Starting phenix.real_space_refine on Thu Feb 5 08:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0p_64667/02_2026/9v0p_64667.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0p_64667/02_2026/9v0p_64667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v0p_64667/02_2026/9v0p_64667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0p_64667/02_2026/9v0p_64667.map" model { file = "/net/cci-nas-00/data/ceres_data/9v0p_64667/02_2026/9v0p_64667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0p_64667/02_2026/9v0p_64667.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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 96 5.16 5 C 10005 2.51 5 N 2658 2.21 5 O 3126 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: 15885 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 860 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "A" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Chain: "D" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "F" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 860 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "G" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 860 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "C" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Time building chain proxies: 3.07, per 1000 atoms: 0.19 Number of scatterers: 15885 At special positions: 0 Unit cell: (116.63, 115.56, 157.29, 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 96 16.00 O 3126 8.00 N 2658 7.00 C 10005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.45 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.04 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.04 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.49 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.04 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.04 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.33 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.04 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.04 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " 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: 1.07 Conformation dependent library (CDL) restraints added in 513.1 milliseconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3828 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 32 sheets defined 19.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 73 through 97 removed outlier: 3.530A pdb=" N MET A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.756A pdb=" N GLN A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 217 through 240 removed outlier: 3.797A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.724A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 492 through 513 Processing helix chain 'B' and resid 73 through 97 removed outlier: 3.589A pdb=" N MET B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.515A pdb=" N GLN B 202 " --> pdb=" O TYR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.777A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.746A pdb=" N LYS B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 492 through 513 Processing helix chain 'C' and resid 73 through 97 Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.698A pdb=" N GLN C 202 " --> pdb=" O TYR C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.549A pdb=" N ASN C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 240 removed outlier: 3.758A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.623A pdb=" N LYS C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 276 " --> pdb=" O LYS C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 492 through 513 Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.620A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 98 through 103 Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.592A pdb=" N ALA L 19 " --> pdb=" O ILE L 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 50 through 53 removed outlier: 6.573A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.738A pdb=" N LEU A 316 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 340 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS A 343 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 351 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 47 through 51 removed outlier: 5.585A pdb=" N THR A 50 " --> pdb=" O TYR A 306 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N TYR A 306 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 176 through 179 removed outlier: 3.890A pdb=" N ALA A 177 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 189 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 179 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 187 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS A 290 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 287 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 244 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AB1, first strand: chain 'A' and resid 422 through 425 removed outlier: 4.144A pdb=" N THR A 449 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.599A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AB4, first strand: chain 'D' and resid 98 through 103 Processing sheet with id=AB5, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.587A pdb=" N ALA F 19 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 58 through 59 removed outlier: 3.542A pdb=" N HIS F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR F 54 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP F 40 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR F 54 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU F 38 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 33 removed outlier: 3.768A pdb=" N LEU B 316 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 340 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS B 343 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 351 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 51 removed outlier: 5.605A pdb=" N THR B 50 " --> pdb=" O TYR B 306 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N TYR B 306 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 176 through 179 removed outlier: 3.884A pdb=" N ALA B 177 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 189 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 179 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 187 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 290 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 287 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 244 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.645A pdb=" N LEU B 334 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC3, first strand: chain 'B' and resid 422 through 425 removed outlier: 4.112A pdb=" N THR B 449 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.622A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 17 through 23 Processing sheet with id=AC6, first strand: chain 'E' and resid 98 through 103 Processing sheet with id=AC7, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.599A pdb=" N ALA G 19 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 58 through 59 removed outlier: 3.554A pdb=" N HIS G 58 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR G 54 " --> pdb=" O HIS G 58 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP G 40 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR G 54 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU G 38 " --> pdb=" O TYR G 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 29 through 33 removed outlier: 3.751A pdb=" N LEU C 316 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY C 340 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS C 343 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 351 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 47 through 51 removed outlier: 5.612A pdb=" N THR C 50 " --> pdb=" O TYR C 306 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR C 306 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 176 through 179 removed outlier: 3.952A pdb=" N ALA C 177 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 189 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 179 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 187 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS C 290 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 287 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 244 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.662A pdb=" N LEU C 334 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AD5, first strand: chain 'C' and resid 422 through 425 removed outlier: 4.165A pdb=" N THR C 449 " --> pdb=" O SER C 425 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1548 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: 2.29 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5139 1.35 - 1.47: 3691 1.47 - 1.58: 7196 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 16158 Sorted by residual: bond pdb=" CA VAL H 5 " pdb=" CB VAL H 5 " ideal model delta sigma weight residual 1.532 1.547 -0.015 1.08e-02 8.57e+03 1.86e+00 bond pdb=" N ILE A 386 " pdb=" CA ILE A 386 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.25e-02 6.40e+03 1.54e+00 bond pdb=" N ILE B 386 " pdb=" CA ILE B 386 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.31e+00 bond pdb=" N ILE C 386 " pdb=" CA ILE C 386 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.23e+00 bond pdb=" CB MET A 396 " pdb=" CG MET A 396 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 ... (remaining 16153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 21409 1.77 - 3.54: 433 3.54 - 5.30: 52 5.30 - 7.07: 9 7.07 - 8.84: 3 Bond angle restraints: 21906 Sorted by residual: angle pdb=" N VAL H 5 " pdb=" CA VAL H 5 " pdb=" C VAL H 5 " ideal model delta sigma weight residual 106.42 110.81 -4.39 1.51e+00 4.39e-01 8.43e+00 angle pdb=" CB MET A 396 " pdb=" CG MET A 396 " pdb=" SD MET A 396 " ideal model delta sigma weight residual 112.70 120.62 -7.92 3.00e+00 1.11e-01 6.98e+00 angle pdb=" C GLN L 98 " pdb=" N THR L 99 " pdb=" CA THR L 99 " ideal model delta sigma weight residual 121.80 115.76 6.04 2.44e+00 1.68e-01 6.12e+00 angle pdb=" N CYS B 290 " pdb=" CA CYS B 290 " pdb=" C CYS B 290 " ideal model delta sigma weight residual 109.65 113.46 -3.81 1.56e+00 4.11e-01 5.97e+00 angle pdb=" C TYR C 342 " pdb=" N CYS C 343 " pdb=" CA CYS C 343 " ideal model delta sigma weight residual 121.91 116.96 4.95 2.03e+00 2.43e-01 5.96e+00 ... (remaining 21901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8850 17.94 - 35.88: 803 35.88 - 53.82: 168 53.82 - 71.76: 31 71.76 - 89.69: 9 Dihedral angle restraints: 9861 sinusoidal: 3906 harmonic: 5955 Sorted by residual: dihedral pdb=" CB CYS C 155 " pdb=" SG CYS C 155 " pdb=" SG CYS C 290 " pdb=" CB CYS C 290 " ideal model delta sinusoidal sigma weight residual -86.00 -18.09 -67.91 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CB CYS B 155 " pdb=" SG CYS B 155 " pdb=" SG CYS B 290 " pdb=" CB CYS B 290 " ideal model delta sinusoidal sigma weight residual -86.00 -19.11 -66.89 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS A 155 " pdb=" SG CYS A 155 " pdb=" SG CYS A 290 " pdb=" CB CYS A 290 " ideal model delta sinusoidal sigma weight residual -86.00 -23.72 -62.28 1 1.00e+01 1.00e-02 5.13e+01 ... (remaining 9858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1931 0.042 - 0.085: 442 0.085 - 0.127: 175 0.127 - 0.169: 14 0.169 - 0.212: 3 Chirality restraints: 2565 Sorted by residual: chirality pdb=" CB ILE B 292 " pdb=" CA ILE B 292 " pdb=" CG1 ILE B 292 " pdb=" CG2 ILE B 292 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE A 292 " pdb=" CA ILE A 292 " pdb=" CG1 ILE A 292 " pdb=" CG2 ILE A 292 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CB ILE C 292 " pdb=" CA ILE C 292 " pdb=" CG1 ILE C 292 " pdb=" CG2 ILE C 292 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 2562 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 386 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C ILE A 386 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 386 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 387 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 386 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C ILE C 386 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE C 386 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE C 387 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 14 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO G 15 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO G 15 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 15 " -0.026 5.00e-02 4.00e+02 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1186 2.74 - 3.28: 15033 3.28 - 3.82: 23391 3.82 - 4.36: 25959 4.36 - 4.90: 47018 Nonbonded interactions: 112587 Sorted by model distance: nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 2.208 3.040 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 2.210 3.040 nonbonded pdb=" O SER F 57 " pdb=" OG SER F 57 " model vdw 2.280 3.040 nonbonded pdb=" O SER G 57 " pdb=" OG SER G 57 " model vdw 2.282 3.040 ... (remaining 112582 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.990 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.006 0.455 16188 Z= 0.295 Angle : 0.692 30.224 21966 Z= 0.356 Chirality : 0.043 0.212 2565 Planarity : 0.004 0.046 2784 Dihedral : 13.974 89.694 5943 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.21 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.38 (0.19), residues: 2031 helix: 1.66 (0.28), residues: 393 sheet: -0.06 (0.23), residues: 582 loop : -2.57 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.008 0.001 TYR H 99 PHE 0.012 0.001 PHE C 483 TRP 0.029 0.002 TRP H 47 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00215 (16158) covalent geometry : angle 0.59083 (21906) SS BOND : bond 0.12600 ( 30) SS BOND : angle 6.91947 ( 60) hydrogen bonds : bond 0.09668 ( 575) hydrogen bonds : angle 5.09572 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8147 (mp10) cc_final: 0.7763 (mp10) REVERT: H 64 PHE cc_start: 0.7757 (m-80) cc_final: 0.7538 (m-10) REVERT: A 49 ARG cc_start: 0.7645 (tmm-80) cc_final: 0.6984 (tmm-80) REVERT: A 264 MET cc_start: 0.8021 (ttp) cc_final: 0.7803 (ttm) REVERT: A 368 ASP cc_start: 0.8315 (t0) cc_final: 0.7900 (t0) REVERT: A 388 ASN cc_start: 0.7417 (t0) cc_final: 0.6554 (p0) REVERT: D 81 ILE cc_start: 0.8232 (pt) cc_final: 0.7943 (tt) REVERT: B 235 ARG cc_start: 0.8113 (tmm-80) cc_final: 0.7868 (tmm-80) REVERT: B 274 MET cc_start: 0.8803 (ttm) cc_final: 0.8598 (ttp) REVERT: B 388 ASN cc_start: 0.7318 (t0) cc_final: 0.6600 (p0) REVERT: E 81 ILE cc_start: 0.8626 (pt) cc_final: 0.8222 (tt) REVERT: C 49 ARG cc_start: 0.7464 (tmm-80) cc_final: 0.6980 (tmm-80) REVERT: C 302 GLN cc_start: 0.7639 (tt0) cc_final: 0.7081 (mt0) REVERT: C 388 ASN cc_start: 0.7466 (t0) cc_final: 0.6851 (p0) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1234 time to fit residues: 67.5958 Evaluate side-chains 202 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS A 279 GLN A 302 GLN A 345 ASN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 277 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 279 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108636 restraints weight = 23056.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112192 restraints weight = 16854.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113083 restraints weight = 12138.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114653 restraints weight = 9419.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114841 restraints weight = 7971.632| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16188 Z= 0.222 Angle : 0.696 13.042 21966 Z= 0.363 Chirality : 0.046 0.204 2565 Planarity : 0.005 0.050 2784 Dihedral : 5.068 38.438 2205 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.77 % Favored : 88.08 % Rotamer: Outliers : 2.95 % Allowed : 12.62 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.70 (0.19), residues: 2031 helix: 1.51 (0.28), residues: 399 sheet: -0.65 (0.22), residues: 597 loop : -2.62 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 72 TYR 0.018 0.002 TYR H 99 PHE 0.022 0.002 PHE A 366 TRP 0.019 0.002 TRP H 47 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00526 (16158) covalent geometry : angle 0.68933 (21906) SS BOND : bond 0.00464 ( 30) SS BOND : angle 1.99416 ( 60) hydrogen bonds : bond 0.05026 ( 575) hydrogen bonds : angle 5.00040 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8387 (mp10) cc_final: 0.7423 (mp10) REVERT: H 90 ASP cc_start: 0.7341 (m-30) cc_final: 0.7085 (m-30) REVERT: A 388 ASN cc_start: 0.7733 (t0) cc_final: 0.7015 (p0) REVERT: D 69 THR cc_start: 0.6783 (m) cc_final: 0.6545 (p) REVERT: D 100 ASP cc_start: 0.8558 (t0) cc_final: 0.8345 (t0) REVERT: B 178 VAL cc_start: 0.8861 (t) cc_final: 0.8659 (p) REVERT: B 235 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.8057 (ttp80) REVERT: B 388 ASN cc_start: 0.7792 (t0) cc_final: 0.7098 (p0) REVERT: E 72 ARG cc_start: 0.7672 (ptm160) cc_final: 0.7285 (ttp80) REVERT: E 90 ASP cc_start: 0.7359 (m-30) cc_final: 0.6836 (m-30) REVERT: C 200 ASP cc_start: 0.8004 (t70) cc_final: 0.7216 (t0) REVERT: C 302 GLN cc_start: 0.8182 (tt0) cc_final: 0.7925 (tt0) REVERT: C 388 ASN cc_start: 0.7960 (t0) cc_final: 0.7235 (p0) outliers start: 54 outliers final: 47 residues processed: 232 average time/residue: 0.1130 time to fit residues: 40.2503 Evaluate side-chains 206 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 425 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 77 optimal weight: 0.0170 chunk 104 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN E 6 GLN ** C 345 ASN ** 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 = 0.3650 r_free = 0.3650 target = 0.138354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114188 restraints weight = 22891.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117423 restraints weight = 17227.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118957 restraints weight = 10915.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119518 restraints weight = 9251.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120018 restraints weight = 8434.416| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 16188 Z= 0.113 Angle : 0.585 11.039 21966 Z= 0.300 Chirality : 0.043 0.218 2565 Planarity : 0.004 0.041 2784 Dihedral : 4.600 36.314 2205 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.90 % Allowed : 15.30 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.36 (0.19), residues: 2031 helix: 1.38 (0.28), residues: 423 sheet: -0.33 (0.22), residues: 615 loop : -2.40 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.008 0.001 TYR H 99 PHE 0.016 0.001 PHE A 366 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00243 (16158) covalent geometry : angle 0.57920 (21906) SS BOND : bond 0.00399 ( 30) SS BOND : angle 1.68405 ( 60) hydrogen bonds : bond 0.03456 ( 575) hydrogen bonds : angle 4.39636 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8347 (mp10) cc_final: 0.7317 (mp10) REVERT: A 49 ARG cc_start: 0.7611 (tmm-80) cc_final: 0.7359 (tmm-80) REVERT: A 388 ASN cc_start: 0.7593 (t0) cc_final: 0.6901 (p0) REVERT: D 69 THR cc_start: 0.6834 (m) cc_final: 0.6624 (p) REVERT: F 17 GLU cc_start: 0.7383 (mp0) cc_final: 0.6966 (mp0) REVERT: B 178 VAL cc_start: 0.8815 (t) cc_final: 0.8608 (p) REVERT: B 235 ARG cc_start: 0.8301 (tmm-80) cc_final: 0.7919 (ttp80) REVERT: B 388 ASN cc_start: 0.7872 (t0) cc_final: 0.7085 (p0) REVERT: B 503 LEU cc_start: 0.8428 (mt) cc_final: 0.8184 (mt) REVERT: E 48 MET cc_start: 0.7685 (tmm) cc_final: 0.7272 (tmm) REVERT: E 72 ARG cc_start: 0.7658 (ptm160) cc_final: 0.7312 (ttp80) REVERT: E 81 ILE cc_start: 0.8308 (pt) cc_final: 0.8081 (tt) REVERT: C 302 GLN cc_start: 0.8038 (tt0) cc_final: 0.7371 (mt0) REVERT: C 388 ASN cc_start: 0.7907 (t0) cc_final: 0.7209 (p0) outliers start: 53 outliers final: 34 residues processed: 237 average time/residue: 0.1060 time to fit residues: 38.2974 Evaluate side-chains 209 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 393 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 71 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 167 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN E 6 GLN ** C 345 ASN ** 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 = 0.3656 r_free = 0.3656 target = 0.138786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113831 restraints weight = 22911.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116902 restraints weight = 17268.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117783 restraints weight = 13281.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119748 restraints weight = 10012.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119986 restraints weight = 8094.648| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16188 Z= 0.109 Angle : 0.574 10.213 21966 Z= 0.291 Chirality : 0.043 0.219 2565 Planarity : 0.004 0.040 2784 Dihedral : 4.447 35.631 2205 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.50 % Allowed : 17.21 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.28 (0.20), residues: 2031 helix: 1.47 (0.28), residues: 420 sheet: -0.21 (0.22), residues: 633 loop : -2.45 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 235 TYR 0.013 0.001 TYR H 99 PHE 0.011 0.001 PHE C 351 TRP 0.009 0.001 TRP H 36 HIS 0.011 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00234 (16158) covalent geometry : angle 0.56839 (21906) SS BOND : bond 0.00358 ( 30) SS BOND : angle 1.65068 ( 60) hydrogen bonds : bond 0.03267 ( 575) hydrogen bonds : angle 4.18753 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 187 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8314 (mp10) cc_final: 0.7320 (mp10) REVERT: L 52 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8006 (mt) REVERT: L 94 MET cc_start: 0.8453 (ttt) cc_final: 0.8055 (ttt) REVERT: A 49 ARG cc_start: 0.7300 (tmm-80) cc_final: 0.7066 (ttp80) REVERT: A 388 ASN cc_start: 0.7691 (t0) cc_final: 0.6995 (p0) REVERT: D 6 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8544 (tp-100) REVERT: D 69 THR cc_start: 0.6809 (m) cc_final: 0.6604 (p) REVERT: F 17 GLU cc_start: 0.7394 (mp0) cc_final: 0.6967 (mp0) REVERT: B 178 VAL cc_start: 0.8829 (t) cc_final: 0.8607 (p) REVERT: B 235 ARG cc_start: 0.8304 (tmm-80) cc_final: 0.7758 (ttp80) REVERT: B 388 ASN cc_start: 0.7918 (t0) cc_final: 0.7225 (p0) REVERT: E 48 MET cc_start: 0.7717 (tmm) cc_final: 0.7283 (tmm) REVERT: E 81 ILE cc_start: 0.8267 (pt) cc_final: 0.8048 (tt) REVERT: C 302 GLN cc_start: 0.8013 (tt0) cc_final: 0.7389 (mt0) REVERT: C 388 ASN cc_start: 0.7967 (t0) cc_final: 0.7255 (p0) outliers start: 64 outliers final: 40 residues processed: 229 average time/residue: 0.1112 time to fit residues: 38.3735 Evaluate side-chains 210 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 393 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 50 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN D 35 HIS B 279 GLN E 6 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109594 restraints weight = 22919.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110454 restraints weight = 22929.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111065 restraints weight = 20181.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111385 restraints weight = 17691.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112075 restraints weight = 15525.839| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 16188 Z= 0.242 Angle : 0.683 10.881 21966 Z= 0.355 Chirality : 0.046 0.238 2565 Planarity : 0.004 0.050 2784 Dihedral : 5.120 40.441 2205 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.06 % Favored : 87.79 % Rotamer: Outliers : 5.14 % Allowed : 16.94 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.66 (0.19), residues: 2031 helix: 1.32 (0.28), residues: 417 sheet: -0.20 (0.24), residues: 528 loop : -2.71 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.025 0.002 TYR H 99 PHE 0.015 0.001 PHE C 351 TRP 0.013 0.002 TRP H 36 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00575 (16158) covalent geometry : angle 0.67479 (21906) SS BOND : bond 0.00434 ( 30) SS BOND : angle 2.07030 ( 60) hydrogen bonds : bond 0.05103 ( 575) hydrogen bonds : angle 4.86482 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 166 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8448 (mp10) cc_final: 0.7771 (mp10) REVERT: L 82 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8038 (ttp80) REVERT: L 94 MET cc_start: 0.8442 (ttt) cc_final: 0.7993 (ttt) REVERT: A 388 ASN cc_start: 0.7772 (t0) cc_final: 0.7168 (p0) REVERT: D 81 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8163 (tt) REVERT: F 17 GLU cc_start: 0.7379 (mp0) cc_final: 0.6932 (mp0) REVERT: B 159 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: B 235 ARG cc_start: 0.8545 (tmm-80) cc_final: 0.8155 (ttp80) REVERT: B 289 MET cc_start: 0.8843 (tpp) cc_final: 0.7941 (tpp) REVERT: B 388 ASN cc_start: 0.7720 (t0) cc_final: 0.7275 (p0) REVERT: E 48 MET cc_start: 0.7569 (tmm) cc_final: 0.7039 (tmm) REVERT: E 51 ILE cc_start: 0.8593 (pt) cc_final: 0.8353 (pt) REVERT: E 81 ILE cc_start: 0.8607 (pt) cc_final: 0.8362 (tt) REVERT: C 388 ASN cc_start: 0.7840 (t0) cc_final: 0.7456 (p0) outliers start: 94 outliers final: 73 residues processed: 238 average time/residue: 0.1040 time to fit residues: 38.3781 Evaluate side-chains 226 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 151 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 482 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN C 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113115 restraints weight = 22515.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114173 restraints weight = 21639.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114725 restraints weight = 19129.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115164 restraints weight = 16103.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115643 restraints weight = 14393.441| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16188 Z= 0.137 Angle : 0.600 10.220 21966 Z= 0.307 Chirality : 0.044 0.253 2565 Planarity : 0.004 0.045 2784 Dihedral : 4.770 38.204 2205 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 3.93 % Allowed : 18.74 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.55 (0.19), residues: 2031 helix: 1.37 (0.28), residues: 420 sheet: -0.46 (0.23), residues: 603 loop : -2.56 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 235 TYR 0.017 0.001 TYR H 99 PHE 0.012 0.001 PHE C 351 TRP 0.010 0.001 TRP H 36 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00313 (16158) covalent geometry : angle 0.59412 (21906) SS BOND : bond 0.00344 ( 30) SS BOND : angle 1.73064 ( 60) hydrogen bonds : bond 0.03789 ( 575) hydrogen bonds : angle 4.46087 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 174 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8383 (mp10) cc_final: 0.7650 (mp10) REVERT: L 94 MET cc_start: 0.8471 (ttt) cc_final: 0.7958 (ttt) REVERT: A 235 ARG cc_start: 0.8230 (ttp80) cc_final: 0.8002 (tmm-80) REVERT: A 388 ASN cc_start: 0.7702 (t0) cc_final: 0.7072 (p0) REVERT: F 17 GLU cc_start: 0.7351 (mp0) cc_final: 0.6865 (mp0) REVERT: B 159 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7612 (t-90) REVERT: B 235 ARG cc_start: 0.8413 (tmm-80) cc_final: 0.8014 (ttp80) REVERT: B 289 MET cc_start: 0.8905 (tpp) cc_final: 0.7983 (tpp) REVERT: B 388 ASN cc_start: 0.7807 (t0) cc_final: 0.7378 (p0) REVERT: E 51 ILE cc_start: 0.8409 (pt) cc_final: 0.8131 (pt) REVERT: C 264 MET cc_start: 0.7997 (ttp) cc_final: 0.7759 (ttm) REVERT: C 289 MET cc_start: 0.8947 (tpp) cc_final: 0.7861 (tpp) REVERT: C 388 ASN cc_start: 0.7876 (t0) cc_final: 0.7480 (p0) REVERT: C 396 MET cc_start: 0.7898 (ttt) cc_final: 0.7658 (tmm) outliers start: 72 outliers final: 58 residues processed: 228 average time/residue: 0.1056 time to fit residues: 37.3782 Evaluate side-chains 229 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 482 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 chunk 109 optimal weight: 0.3980 chunk 134 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 83 optimal weight: 0.0020 chunk 161 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN D 6 GLN B 501 GLN C 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115701 restraints weight = 22799.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117452 restraints weight = 20776.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118337 restraints weight = 17845.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119224 restraints weight = 13087.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119466 restraints weight = 12425.531| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16188 Z= 0.101 Angle : 0.577 9.514 21966 Z= 0.291 Chirality : 0.043 0.264 2565 Planarity : 0.004 0.040 2784 Dihedral : 4.486 35.394 2205 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.39 % Allowed : 19.84 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.22 (0.20), residues: 2031 helix: 1.44 (0.28), residues: 420 sheet: 0.27 (0.24), residues: 564 loop : -2.53 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 235 TYR 0.016 0.001 TYR A 417 PHE 0.010 0.001 PHE C 351 TRP 0.014 0.001 TRP C 341 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00211 (16158) covalent geometry : angle 0.56913 (21906) SS BOND : bond 0.00390 ( 30) SS BOND : angle 1.93316 ( 60) hydrogen bonds : bond 0.02948 ( 575) hydrogen bonds : angle 4.05464 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8298 (mp10) cc_final: 0.7403 (mp10) REVERT: L 52 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7881 (mt) REVERT: L 94 MET cc_start: 0.8395 (ttt) cc_final: 0.7977 (ttt) REVERT: A 289 MET cc_start: 0.8683 (tpp) cc_final: 0.8049 (tpp) REVERT: A 388 ASN cc_start: 0.7751 (t0) cc_final: 0.7123 (p0) REVERT: A 426 ASN cc_start: 0.8987 (t0) cc_final: 0.8626 (t0) REVERT: F 17 GLU cc_start: 0.7344 (mp0) cc_final: 0.6739 (mp0) REVERT: B 159 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7372 (t-90) REVERT: B 235 ARG cc_start: 0.8275 (tmm-80) cc_final: 0.7831 (ttp80) REVERT: B 388 ASN cc_start: 0.7949 (t0) cc_final: 0.7277 (p0) REVERT: E 51 ILE cc_start: 0.8256 (pt) cc_final: 0.8002 (pt) REVERT: G 94 MET cc_start: 0.8441 (ttt) cc_final: 0.8181 (ttt) REVERT: C 224 GLN cc_start: 0.5819 (OUTLIER) cc_final: 0.5499 (mt0) REVERT: C 264 MET cc_start: 0.7905 (ttp) cc_final: 0.7641 (ttm) REVERT: C 289 MET cc_start: 0.8840 (tpp) cc_final: 0.8074 (tpp) REVERT: C 388 ASN cc_start: 0.7891 (t0) cc_final: 0.7301 (p0) outliers start: 62 outliers final: 47 residues processed: 231 average time/residue: 0.1040 time to fit residues: 37.5818 Evaluate side-chains 221 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 482 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 88 optimal weight: 0.0470 chunk 100 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 172 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 131 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN D 6 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN C 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117582 restraints weight = 22202.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.118989 restraints weight = 20233.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120263 restraints weight = 17470.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122304 restraints weight = 13460.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122351 restraints weight = 11829.781| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16188 Z= 0.102 Angle : 0.580 9.469 21966 Z= 0.291 Chirality : 0.043 0.276 2565 Planarity : 0.004 0.064 2784 Dihedral : 4.358 34.802 2205 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.55 % Allowed : 20.11 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.19 (0.20), residues: 2031 helix: 1.45 (0.28), residues: 420 sheet: -0.02 (0.23), residues: 603 loop : -2.38 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 507 TYR 0.015 0.001 TYR H 99 PHE 0.011 0.001 PHE C 351 TRP 0.008 0.001 TRP C 341 HIS 0.010 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00217 (16158) covalent geometry : angle 0.57268 (21906) SS BOND : bond 0.00323 ( 30) SS BOND : angle 1.80525 ( 60) hydrogen bonds : bond 0.02944 ( 575) hydrogen bonds : angle 3.97204 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8267 (mp10) cc_final: 0.7372 (mp10) REVERT: L 52 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7875 (mt) REVERT: L 94 MET cc_start: 0.8390 (ttt) cc_final: 0.8025 (ttt) REVERT: A 289 MET cc_start: 0.8635 (tpp) cc_final: 0.8134 (tpp) REVERT: A 388 ASN cc_start: 0.7761 (t0) cc_final: 0.7150 (p0) REVERT: A 426 ASN cc_start: 0.8975 (t0) cc_final: 0.8608 (t0) REVERT: D 43 GLN cc_start: 0.8208 (mp10) cc_final: 0.7851 (mp10) REVERT: B 159 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7283 (t-90) REVERT: B 235 ARG cc_start: 0.8273 (tmm-80) cc_final: 0.7808 (ttp80) REVERT: B 264 MET cc_start: 0.8049 (mmm) cc_final: 0.7738 (tpp) REVERT: B 388 ASN cc_start: 0.7854 (t0) cc_final: 0.7239 (p0) REVERT: E 43 GLN cc_start: 0.8215 (mp10) cc_final: 0.7796 (mp10) REVERT: E 51 ILE cc_start: 0.8239 (pt) cc_final: 0.7935 (pt) REVERT: G 94 MET cc_start: 0.8458 (ttt) cc_final: 0.8210 (ttt) REVERT: C 264 MET cc_start: 0.7890 (ttp) cc_final: 0.7651 (ttm) REVERT: C 289 MET cc_start: 0.8819 (tpp) cc_final: 0.8062 (tpp) REVERT: C 388 ASN cc_start: 0.7831 (t0) cc_final: 0.7302 (p0) outliers start: 65 outliers final: 48 residues processed: 236 average time/residue: 0.1054 time to fit residues: 39.1186 Evaluate side-chains 221 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 393 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 49 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 0.0770 chunk 78 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 170 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117325 restraints weight = 22146.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119055 restraints weight = 20088.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120113 restraints weight = 16036.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120597 restraints weight = 12485.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120849 restraints weight = 11554.576| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16188 Z= 0.108 Angle : 0.576 9.728 21966 Z= 0.290 Chirality : 0.044 0.283 2565 Planarity : 0.004 0.054 2784 Dihedral : 4.383 35.613 2205 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.39 % Allowed : 20.00 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.19 (0.20), residues: 2031 helix: 1.49 (0.28), residues: 420 sheet: -0.16 (0.22), residues: 633 loop : -2.35 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 507 TYR 0.015 0.001 TYR A 417 PHE 0.011 0.001 PHE C 351 TRP 0.024 0.001 TRP E 36 HIS 0.011 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00238 (16158) covalent geometry : angle 0.57042 (21906) SS BOND : bond 0.00329 ( 30) SS BOND : angle 1.68705 ( 60) hydrogen bonds : bond 0.03013 ( 575) hydrogen bonds : angle 4.00584 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8286 (mp10) cc_final: 0.7395 (mp10) REVERT: L 52 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7925 (mt) REVERT: L 94 MET cc_start: 0.8386 (ttt) cc_final: 0.8014 (ttt) REVERT: A 200 ASP cc_start: 0.7777 (t0) cc_final: 0.7421 (t0) REVERT: A 289 MET cc_start: 0.8682 (tpp) cc_final: 0.8152 (tpp) REVERT: A 388 ASN cc_start: 0.7785 (t0) cc_final: 0.7157 (p0) REVERT: A 426 ASN cc_start: 0.8976 (t0) cc_final: 0.8612 (t0) REVERT: D 43 GLN cc_start: 0.8215 (mp10) cc_final: 0.7856 (mp10) REVERT: B 159 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7314 (t-90) REVERT: B 235 ARG cc_start: 0.8298 (tmm-80) cc_final: 0.7833 (ttp80) REVERT: B 264 MET cc_start: 0.8064 (mmm) cc_final: 0.7705 (tpp) REVERT: B 289 MET cc_start: 0.8872 (tpp) cc_final: 0.8010 (tpp) REVERT: B 388 ASN cc_start: 0.7871 (t0) cc_final: 0.7242 (p0) REVERT: E 43 GLN cc_start: 0.8177 (mp10) cc_final: 0.7771 (mp10) REVERT: C 264 MET cc_start: 0.7903 (ttp) cc_final: 0.7666 (ttm) REVERT: C 289 MET cc_start: 0.8860 (tpp) cc_final: 0.8077 (tpp) REVERT: C 388 ASN cc_start: 0.7837 (t0) cc_final: 0.7301 (p0) outliers start: 62 outliers final: 54 residues processed: 229 average time/residue: 0.1113 time to fit residues: 39.6695 Evaluate side-chains 226 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 482 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 112 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116281 restraints weight = 22463.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117291 restraints weight = 22058.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118009 restraints weight = 19040.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118261 restraints weight = 15820.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119843 restraints weight = 14391.668| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16188 Z= 0.132 Angle : 0.605 9.749 21966 Z= 0.305 Chirality : 0.044 0.287 2565 Planarity : 0.004 0.050 2784 Dihedral : 4.485 35.998 2205 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 3.55 % Allowed : 19.73 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.22 (0.20), residues: 2031 helix: 1.49 (0.28), residues: 420 sheet: -0.14 (0.22), residues: 642 loop : -2.43 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 507 TYR 0.018 0.001 TYR H 99 PHE 0.013 0.001 PHE C 351 TRP 0.019 0.002 TRP E 36 HIS 0.011 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00304 (16158) covalent geometry : angle 0.59586 (21906) SS BOND : bond 0.00378 ( 30) SS BOND : angle 2.05893 ( 60) hydrogen bonds : bond 0.03386 ( 575) hydrogen bonds : angle 4.14845 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8320 (mp10) cc_final: 0.7481 (mp10) REVERT: L 52 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8022 (mt) REVERT: L 94 MET cc_start: 0.8430 (ttt) cc_final: 0.8027 (ttt) REVERT: A 289 MET cc_start: 0.8693 (tpp) cc_final: 0.8061 (tpp) REVERT: A 388 ASN cc_start: 0.7702 (t0) cc_final: 0.7069 (p0) REVERT: D 43 GLN cc_start: 0.8208 (mp10) cc_final: 0.7824 (mp10) REVERT: D 89 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 159 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7351 (t-90) REVERT: B 235 ARG cc_start: 0.8348 (tmm-80) cc_final: 0.7987 (ttp80) REVERT: B 289 MET cc_start: 0.8898 (tpp) cc_final: 0.8123 (tpp) REVERT: B 388 ASN cc_start: 0.7786 (t0) cc_final: 0.7310 (p0) REVERT: C 264 MET cc_start: 0.7883 (ttp) cc_final: 0.7620 (ttm) REVERT: C 289 MET cc_start: 0.8894 (tpp) cc_final: 0.8068 (tpp) REVERT: C 388 ASN cc_start: 0.7870 (t0) cc_final: 0.7486 (p0) outliers start: 65 outliers final: 56 residues processed: 225 average time/residue: 0.1063 time to fit residues: 37.6985 Evaluate side-chains 223 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 482 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 26 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** E 35 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 = 0.3602 r_free = 0.3602 target = 0.135740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116469 restraints weight = 22364.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117371 restraints weight = 21797.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117991 restraints weight = 19285.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118831 restraints weight = 16130.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118995 restraints weight = 14075.049| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16188 Z= 0.129 Angle : 0.603 9.846 21966 Z= 0.305 Chirality : 0.044 0.291 2565 Planarity : 0.004 0.074 2784 Dihedral : 4.537 36.520 2205 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.28 % Allowed : 19.95 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.23 (0.20), residues: 2031 helix: 1.48 (0.28), residues: 420 sheet: -0.17 (0.22), residues: 642 loop : -2.43 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 507 TYR 0.023 0.001 TYR H 99 PHE 0.030 0.001 PHE B 366 TRP 0.017 0.001 TRP E 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00296 (16158) covalent geometry : angle 0.59500 (21906) SS BOND : bond 0.00334 ( 30) SS BOND : angle 1.99171 ( 60) hydrogen bonds : bond 0.03370 ( 575) hydrogen bonds : angle 4.17317 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.17 seconds wall clock time: 34 minutes 58.37 seconds (2098.37 seconds total)