-chains 255 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 175 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 97 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS D 38 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.192686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130819 restraints weight = 79120.475| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 5.58 r_work: 0.3355 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16107 Z= 0.223 Angle : 0.756 9.453 21954 Z= 0.393 Chirality : 0.049 0.284 2318 Planarity : 0.006 0.066 2822 Dihedral : 7.527 57.374 2176 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.67 % Favored : 87.02 % Rotamer: Outliers : 7.10 % Allowed : 28.62 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.36 (0.18), residues: 1983 helix: 0.19 (0.37), residues: 201 sheet: -1.68 (0.24), residues: 428 loop : -1.91 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 249 TYR 0.043 0.002 TYR D 94 PHE 0.020 0.002 PHE A 326 TRP 0.012 0.002 TRP B 236 HIS 0.007 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00531 (16083) covalent geometry : angle 0.75241 (21906) SS BOND : bond 0.00379 ( 24) SS BOND : angle 1.79854 ( 48) hydrogen bonds : bond 0.04170 ( 427) hydrogen bonds : angle 6.30364 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 192 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8590 (tt) REVERT: A 174 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6933 (pttt) REVERT: A 253 CYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6441 (m) REVERT: B 78 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6719 (pt) REVERT: B 181 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8393 (mt) REVERT: B 206 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7538 (ptt90) REVERT: B 393 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8398 (t0) REVERT: C 58 MET cc_start: 0.8256 (tpp) cc_final: 0.7926 (mmt) REVERT: C 417 LEU cc_start: 0.6613 (tp) cc_final: 0.6300 (tt) REVERT: D 9 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6890 (mmtp) REVERT: D 11 MET cc_start: 0.5826 (OUTLIER) cc_final: 0.5555 (ttt) REVERT: D 27 GLN cc_start: 0.6562 (tm130) cc_final: 0.5653 (tm-30) REVERT: D 28 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7039 (p0) REVERT: E 47 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7142 (mm-30) REVERT: F 24 LYS cc_start: 0.6666 (tptt) cc_final: 0.6184 (mtpt) REVERT: F 37 GLN cc_start: 0.6716 (tp-100) cc_final: 0.6471 (tp40) REVERT: F 38 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6201 (tp40) REVERT: F 104 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6902 (pt) REVERT: G 28 SER cc_start: 0.7922 (OUTLIER) cc_final: 0.7445 (p) REVERT: G 36 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7973 (m-70) REVERT: G 47 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7231 (tm-30) outliers start: 111 outliers final: 56 residues processed: 268 average time/residue: 0.4342 time to fit residues: 131.5526 Evaluate side-chains 258 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 187 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 177 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS D 37 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.197132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.137835 restraints weight = 90522.347| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 6.84 r_work: 0.3399 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16107 Z= 0.136 Angle : 0.697 9.716 21954 Z= 0.359 Chirality : 0.047 0.241 2318 Planarity : 0.005 0.064 2822 Dihedral : 7.254 58.226 2175 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.82 % Favored : 88.87 % Rotamer: Outliers : 5.25 % Allowed : 29.95 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.17 (0.18), residues: 1983 helix: 0.73 (0.39), residues: 189 sheet: -1.71 (0.26), residues: 376 loop : -1.79 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 83 TYR 0.035 0.002 TYR D 94 PHE 0.015 0.001 PHE D 87 TRP 0.013 0.001 TRP B 236 HIS 0.005 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00309 (16083) covalent geometry : angle 0.69408 (21906) SS BOND : bond 0.00290 ( 24) SS BOND : angle 1.56747 ( 48) hydrogen bonds : bond 0.03597 ( 427) hydrogen bonds : angle 5.98785 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 202 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8702 (tt) REVERT: A 174 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.6976 (pttt) REVERT: A 253 CYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6387 (m) REVERT: B 20 ASN cc_start: 0.8662 (t0) cc_final: 0.8312 (t160) REVERT: B 78 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6789 (pt) REVERT: B 181 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 206 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7652 (ptt90) REVERT: B 393 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8424 (t0) REVERT: C 58 MET cc_start: 0.8232 (tpp) cc_final: 0.7899 (mmt) REVERT: C 222 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6808 (tp-100) REVERT: C 417 LEU cc_start: 0.6602 (tp) cc_final: 0.6303 (tt) REVERT: D 9 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6880 (mmtp) REVERT: D 11 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.5128 (ptp) REVERT: E 47 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: F 24 LYS cc_start: 0.6211 (tptt) cc_final: 0.5949 (mtpt) REVERT: F 27 GLN cc_start: 0.8366 (tp40) cc_final: 0.7635 (tp40) REVERT: F 36 TYR cc_start: 0.7280 (m-80) cc_final: 0.6834 (m-80) REVERT: F 38 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6282 (tp40) REVERT: G 36 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7739 (m-70) REVERT: G 47 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7114 (tm-30) REVERT: I 109 MET cc_start: 0.0702 (mpp) cc_final: -0.0365 (ttp) outliers start: 79 outliers final: 43 residues processed: 253 average time/residue: 0.4187 time to fit residues: 120.3453 Evaluate side-chains 242 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 39 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 0.0040 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 HIS ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.197528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139770 restraints weight = 78601.466| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 5.86 r_work: 0.3428 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16107 Z= 0.134 Angle : 0.689 10.527 21954 Z= 0.353 Chirality : 0.046 0.237 2318 Planarity : 0.005 0.067 2822 Dihedral : 6.679 58.295 2165 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.87 % Favored : 88.77 % Rotamer: Outliers : 5.25 % Allowed : 29.83 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.08 (0.18), residues: 1983 helix: 0.89 (0.39), residues: 189 sheet: -1.64 (0.25), residues: 394 loop : -1.72 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 83 TYR 0.034 0.002 TYR D 94 PHE 0.014 0.001 PHE A 326 TRP 0.012 0.001 TRP B 236 HIS 0.009 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00306 (16083) covalent geometry : angle 0.68573 (21906) SS BOND : bond 0.00217 ( 24) SS BOND : angle 1.66119 ( 48) hydrogen bonds : bond 0.03542 ( 427) hydrogen bonds : angle 5.80724 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 200 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8692 (tt) REVERT: A 174 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.6932 (pttt) REVERT: A 253 CYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6323 (m) REVERT: B 20 ASN cc_start: 0.8603 (t0) cc_final: 0.8276 (t160) REVERT: B 78 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6772 (pt) REVERT: B 181 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8381 (mt) REVERT: B 206 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7567 (ptt90) REVERT: C 58 MET cc_start: 0.8191 (tpp) cc_final: 0.7862 (mmt) REVERT: C 217 LYS cc_start: 0.8521 (mmpt) cc_final: 0.8315 (mmpt) REVERT: C 417 LEU cc_start: 0.6704 (tp) cc_final: 0.6422 (tt) REVERT: D 62 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.4825 (p90) REVERT: E 39 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6914 (ptt180) REVERT: E 47 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: E 57 LEU cc_start: 0.8850 (mt) cc_final: 0.8527 (mt) REVERT: E 105 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7871 (t0) REVERT: E 109 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.4911 (mpt) REVERT: F 24 LYS cc_start: 0.6439 (tptt) cc_final: 0.5806 (ttmm) REVERT: F 27 GLN cc_start: 0.8296 (tp40) cc_final: 0.7568 (tp40) REVERT: F 36 TYR cc_start: 0.7516 (m-80) cc_final: 0.6947 (m-80) REVERT: F 37 GLN cc_start: 0.6567 (tp-100) cc_final: 0.6001 (tp40) REVERT: F 38 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6325 (tp40) REVERT: F 89 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.5938 (tt0) REVERT: G 28 SER cc_start: 0.7894 (OUTLIER) cc_final: 0.7481 (p) REVERT: G 36 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7786 (m-70) REVERT: G 47 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7099 (tm-30) REVERT: G 107 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6611 (m-80) REVERT: I 109 MET cc_start: 0.0690 (mpp) cc_final: -0.0433 (ttp) outliers start: 79 outliers final: 42 residues processed: 253 average time/residue: 0.4753 time to fit residues: 135.7614 Evaluate side-chains 246 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 107 TYR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 85 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 150 optimal weight: 0.0870 chunk 157 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 173 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.197380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.140031 restraints weight = 89819.701| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 6.69 r_work: 0.3421 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16107 Z= 0.127 Angle : 0.683 12.641 21954 Z= 0.350 Chirality : 0.046 0.234 2318 Planarity : 0.005 0.067 2822 Dihedral : 6.496 56.522 2162 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.41 % Favored : 89.23 % Rotamer: Outliers : 4.50 % Allowed : 30.06 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.18), residues: 1983 helix: 1.50 (0.40), residues: 174 sheet: -1.48 (0.27), residues: 372 loop : -1.71 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.032 0.002 TYR D 94 PHE 0.016 0.001 PHE D 87 TRP 0.012 0.001 TRP C 360 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00287 (16083) covalent geometry : angle 0.68054 (21906) SS BOND : bond 0.00155 ( 24) SS BOND : angle 1.42442 ( 48) hydrogen bonds : bond 0.03436 ( 427) hydrogen bonds : angle 5.63367 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 199 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6893 (pttt) REVERT: A 253 CYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6033 (m) REVERT: B 20 ASN cc_start: 0.8652 (t0) cc_final: 0.8332 (t160) REVERT: B 69 ASP cc_start: 0.3736 (OUTLIER) cc_final: 0.3512 (p0) REVERT: B 181 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8332 (mt) REVERT: B 206 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7599 (ptt90) REVERT: C 58 MET cc_start: 0.8126 (tpp) cc_final: 0.7804 (mmt) REVERT: C 217 LYS cc_start: 0.8438 (mmpt) cc_final: 0.8151 (tppp) REVERT: C 417 LEU cc_start: 0.6374 (tp) cc_final: 0.6073 (tt) REVERT: D 27 GLN cc_start: 0.6053 (tm-30) cc_final: 0.5728 (tm130) REVERT: D 28 ASP cc_start: 0.7355 (t70) cc_final: 0.6922 (p0) REVERT: D 62 PHE cc_start: 0.5403 (OUTLIER) cc_final: 0.4483 (p90) REVERT: E 39 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6938 (ptt180) REVERT: E 47 GLU cc_start: 0.7676 (tp30) cc_final: 0.7006 (mm-30) REVERT: E 57 LEU cc_start: 0.8867 (mt) cc_final: 0.8529 (mt) REVERT: E 105 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7645 (t0) REVERT: F 24 LYS cc_start: 0.6383 (tptt) cc_final: 0.5731 (ttmm) REVERT: F 36 TYR cc_start: 0.7395 (m-80) cc_final: 0.6674 (m-80) REVERT: F 38 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.6519 (tp40) REVERT: F 89 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6119 (tt0) REVERT: G 28 SER cc_start: 0.7770 (OUTLIER) cc_final: 0.7345 (p) REVERT: G 36 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7719 (m-70) REVERT: G 47 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7112 (tm-30) REVERT: G 107 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: I 109 MET cc_start: 0.0632 (mpp) cc_final: -0.0431 (ttp) outliers start: 66 outliers final: 37 residues processed: 246 average time/residue: 0.4841 time to fit residues: 133.7402 Evaluate side-chains 238 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 107 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 78 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 149 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN G 61 ASN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.191525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134210 restraints weight = 86788.976| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 6.25 r_work: 0.3350 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16107 Z= 0.249 Angle : 0.775 13.336 21954 Z= 0.400 Chirality : 0.050 0.290 2318 Planarity : 0.006 0.072 2822 Dihedral : 6.758 56.085 2161 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.36 % Favored : 87.27 % Rotamer: Outliers : 4.67 % Allowed : 30.24 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.12 (0.18), residues: 1983 helix: 1.16 (0.40), residues: 168 sheet: -1.52 (0.24), residues: 424 loop : -1.81 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 83 TYR 0.041 0.003 TYR D 94 PHE 0.020 0.002 PHE A 326 TRP 0.017 0.002 TRP B 72 HIS 0.008 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00598 (16083) covalent geometry : angle 0.77118 (21906) SS BOND : bond 0.00358 ( 24) SS BOND : angle 1.91026 ( 48) hydrogen bonds : bond 0.04286 ( 427) hydrogen bonds : angle 6.01311 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 52 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8630 (tt) REVERT: A 174 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.6917 (pttt) REVERT: B 181 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 206 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7430 (ptt90) REVERT: C 39 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7124 (p) REVERT: C 58 MET cc_start: 0.8251 (tpp) cc_final: 0.7891 (mmt) REVERT: D 28 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7119 (p0) REVERT: D 62 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.4655 (p90) REVERT: E 39 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7137 (ptt180) REVERT: E 47 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: E 54 TYR cc_start: 0.7598 (p90) cc_final: 0.7379 (p90) REVERT: E 57 LEU cc_start: 0.8849 (mt) cc_final: 0.8471 (mt) REVERT: F 24 LYS cc_start: 0.6427 (tptt) cc_final: 0.6119 (mtpt) REVERT: F 89 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6414 (tt0) REVERT: G 47 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7150 (tm-30) REVERT: I 109 MET cc_start: 0.0714 (mpp) cc_final: -0.0407 (ttp) outliers start: 69 outliers final: 39 residues processed: 236 average time/residue: 0.5575 time to fit residues: 146.8225 Evaluate side-chains 235 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 85 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 65 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 170 optimal weight: 6.9990 chunk 110 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN B 180 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN G 38 ASN ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.197775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140764 restraints weight = 92392.691| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 6.98 r_work: 0.3413 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16107 Z= 0.127 Angle : 0.690 13.882 21954 Z= 0.354 Chirality : 0.046 0.218 2318 Planarity : 0.005 0.066 2822 Dihedral : 6.195 57.744 2156 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.20 % Favored : 89.39 % Rotamer: Outliers : 3.69 % Allowed : 31.22 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.03 (0.18), residues: 1983 helix: 0.88 (0.39), residues: 189 sheet: -1.75 (0.26), residues: 388 loop : -1.63 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 249 TYR 0.030 0.002 TYR D 94 PHE 0.013 0.001 PHE A 326 TRP 0.018 0.001 TRP C 357 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00285 (16083) covalent geometry : angle 0.68767 (21906) SS BOND : bond 0.00327 ( 24) SS BOND : angle 1.46391 ( 48) hydrogen bonds : bond 0.03464 ( 427) hydrogen bonds : angle 5.61592 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 150 ASN cc_start: 0.8633 (m-40) cc_final: 0.7955 (t0) REVERT: A 174 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6943 (pttt) REVERT: B 20 ASN cc_start: 0.8626 (t0) cc_final: 0.8258 (t160) REVERT: B 206 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7596 (ptt90) REVERT: C 39 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6971 (p) REVERT: C 58 MET cc_start: 0.8147 (tpp) cc_final: 0.7823 (mmt) REVERT: C 191 GLU cc_start: 0.6825 (tp30) cc_final: 0.6419 (mp0) REVERT: C 217 LYS cc_start: 0.8613 (mppt) cc_final: 0.7964 (tppp) REVERT: C 417 LEU cc_start: 0.6547 (tp) cc_final: 0.6313 (tt) REVERT: D 27 GLN cc_start: 0.6172 (tm-30) cc_final: 0.5848 (tm130) REVERT: D 28 ASP cc_start: 0.7648 (t70) cc_final: 0.7284 (p0) REVERT: D 62 PHE cc_start: 0.5518 (OUTLIER) cc_final: 0.4533 (p90) REVERT: E 39 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7000 (ptt180) REVERT: E 47 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: E 57 LEU cc_start: 0.8856 (mt) cc_final: 0.8549 (mt) REVERT: F 24 LYS cc_start: 0.6456 (tptt) cc_final: 0.5774 (ttmm) REVERT: F 36 TYR cc_start: 0.7690 (m-80) cc_final: 0.7252 (m-80) REVERT: G 28 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7447 (p) REVERT: G 47 GLU cc_start: 0.7616 (tm-30) cc_final: 0.6885 (tm-30) REVERT: G 49 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6509 (pmm) REVERT: I 109 MET cc_start: 0.0602 (mpp) cc_final: -0.0514 (ttp) outliers start: 52 outliers final: 28 residues processed: 231 average time/residue: 0.4952 time to fit residues: 128.6889 Evaluate side-chains 227 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain I residue 39 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 157 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 178 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.195892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.134946 restraints weight = 102592.237| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 6.58 r_work: 0.3404 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16107 Z= 0.146 Angle : 0.702 15.110 21954 Z= 0.359 Chirality : 0.047 0.241 2318 Planarity : 0.005 0.070 2822 Dihedral : 6.113 58.788 2155 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.82 % Favored : 88.77 % Rotamer: Outliers : 3.40 % Allowed : 31.56 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.18), residues: 1983 helix: 1.42 (0.40), residues: 174 sheet: -1.55 (0.25), residues: 418 loop : -1.62 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.032 0.002 TYR D 94 PHE 0.015 0.001 PHE A 326 TRP 0.015 0.001 TRP C 357 HIS 0.004 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00339 (16083) covalent geometry : angle 0.69963 (21906) SS BOND : bond 0.00217 ( 24) SS BOND : angle 1.36460 ( 48) hydrogen bonds : bond 0.03652 ( 427) hydrogen bonds : angle 5.61591 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8141 (tpt) REVERT: A 150 ASN cc_start: 0.8616 (m-40) cc_final: 0.7993 (t0) REVERT: A 174 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6897 (pttt) REVERT: B 20 ASN cc_start: 0.8624 (t0) cc_final: 0.8249 (t160) REVERT: B 206 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7544 (ptt90) REVERT: C 39 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.7073 (p) REVERT: C 58 MET cc_start: 0.8226 (tpp) cc_final: 0.7973 (mmt) REVERT: C 217 LYS cc_start: 0.8616 (mppt) cc_final: 0.7930 (tppp) REVERT: C 417 LEU cc_start: 0.6679 (tp) cc_final: 0.6411 (tt) REVERT: D 27 GLN cc_start: 0.6209 (tm-30) cc_final: 0.5883 (tm130) REVERT: D 28 ASP cc_start: 0.7641 (t70) cc_final: 0.7298 (p0) REVERT: D 62 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.4440 (p90) REVERT: E 39 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7143 (ptt180) REVERT: E 47 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: E 57 LEU cc_start: 0.8913 (mt) cc_final: 0.8613 (mt) REVERT: F 24 LYS cc_start: 0.6530 (tptt) cc_final: 0.5862 (ttmm) REVERT: G 28 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7605 (p) REVERT: G 47 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7120 (tm-30) REVERT: G 49 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6635 (pmm) outliers start: 47 outliers final: 30 residues processed: 216 average time/residue: 0.4799 time to fit residues: 117.3074 Evaluate side-chains 229 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 106 TYR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain I residue 39 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 102 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 106 optimal weight: 0.0170 chunk 173 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.195628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139473 restraints weight = 92121.828| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 6.81 r_work: 0.3408 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16107 Z= 0.180 Angle : 0.720 13.828 21954 Z= 0.371 Chirality : 0.048 0.242 2318 Planarity : 0.006 0.071 2822 Dihedral : 6.194 59.801 2155 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.28 % Favored : 88.46 % Rotamer: Outliers : 2.89 % Allowed : 32.43 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.18), residues: 1983 helix: 1.31 (0.40), residues: 174 sheet: -1.49 (0.25), residues: 406 loop : -1.69 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 83 TYR 0.034 0.002 TYR D 94 PHE 0.016 0.002 PHE A 326 TRP 0.017 0.002 TRP C 357 HIS 0.006 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00425 (16083) covalent geometry : angle 0.71792 (21906) SS BOND : bond 0.00254 ( 24) SS BOND : angle 1.47375 ( 48) hydrogen bonds : bond 0.03811 ( 427) hydrogen bonds : angle 5.68090 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6227.34 seconds wall clock time: 106 minutes 41.79 seconds (6401.79 seconds total)