Starting phenix.real_space_refine on Thu Feb 5 08:19:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0q_64668/02_2026/9v0q_64668.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0q_64668/02_2026/9v0q_64668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v0q_64668/02_2026/9v0q_64668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0q_64668/02_2026/9v0q_64668.map" model { file = "/net/cci-nas-00/data/ceres_data/9v0q_64668/02_2026/9v0q_64668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0q_64668/02_2026/9v0q_64668.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 84 5.16 5 C 10008 2.51 5 N 2613 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s 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: 15855 Number of models: 1 Model: "" Number of chains: 9 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: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "C" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "F" 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: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "G" 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: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "I" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Time building chain proxies: 4.05, per 1000 atoms: 0.26 Number of scatterers: 15855 At special positions: 0 Unit cell: (128.464, 125.356, 145.04, 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 84 16.00 O 3150 8.00 N 2613 7.00 C 10008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.05 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.04 Simple disulfide: pdb=" SG CYS F 37 " - pdb=" SG CYS F 439 " distance=2.03 Simple disulfide: pdb=" SG CYS F 69 " - pdb=" SG CYS F 212 " distance=2.02 Simple disulfide: pdb=" SG CYS F 155 " - pdb=" SG CYS F 290 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 343 " distance=2.05 Simple disulfide: pdb=" SG CYS F 322 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 367 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 393 " distance=2.03 Simple disulfide: pdb=" SG CYS F 416 " - pdb=" SG CYS F 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 37 " - pdb=" SG CYS G 439 " distance=2.03 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 212 " distance=2.04 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 290 " distance=2.03 Simple disulfide: pdb=" SG CYS G 313 " - pdb=" SG CYS G 343 " distance=2.05 Simple disulfide: pdb=" SG CYS G 322 " - pdb=" SG CYS G 333 " distance=2.03 Simple disulfide: pdb=" SG CYS G 358 " - pdb=" SG CYS G 367 " distance=2.03 Simple disulfide: pdb=" SG CYS G 382 " - pdb=" SG CYS G 393 " distance=2.03 Simple disulfide: pdb=" SG CYS G 416 " - pdb=" SG CYS G 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 763.0 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: 3822 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 38 sheets defined 23.5% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 78 through 97 removed outlier: 3.732A 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 163 through 171 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 216 through 240 removed outlier: 4.360A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.583A pdb=" N GLU B 295 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 296' Processing helix chain 'B' and resid 379 through 385 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 513 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.813A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.706A pdb=" N GLU C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 97 removed outlier: 3.641A pdb=" N LEU F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 163 through 171 removed outlier: 3.557A pdb=" N LEU F 171 " --> pdb=" O ILE F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 202 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 217 through 240 removed outlier: 3.790A pdb=" N ILE F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ARG F 229 " --> pdb=" O GLN F 225 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU F 230 " --> pdb=" O LYS F 226 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 262 Processing helix chain 'F' and resid 267 through 276 Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 379 through 385 Processing helix chain 'F' and resid 445 through 447 No H-bonds generated for 'chain 'F' and resid 445 through 447' Processing helix chain 'F' and resid 473 through 477 Processing helix chain 'F' and resid 491 through 513 removed outlier: 3.508A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.828A pdb=" N ASP D 90 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR D 91 " --> pdb=" O ARG D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.754A pdb=" N GLU H 85 " --> pdb=" O PRO H 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 97 removed outlier: 3.652A pdb=" N MET G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 163 through 171 Processing helix chain 'G' and resid 195 through 202 Processing helix chain 'G' and resid 203 through 208 Processing helix chain 'G' and resid 217 through 240 removed outlier: 3.620A pdb=" N ILE G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU G 230 " --> pdb=" O LYS G 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 262 removed outlier: 3.618A pdb=" N ASN G 262 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 276 Processing helix chain 'G' and resid 277 through 284 Processing helix chain 'G' and resid 292 through 294 No H-bonds generated for 'chain 'G' and resid 292 through 294' Processing helix chain 'G' and resid 379 through 385 Processing helix chain 'G' and resid 445 through 447 No H-bonds generated for 'chain 'G' and resid 445 through 447' Processing helix chain 'G' and resid 473 through 477 Processing helix chain 'G' and resid 491 through 513 Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.822A pdb=" N GLU I 85 " --> pdb=" O PRO I 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.731A pdb=" N LYS B 315 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 40 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 31 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 176 through 177 removed outlier: 7.448A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA5, first strand: chain 'B' and resid 405 through 407 Processing sheet with id=AA6, first strand: chain 'B' and resid 430 through 433 removed outlier: 7.028A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 12 removed outlier: 7.809A pdb=" N PHE A 34 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU A 50 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.906A pdb=" N ARG A 98 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 115 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.700A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 73 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.520A pdb=" N GLN C 39 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU C 48 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.579A pdb=" N THR C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AB4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.148A pdb=" N GLU F 30 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 38 through 40 Processing sheet with id=AB6, first strand: chain 'F' and resid 176 through 177 removed outlier: 7.774A pdb=" N GLU F 60 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP F 194 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL F 300 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N MET F 289 " --> pdb=" O VAL F 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 333 through 336 Processing sheet with id=AB8, first strand: chain 'F' and resid 359 through 361 Processing sheet with id=AB9, first strand: chain 'F' and resid 405 through 407 Processing sheet with id=AC1, first strand: chain 'F' and resid 430 through 434 removed outlier: 4.994A pdb=" N ILE F 431 " --> pdb=" O ASN F 426 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASN F 426 " --> pdb=" O ILE F 431 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.021A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.589A pdb=" N ARG D 98 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL D 115 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 18 through 21 removed outlier: 3.559A pdb=" N LEU D 18 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 83 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 73 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.908A pdb=" N GLN H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU H 48 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.629A pdb=" N THR H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.716A pdb=" N ILE H 18 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.070A pdb=" N GLU G 30 " --> pdb=" O LEU G 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 38 through 40 Processing sheet with id=AD1, first strand: chain 'G' and resid 176 through 180 removed outlier: 3.584A pdb=" N VAL G 179 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 187 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLU G 60 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP G 194 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR G 244 " --> pdb=" O SER G 287 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 333 through 336 Processing sheet with id=AD3, first strand: chain 'G' and resid 359 through 361 Processing sheet with id=AD4, first strand: chain 'G' and resid 405 through 407 Processing sheet with id=AD5, first strand: chain 'G' and resid 430 through 434 removed outlier: 4.944A pdb=" N ILE G 431 " --> pdb=" O ASN G 426 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN G 426 " --> pdb=" O ILE G 431 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.123A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.816A pdb=" N ARG E 98 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL E 115 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 18 through 23 removed outlier: 3.638A pdb=" N LEU E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU E 83 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.302A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.675A pdb=" N THR I 98 " --> pdb=" O SER I 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.859A pdb=" N ILE I 18 " --> pdb=" O ILE I 77 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE I 77 " --> pdb=" O ILE I 18 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5088 1.35 - 1.47: 3864 1.47 - 1.59: 7070 1.59 - 1.72: 1 1.72 - 1.84: 108 Bond restraints: 16131 Sorted by residual: bond pdb=" N ILE F 214 " pdb=" CA ILE F 214 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.25e-02 6.40e+03 8.14e+00 bond pdb=" N ILE B 214 " pdb=" CA ILE B 214 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 bond pdb=" N THR G 219 " pdb=" CA THR G 219 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.17e-02 7.31e+03 7.17e+00 bond pdb=" N ASN F 216 " pdb=" CA ASN F 216 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.26e-02 6.30e+03 7.12e+00 bond pdb=" N ILE G 214 " pdb=" CA ILE G 214 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 ... (remaining 16126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 21429 2.13 - 4.25: 412 4.25 - 6.38: 34 6.38 - 8.51: 8 8.51 - 10.64: 5 Bond angle restraints: 21888 Sorted by residual: angle pdb=" C ASP G 73 " pdb=" CA ASP G 73 " pdb=" CB ASP G 73 " ideal model delta sigma weight residual 115.79 110.06 5.73 1.19e+00 7.06e-01 2.32e+01 angle pdb=" C ASP B 73 " pdb=" CA ASP B 73 " pdb=" CB ASP B 73 " ideal model delta sigma weight residual 115.89 110.14 5.75 1.32e+00 5.74e-01 1.90e+01 angle pdb=" C ASP F 73 " pdb=" CA ASP F 73 " pdb=" CB ASP F 73 " ideal model delta sigma weight residual 115.79 110.81 4.98 1.19e+00 7.06e-01 1.75e+01 angle pdb=" N ILE F 217 " pdb=" CA ILE F 217 " pdb=" C ILE F 217 " ideal model delta sigma weight residual 113.22 108.19 5.03 1.23e+00 6.61e-01 1.67e+01 angle pdb=" CA GLN F 210 " pdb=" C GLN F 210 " pdb=" O GLN F 210 " ideal model delta sigma weight residual 121.87 117.63 4.24 1.16e+00 7.43e-01 1.33e+01 ... (remaining 21883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8413 17.79 - 35.58: 1057 35.58 - 53.37: 231 53.37 - 71.16: 43 71.16 - 88.95: 9 Dihedral angle restraints: 9753 sinusoidal: 3789 harmonic: 5964 Sorted by residual: dihedral pdb=" CB CYS G 69 " pdb=" SG CYS G 69 " pdb=" SG CYS G 212 " pdb=" CB CYS G 212 " ideal model delta sinusoidal sigma weight residual 93.00 175.41 -82.41 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS F 382 " pdb=" SG CYS F 382 " pdb=" SG CYS F 393 " pdb=" CB CYS F 393 " ideal model delta sinusoidal sigma weight residual 93.00 164.07 -71.07 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 393 " pdb=" CB CYS B 393 " ideal model delta sinusoidal sigma weight residual 93.00 163.87 -70.87 1 1.00e+01 1.00e-02 6.45e+01 ... (remaining 9750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1814 0.040 - 0.080: 553 0.080 - 0.119: 172 0.119 - 0.159: 22 0.159 - 0.199: 7 Chirality restraints: 2568 Sorted by residual: chirality pdb=" CA ILE G 214 " pdb=" N ILE G 214 " pdb=" C ILE G 214 " pdb=" CB ILE G 214 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA ILE F 217 " pdb=" N ILE F 217 " pdb=" C ILE F 217 " pdb=" CB ILE F 217 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ILE F 214 " pdb=" N ILE F 214 " pdb=" C ILE F 214 " pdb=" CB ILE F 214 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 2565 not shown) Planarity restraints: 2766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 363 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ASN G 363 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN G 363 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG G 364 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 363 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" C ASN F 363 " -0.041 2.00e-02 2.50e+03 pdb=" O ASN F 363 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG F 364 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 38 " 0.025 2.00e-02 2.50e+03 1.47e-02 4.35e+00 pdb=" CG TYR C 38 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 38 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 38 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 38 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 38 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 38 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 38 " 0.010 2.00e-02 2.50e+03 ... (remaining 2763 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5638 2.85 - 3.36: 14731 3.36 - 3.88: 24841 3.88 - 4.39: 27408 4.39 - 4.90: 48098 Nonbonded interactions: 120716 Sorted by model distance: nonbonded pdb=" O ASN G 363 " pdb=" OD1 ASN G 363 " model vdw 2.340 3.040 nonbonded pdb=" O ASN F 363 " pdb=" OD1 ASN F 363 " model vdw 2.346 3.040 nonbonded pdb=" O ASN B 363 " pdb=" OD1 ASN B 363 " model vdw 2.440 3.040 nonbonded pdb=" O SER G 415 " pdb=" OG SER G 415 " model vdw 2.474 3.040 nonbonded pdb=" O GLN G 210 " pdb=" OG SER G 211 " model vdw 2.512 3.040 ... (remaining 120711 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.730 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.250 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.003 0.094 16161 Z= 0.187 Angle : 0.705 10.636 21948 Z= 0.403 Chirality : 0.043 0.199 2568 Planarity : 0.004 0.046 2766 Dihedral : 15.907 88.955 5841 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.87 % Allowed : 19.38 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.19), residues: 2031 helix: 0.09 (0.27), residues: 390 sheet: -0.79 (0.22), residues: 540 loop : -1.48 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 507 TYR 0.032 0.002 TYR C 38 PHE 0.019 0.002 PHE B 190 TRP 0.029 0.002 TRP E 36 HIS 0.005 0.002 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00346 (16131) covalent geometry : angle 0.70116 (21888) SS BOND : bond 0.00661 ( 30) SS BOND : angle 1.58267 ( 60) hydrogen bonds : bond 0.13054 ( 601) hydrogen bonds : angle 6.91590 ( 1650) *********************** 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 277 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: B 53 TYR cc_start: 0.7950 (t80) cc_final: 0.7385 (t80) REVERT: B 396 MET cc_start: 0.7633 (ppp) cc_final: 0.7242 (ppp) REVERT: A 98 ARG cc_start: 0.8169 (ttt-90) cc_final: 0.7936 (ttt-90) REVERT: A 113 MET cc_start: 0.8026 (mmm) cc_final: 0.7553 (mmm) REVERT: C 41 TYR cc_start: 0.5833 (m-10) cc_final: 0.5325 (m-10) REVERT: C 63 ARG cc_start: 0.7082 (mtm-85) cc_final: 0.6845 (mtm110) REVERT: C 100 LYS cc_start: 0.6446 (mmmm) cc_final: 0.6078 (mmtp) REVERT: F 216 ASN cc_start: 0.6520 (OUTLIER) cc_final: 0.5776 (m-40) REVERT: F 217 ILE cc_start: 0.8495 (tp) cc_final: 0.8213 (tp) REVERT: F 251 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7523 (mtm) REVERT: F 292 ILE cc_start: 0.8599 (tp) cc_final: 0.8373 (tp) REVERT: D 36 TRP cc_start: 0.8170 (m100) cc_final: 0.7086 (m100) REVERT: D 38 ARG cc_start: 0.6808 (ptt90) cc_final: 0.6514 (ptt180) REVERT: D 65 LYS cc_start: 0.7447 (tptp) cc_final: 0.6785 (ttpt) REVERT: D 113 MET cc_start: 0.7887 (mtt) cc_final: 0.7464 (mtt) REVERT: G 97 MET cc_start: 0.6282 (mmm) cc_final: 0.5879 (mmm) REVERT: G 148 ILE cc_start: 0.8568 (pt) cc_final: 0.8315 (pp) REVERT: G 176 LYS cc_start: 0.8450 (pttt) cc_final: 0.7971 (pttp) REVERT: G 279 GLN cc_start: 0.6997 (pm20) cc_final: 0.6621 (pm20) REVERT: G 462 GLN cc_start: 0.9019 (pp30) cc_final: 0.8545 (pt0) REVERT: E 39 GLN cc_start: 0.8663 (pt0) cc_final: 0.8238 (pt0) REVERT: E 65 LYS cc_start: 0.7683 (tptp) cc_final: 0.7113 (ttpt) REVERT: I 41 TYR cc_start: 0.5548 (m-10) cc_final: 0.5203 (m-10) outliers start: 34 outliers final: 26 residues processed: 259 average time/residue: 0.1426 time to fit residues: 54.1535 Evaluate side-chains 255 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain I residue 49 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN F 225 GLN ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN G 225 GLN ** G 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.202577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.160047 restraints weight = 21023.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.161810 restraints weight = 14784.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163042 restraints weight = 12108.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163973 restraints weight = 9071.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164179 restraints weight = 8160.520| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16161 Z= 0.219 Angle : 0.679 9.106 21948 Z= 0.357 Chirality : 0.044 0.173 2568 Planarity : 0.004 0.047 2766 Dihedral : 6.544 59.121 2248 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 5.33 % Allowed : 19.88 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.18), residues: 2031 helix: 0.18 (0.26), residues: 405 sheet: -0.79 (0.22), residues: 573 loop : -1.63 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 507 TYR 0.021 0.002 TYR C 38 PHE 0.018 0.002 PHE B 505 TRP 0.020 0.002 TRP E 36 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00527 (16131) covalent geometry : angle 0.67279 (21888) SS BOND : bond 0.00715 ( 30) SS BOND : angle 1.84031 ( 60) hydrogen bonds : bond 0.04215 ( 601) hydrogen bonds : angle 5.48900 ( 1650) *********************** 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 345 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 248 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: B 97 MET cc_start: 0.5964 (mmm) cc_final: 0.5529 (mmm) REVERT: B 148 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8225 (pp) REVERT: B 399 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6809 (mtpt) REVERT: A 65 LYS cc_start: 0.7635 (tptp) cc_final: 0.7095 (ttpt) REVERT: A 98 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7835 (ttt-90) REVERT: C 41 TYR cc_start: 0.6057 (m-10) cc_final: 0.5581 (m-10) REVERT: C 63 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6819 (mtm110) REVERT: C 100 LYS cc_start: 0.6781 (mmmm) cc_final: 0.6347 (mmtp) REVERT: F 93 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8309 (tt) REVERT: F 292 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8417 (tp) REVERT: F 507 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.6998 (ptp-170) REVERT: D 36 TRP cc_start: 0.8341 (m100) cc_final: 0.7477 (m100) REVERT: D 39 GLN cc_start: 0.8696 (pp30) cc_final: 0.8135 (pp30) REVERT: D 65 LYS cc_start: 0.7567 (tptp) cc_final: 0.7094 (ttpt) REVERT: D 113 MET cc_start: 0.8331 (mtt) cc_final: 0.8043 (mtt) REVERT: G 97 MET cc_start: 0.6233 (mmm) cc_final: 0.5659 (mmm) REVERT: G 176 LYS cc_start: 0.8616 (pttt) cc_final: 0.7748 (mptt) REVERT: G 279 GLN cc_start: 0.7175 (pm20) cc_final: 0.6841 (pm20) REVERT: E 18 LEU cc_start: 0.7534 (tp) cc_final: 0.6768 (pp) REVERT: E 19 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7071 (p) REVERT: E 39 GLN cc_start: 0.8772 (pt0) cc_final: 0.8539 (pt0) REVERT: E 65 LYS cc_start: 0.7845 (tptp) cc_final: 0.7422 (ttpt) REVERT: I 41 TYR cc_start: 0.5905 (m-10) cc_final: 0.5510 (m-10) outliers start: 97 outliers final: 52 residues processed: 315 average time/residue: 0.1326 time to fit residues: 62.5458 Evaluate side-chains 279 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 100 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 123 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN F 225 GLN F 437 ASN F 462 GLN D 82 HIS ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.206673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164162 restraints weight = 21201.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165976 restraints weight = 14432.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167308 restraints weight = 11715.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168194 restraints weight = 8634.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.168328 restraints weight = 7874.424| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16161 Z= 0.135 Angle : 0.596 7.337 21948 Z= 0.313 Chirality : 0.041 0.153 2568 Planarity : 0.004 0.047 2766 Dihedral : 5.691 58.915 2222 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.28 % Allowed : 22.24 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2031 helix: 0.50 (0.26), residues: 414 sheet: -0.75 (0.22), residues: 558 loop : -1.57 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 98 TYR 0.023 0.002 TYR C 38 PHE 0.013 0.001 PHE B 351 TRP 0.031 0.002 TRP E 36 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00324 (16131) covalent geometry : angle 0.58924 (21888) SS BOND : bond 0.00667 ( 30) SS BOND : angle 1.75025 ( 60) hydrogen bonds : bond 0.03525 ( 601) hydrogen bonds : angle 5.13155 ( 1650) *********************** 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 320 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 242 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8218 (mt) REVERT: B 97 MET cc_start: 0.5907 (mmm) cc_final: 0.5557 (mmm) REVERT: B 148 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8155 (pp) REVERT: B 171 LEU cc_start: 0.8311 (tp) cc_final: 0.7931 (tp) REVERT: B 396 MET cc_start: 0.7640 (ppp) cc_final: 0.7217 (ppp) REVERT: B 399 LYS cc_start: 0.7244 (mtpt) cc_final: 0.6771 (mtpt) REVERT: A 65 LYS cc_start: 0.7678 (tptp) cc_final: 0.7146 (ttpt) REVERT: A 98 ARG cc_start: 0.8152 (ttt-90) cc_final: 0.7837 (ttt-90) REVERT: A 113 MET cc_start: 0.8068 (mmm) cc_final: 0.7295 (mmm) REVERT: C 41 TYR cc_start: 0.5874 (m-10) cc_final: 0.5543 (m-10) REVERT: C 63 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6839 (mtm110) REVERT: C 100 LYS cc_start: 0.6754 (mmmm) cc_final: 0.6380 (mmtp) REVERT: F 93 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8430 (tt) REVERT: F 217 ILE cc_start: 0.8360 (tp) cc_final: 0.8102 (tp) REVERT: F 251 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7302 (mtm) REVERT: F 292 ILE cc_start: 0.8664 (tp) cc_final: 0.8426 (tp) REVERT: F 507 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6944 (ptp90) REVERT: D 39 GLN cc_start: 0.8665 (pp30) cc_final: 0.8108 (pp30) REVERT: D 65 LYS cc_start: 0.7557 (tptp) cc_final: 0.7076 (ttpt) REVERT: G 97 MET cc_start: 0.6039 (mmm) cc_final: 0.5517 (mmm) REVERT: G 176 LYS cc_start: 0.8515 (pttt) cc_final: 0.8058 (pttp) REVERT: G 279 GLN cc_start: 0.6994 (pm20) cc_final: 0.6731 (pm20) REVERT: G 462 GLN cc_start: 0.9082 (pp30) cc_final: 0.8619 (pt0) REVERT: E 18 LEU cc_start: 0.7516 (tp) cc_final: 0.6822 (pp) REVERT: E 19 THR cc_start: 0.7483 (m) cc_final: 0.6969 (p) REVERT: E 65 LYS cc_start: 0.7834 (tptp) cc_final: 0.7329 (ttpp) REVERT: I 41 TYR cc_start: 0.5881 (m-10) cc_final: 0.5521 (m-10) outliers start: 78 outliers final: 39 residues processed: 299 average time/residue: 0.1329 time to fit residues: 59.8795 Evaluate side-chains 273 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 127 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 153 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN F 277 ASN F 462 GLN G 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.206849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.163411 restraints weight = 21059.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164529 restraints weight = 15088.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166429 restraints weight = 11392.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.167677 restraints weight = 8651.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.168287 restraints weight = 7613.899| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16161 Z= 0.135 Angle : 0.589 7.157 21948 Z= 0.308 Chirality : 0.041 0.148 2568 Planarity : 0.004 0.046 2766 Dihedral : 5.596 56.478 2221 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.61 % Allowed : 23.01 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 2031 helix: 0.79 (0.27), residues: 396 sheet: -0.81 (0.21), residues: 582 loop : -1.59 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 63 TYR 0.025 0.002 TYR C 38 PHE 0.012 0.001 PHE G 351 TRP 0.033 0.002 TRP E 36 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00326 (16131) covalent geometry : angle 0.58304 (21888) SS BOND : bond 0.00637 ( 30) SS BOND : angle 1.64329 ( 60) hydrogen bonds : bond 0.03418 ( 601) hydrogen bonds : angle 4.96800 ( 1650) *********************** 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 326 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 242 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: B 97 MET cc_start: 0.5864 (mmm) cc_final: 0.5502 (mmm) REVERT: B 148 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8177 (pp) REVERT: B 171 LEU cc_start: 0.8351 (tp) cc_final: 0.7909 (tp) REVERT: B 310 ASP cc_start: 0.7769 (t70) cc_final: 0.7534 (t70) REVERT: B 396 MET cc_start: 0.7542 (ppp) cc_final: 0.7051 (ppp) REVERT: B 399 LYS cc_start: 0.7283 (mtpt) cc_final: 0.6842 (mtpt) REVERT: A 65 LYS cc_start: 0.7573 (tptp) cc_final: 0.7058 (ttpt) REVERT: A 98 ARG cc_start: 0.8161 (ttt-90) cc_final: 0.7818 (ttt-90) REVERT: A 113 MET cc_start: 0.8296 (mmm) cc_final: 0.7490 (mmm) REVERT: C 41 TYR cc_start: 0.5579 (m-10) cc_final: 0.5352 (m-10) REVERT: C 100 LYS cc_start: 0.6828 (mmmm) cc_final: 0.6488 (mmmm) REVERT: F 93 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8324 (tt) REVERT: F 217 ILE cc_start: 0.8309 (tp) cc_final: 0.8063 (tp) REVERT: F 251 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7227 (mtm) REVERT: F 396 MET cc_start: 0.7476 (ppp) cc_final: 0.6849 (ppp) REVERT: F 507 ARG cc_start: 0.7295 (ttp-110) cc_final: 0.6999 (ptp90) REVERT: D 39 GLN cc_start: 0.8625 (pp30) cc_final: 0.7942 (pp30) REVERT: D 65 LYS cc_start: 0.7491 (tptp) cc_final: 0.7038 (ttpt) REVERT: D 87 ARG cc_start: 0.7177 (ptt180) cc_final: 0.6393 (mmt90) REVERT: H 41 TYR cc_start: 0.5589 (m-10) cc_final: 0.5330 (m-10) REVERT: G 176 LYS cc_start: 0.8538 (pttt) cc_final: 0.8052 (pttp) REVERT: G 264 MET cc_start: 0.6298 (mtm) cc_final: 0.6052 (mmm) REVERT: G 279 GLN cc_start: 0.6978 (pm20) cc_final: 0.6751 (pm20) REVERT: G 339 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7517 (mtt180) REVERT: G 462 GLN cc_start: 0.9095 (pp30) cc_final: 0.8707 (pt0) REVERT: E 18 LEU cc_start: 0.7436 (tp) cc_final: 0.6803 (pp) REVERT: E 65 LYS cc_start: 0.7781 (tptp) cc_final: 0.7305 (ttpp) REVERT: I 41 TYR cc_start: 0.5761 (m-10) cc_final: 0.5505 (m-10) outliers start: 84 outliers final: 54 residues processed: 298 average time/residue: 0.1303 time to fit residues: 58.5206 Evaluate side-chains 290 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 233 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 25 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 173 optimal weight: 0.1980 chunk 15 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.207527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164749 restraints weight = 20972.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167337 restraints weight = 14273.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.169004 restraints weight = 10343.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169319 restraints weight = 7594.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.169922 restraints weight = 7255.213| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16161 Z= 0.128 Angle : 0.580 7.071 21948 Z= 0.304 Chirality : 0.041 0.148 2568 Planarity : 0.003 0.045 2766 Dihedral : 5.453 56.137 2220 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.78 % Allowed : 23.61 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 2031 helix: 0.93 (0.27), residues: 396 sheet: -0.76 (0.22), residues: 543 loop : -1.55 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 63 TYR 0.027 0.002 TYR C 38 PHE 0.012 0.001 PHE B 351 TRP 0.035 0.002 TRP E 36 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00309 (16131) covalent geometry : angle 0.57449 (21888) SS BOND : bond 0.00627 ( 30) SS BOND : angle 1.56773 ( 60) hydrogen bonds : bond 0.03255 ( 601) hydrogen bonds : angle 4.87288 ( 1650) *********************** 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 335 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 248 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5949 (mmm) cc_final: 0.5578 (mmm) REVERT: B 148 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8164 (pp) REVERT: B 171 LEU cc_start: 0.8337 (tp) cc_final: 0.7865 (tp) REVERT: B 310 ASP cc_start: 0.7671 (t70) cc_final: 0.7420 (t70) REVERT: B 396 MET cc_start: 0.7499 (ppp) cc_final: 0.7050 (ppp) REVERT: B 399 LYS cc_start: 0.7333 (mtpt) cc_final: 0.6885 (mtpt) REVERT: A 38 ARG cc_start: 0.6803 (ptt180) cc_final: 0.6591 (ptt180) REVERT: A 65 LYS cc_start: 0.7590 (tptp) cc_final: 0.7177 (ttpt) REVERT: A 113 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7586 (mtt) REVERT: C 100 LYS cc_start: 0.6859 (mmmm) cc_final: 0.6516 (mmmm) REVERT: F 93 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8353 (tt) REVERT: F 217 ILE cc_start: 0.8251 (tp) cc_final: 0.8022 (tp) REVERT: F 251 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7289 (mtm) REVERT: F 310 ASP cc_start: 0.7718 (t70) cc_final: 0.7392 (t70) REVERT: F 396 MET cc_start: 0.7554 (ppp) cc_final: 0.6891 (ppp) REVERT: F 441 TYR cc_start: 0.8717 (t80) cc_final: 0.8348 (t80) REVERT: D 39 GLN cc_start: 0.8640 (pp30) cc_final: 0.7955 (pp30) REVERT: D 65 LYS cc_start: 0.7541 (tptp) cc_final: 0.7131 (ttpt) REVERT: D 87 ARG cc_start: 0.7072 (ptt180) cc_final: 0.6365 (mmt90) REVERT: H 41 TYR cc_start: 0.5662 (m-10) cc_final: 0.5333 (m-10) REVERT: G 176 LYS cc_start: 0.8531 (pttt) cc_final: 0.8050 (pttp) REVERT: G 279 GLN cc_start: 0.6934 (pm20) cc_final: 0.6704 (pm20) REVERT: G 339 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7510 (mtt180) REVERT: E 18 LEU cc_start: 0.7503 (tp) cc_final: 0.6910 (pp) REVERT: E 65 LYS cc_start: 0.7828 (tptp) cc_final: 0.7366 (ttpp) REVERT: I 41 TYR cc_start: 0.5781 (m-10) cc_final: 0.5570 (m-10) outliers start: 87 outliers final: 58 residues processed: 305 average time/residue: 0.1280 time to fit residues: 58.7315 Evaluate side-chains 296 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 126 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN ** B 361 GLN ** 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 = 0.4265 r_free = 0.4265 target = 0.201568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158796 restraints weight = 21041.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160454 restraints weight = 14338.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.161757 restraints weight = 12070.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162435 restraints weight = 8825.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.162771 restraints weight = 8036.742| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16161 Z= 0.203 Angle : 0.648 9.002 21948 Z= 0.340 Chirality : 0.043 0.172 2568 Planarity : 0.004 0.044 2766 Dihedral : 5.647 58.525 2218 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 5.88 % Allowed : 23.12 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2031 helix: 0.88 (0.27), residues: 390 sheet: -0.86 (0.22), residues: 543 loop : -1.69 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 63 TYR 0.031 0.002 TYR C 38 PHE 0.012 0.001 PHE B 237 TRP 0.034 0.002 TRP E 36 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00497 (16131) covalent geometry : angle 0.64097 (21888) SS BOND : bond 0.00778 ( 30) SS BOND : angle 1.91933 ( 60) hydrogen bonds : bond 0.03823 ( 601) hydrogen bonds : angle 5.10856 ( 1650) *********************** 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 353 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 246 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: B 148 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8301 (pp) REVERT: B 171 LEU cc_start: 0.8489 (tp) cc_final: 0.8078 (tp) REVERT: B 310 ASP cc_start: 0.7987 (t70) cc_final: 0.7783 (t70) REVERT: B 396 MET cc_start: 0.7579 (ppp) cc_final: 0.7205 (ppp) REVERT: B 399 LYS cc_start: 0.7472 (mtpt) cc_final: 0.7028 (mtpt) REVERT: A 36 TRP cc_start: 0.8894 (m100) cc_final: 0.8592 (m-10) REVERT: A 38 ARG cc_start: 0.7050 (ptt180) cc_final: 0.6847 (ptt180) REVERT: A 65 LYS cc_start: 0.7682 (tptp) cc_final: 0.7389 (ttpt) REVERT: A 69 THR cc_start: 0.7587 (t) cc_final: 0.7382 (p) REVERT: A 113 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7426 (mmm) REVERT: F 93 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8145 (tt) REVERT: F 217 ILE cc_start: 0.8133 (tp) cc_final: 0.7876 (tp) REVERT: F 251 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: F 441 TYR cc_start: 0.8813 (t80) cc_final: 0.8422 (t80) REVERT: D 39 GLN cc_start: 0.8670 (pp30) cc_final: 0.7962 (pp30) REVERT: D 65 LYS cc_start: 0.7689 (tptp) cc_final: 0.7319 (ttpt) REVERT: D 87 ARG cc_start: 0.7108 (ptt180) cc_final: 0.6400 (mmt90) REVERT: D 106 TRP cc_start: 0.7930 (OUTLIER) cc_final: 0.7518 (t-100) REVERT: H 41 TYR cc_start: 0.6004 (m-10) cc_final: 0.5733 (m-10) REVERT: H 101 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6993 (m-10) REVERT: G 176 LYS cc_start: 0.8613 (pttt) cc_final: 0.8109 (pttp) REVERT: G 279 GLN cc_start: 0.7086 (pm20) cc_final: 0.6804 (pm20) REVERT: G 295 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7233 (pt0) REVERT: G 339 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7558 (mtt180) REVERT: E 18 LEU cc_start: 0.7580 (tp) cc_final: 0.6942 (pp) REVERT: E 65 LYS cc_start: 0.7819 (tptp) cc_final: 0.7446 (ttpt) REVERT: E 113 MET cc_start: 0.7463 (mmm) cc_final: 0.6167 (mmm) REVERT: I 41 TYR cc_start: 0.6053 (m-10) cc_final: 0.5845 (m-10) outliers start: 107 outliers final: 71 residues processed: 320 average time/residue: 0.1314 time to fit residues: 63.4817 Evaluate side-chains 315 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 238 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 129 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 152 optimal weight: 0.2980 chunk 196 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.202691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159888 restraints weight = 20896.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161612 restraints weight = 14425.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.162873 restraints weight = 11935.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163771 restraints weight = 8732.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163921 restraints weight = 7954.437| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16161 Z= 0.169 Angle : 0.629 7.698 21948 Z= 0.329 Chirality : 0.042 0.175 2568 Planarity : 0.004 0.050 2766 Dihedral : 5.574 59.693 2218 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.11 % Allowed : 24.11 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 2031 helix: 0.87 (0.27), residues: 393 sheet: -0.98 (0.22), residues: 573 loop : -1.64 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 63 TYR 0.034 0.002 TYR C 38 PHE 0.017 0.001 PHE F 137 TRP 0.034 0.002 TRP E 36 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00415 (16131) covalent geometry : angle 0.62160 (21888) SS BOND : bond 0.00713 ( 30) SS BOND : angle 1.91430 ( 60) hydrogen bonds : bond 0.03573 ( 601) hydrogen bonds : angle 5.03756 ( 1650) *********************** 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 345 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 252 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5850 (mmm) cc_final: 0.5483 (mmm) REVERT: B 148 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8328 (pp) REVERT: B 171 LEU cc_start: 0.8416 (tp) cc_final: 0.7989 (tp) REVERT: B 310 ASP cc_start: 0.7899 (t70) cc_final: 0.7664 (t70) REVERT: B 399 LYS cc_start: 0.7498 (mtpt) cc_final: 0.7021 (mtpt) REVERT: A 36 TRP cc_start: 0.8845 (m100) cc_final: 0.8485 (m-10) REVERT: A 38 ARG cc_start: 0.7008 (ptt180) cc_final: 0.6786 (ptt180) REVERT: A 65 LYS cc_start: 0.7684 (tptp) cc_final: 0.7387 (ttpt) REVERT: A 69 THR cc_start: 0.7491 (t) cc_final: 0.7256 (p) REVERT: A 113 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7808 (mtt) REVERT: C 100 LYS cc_start: 0.7129 (mmmm) cc_final: 0.6715 (mmmm) REVERT: F 93 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8220 (tt) REVERT: F 251 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7340 (mtm) REVERT: F 391 TYR cc_start: 0.8490 (t80) cc_final: 0.7870 (t80) REVERT: F 441 TYR cc_start: 0.8814 (t80) cc_final: 0.8474 (t80) REVERT: F 507 ARG cc_start: 0.7300 (ttp-110) cc_final: 0.6895 (ptp-170) REVERT: D 39 GLN cc_start: 0.8642 (pp30) cc_final: 0.7928 (pp30) REVERT: D 65 LYS cc_start: 0.7636 (tptp) cc_final: 0.7317 (ttpt) REVERT: D 87 ARG cc_start: 0.7159 (ptt180) cc_final: 0.6359 (mmt90) REVERT: H 41 TYR cc_start: 0.5968 (m-10) cc_final: 0.5749 (m-10) REVERT: H 101 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: G 176 LYS cc_start: 0.8556 (pttt) cc_final: 0.8000 (pttp) REVERT: G 279 GLN cc_start: 0.7038 (pm20) cc_final: 0.6786 (pm20) REVERT: G 339 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7581 (mtt180) REVERT: E 18 LEU cc_start: 0.7572 (tp) cc_final: 0.6945 (pp) REVERT: E 65 LYS cc_start: 0.7812 (tptp) cc_final: 0.7382 (ttpt) REVERT: I 41 TYR cc_start: 0.6051 (m-10) cc_final: 0.5805 (m-10) outliers start: 93 outliers final: 77 residues processed: 320 average time/residue: 0.1283 time to fit residues: 61.4231 Evaluate side-chains 321 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 239 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 129 optimal weight: 30.0000 chunk 78 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 142 optimal weight: 0.0970 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.206612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163631 restraints weight = 20980.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.165257 restraints weight = 14216.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.167352 restraints weight = 10569.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.167554 restraints weight = 7789.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.168010 restraints weight = 7333.704| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 16161 Z= 0.123 Angle : 0.606 9.042 21948 Z= 0.316 Chirality : 0.041 0.165 2568 Planarity : 0.004 0.047 2766 Dihedral : 5.363 58.439 2218 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.28 % Allowed : 24.93 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 2031 helix: 1.05 (0.27), residues: 396 sheet: -0.86 (0.22), residues: 570 loop : -1.53 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 63 TYR 0.033 0.001 TYR C 38 PHE 0.015 0.001 PHE B 137 TRP 0.033 0.002 TRP E 36 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00295 (16131) covalent geometry : angle 0.60080 (21888) SS BOND : bond 0.00640 ( 30) SS BOND : angle 1.62858 ( 60) hydrogen bonds : bond 0.03160 ( 601) hydrogen bonds : angle 4.83989 ( 1650) *********************** 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 332 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5872 (mmm) cc_final: 0.5523 (mmm) REVERT: B 148 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8243 (pp) REVERT: B 171 LEU cc_start: 0.8341 (tp) cc_final: 0.7902 (tp) REVERT: B 310 ASP cc_start: 0.7722 (t70) cc_final: 0.7505 (t70) REVERT: B 399 LYS cc_start: 0.7419 (mtpt) cc_final: 0.6966 (mtpt) REVERT: B 488 PHE cc_start: 0.7309 (t80) cc_final: 0.6851 (t80) REVERT: A 38 ARG cc_start: 0.6881 (ptt180) cc_final: 0.6678 (ptt180) REVERT: A 65 LYS cc_start: 0.7607 (tptp) cc_final: 0.7279 (ttpt) REVERT: C 100 LYS cc_start: 0.7010 (mmmm) cc_final: 0.6588 (mmmm) REVERT: F 93 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8324 (tt) REVERT: F 251 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7242 (mtm) REVERT: F 310 ASP cc_start: 0.7644 (t70) cc_final: 0.7338 (t70) REVERT: F 391 TYR cc_start: 0.8462 (t80) cc_final: 0.7858 (t80) REVERT: F 441 TYR cc_start: 0.8722 (t80) cc_final: 0.8431 (t80) REVERT: F 507 ARG cc_start: 0.7279 (ttp-110) cc_final: 0.6964 (ptp-170) REVERT: D 39 GLN cc_start: 0.8641 (pp30) cc_final: 0.7937 (pp30) REVERT: D 65 LYS cc_start: 0.7621 (tptp) cc_final: 0.7251 (ttpt) REVERT: D 87 ARG cc_start: 0.7207 (ptt180) cc_final: 0.6314 (mmt90) REVERT: D 113 MET cc_start: 0.8047 (mtt) cc_final: 0.7840 (mtt) REVERT: G 176 LYS cc_start: 0.8497 (pttt) cc_final: 0.7940 (pttp) REVERT: G 279 GLN cc_start: 0.6859 (pm20) cc_final: 0.6651 (pm20) REVERT: G 370 MET cc_start: 0.7440 (tmm) cc_final: 0.6715 (tmm) REVERT: E 18 LEU cc_start: 0.7507 (tp) cc_final: 0.6931 (pp) REVERT: E 65 LYS cc_start: 0.7917 (tptp) cc_final: 0.7476 (ttpp) outliers start: 78 outliers final: 66 residues processed: 307 average time/residue: 0.1407 time to fit residues: 64.9765 Evaluate side-chains 306 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 237 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 115 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 198 optimal weight: 20.0000 chunk 173 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** D 82 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 = 0.4288 r_free = 0.4288 target = 0.204441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161991 restraints weight = 20838.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163856 restraints weight = 14818.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165312 restraints weight = 12036.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166007 restraints weight = 8710.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166309 restraints weight = 8108.916| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 16161 Z= 0.153 Angle : 0.629 9.015 21948 Z= 0.330 Chirality : 0.042 0.168 2568 Planarity : 0.004 0.042 2766 Dihedral : 5.328 59.526 2215 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.45 % Allowed : 25.26 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 2031 helix: 1.06 (0.27), residues: 396 sheet: -0.86 (0.22), residues: 570 loop : -1.56 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 63 TYR 0.024 0.002 TYR C 38 PHE 0.014 0.001 PHE F 137 TRP 0.042 0.002 TRP A 36 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00380 (16131) covalent geometry : angle 0.62376 (21888) SS BOND : bond 0.00665 ( 30) SS BOND : angle 1.68075 ( 60) hydrogen bonds : bond 0.03374 ( 601) hydrogen bonds : angle 4.88520 ( 1650) *********************** 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 322 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 241 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5933 (mmm) cc_final: 0.5597 (mmm) REVERT: B 148 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8244 (pp) REVERT: B 171 LEU cc_start: 0.8399 (tp) cc_final: 0.7971 (tp) REVERT: B 399 LYS cc_start: 0.7514 (mtpt) cc_final: 0.7076 (mtpt) REVERT: B 488 PHE cc_start: 0.7266 (t80) cc_final: 0.6821 (t80) REVERT: A 65 LYS cc_start: 0.7683 (tptp) cc_final: 0.7416 (ttpt) REVERT: C 100 LYS cc_start: 0.7028 (mmmm) cc_final: 0.6639 (mmmm) REVERT: F 93 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8437 (tt) REVERT: F 251 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7258 (mtm) REVERT: F 274 MET cc_start: 0.7760 (ttm) cc_final: 0.7507 (ttt) REVERT: F 310 ASP cc_start: 0.7710 (t70) cc_final: 0.7397 (t70) REVERT: F 391 TYR cc_start: 0.8498 (t80) cc_final: 0.7930 (t80) REVERT: F 441 TYR cc_start: 0.8738 (t80) cc_final: 0.8421 (t80) REVERT: D 39 GLN cc_start: 0.8668 (pp30) cc_final: 0.8278 (pp30) REVERT: D 65 LYS cc_start: 0.7682 (tptp) cc_final: 0.7396 (ttpt) REVERT: D 87 ARG cc_start: 0.7137 (ptt180) cc_final: 0.6365 (mmt90) REVERT: D 98 ARG cc_start: 0.8576 (ttt-90) cc_final: 0.7266 (ttt90) REVERT: G 176 LYS cc_start: 0.8516 (pttt) cc_final: 0.7955 (pttp) REVERT: G 279 GLN cc_start: 0.6990 (pm20) cc_final: 0.6757 (pm20) REVERT: E 18 LEU cc_start: 0.7591 (tp) cc_final: 0.7108 (pp) REVERT: E 65 LYS cc_start: 0.7916 (tptp) cc_final: 0.7574 (ttpp) outliers start: 81 outliers final: 73 residues processed: 300 average time/residue: 0.1258 time to fit residues: 57.2069 Evaluate side-chains 310 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 234 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 18 optimal weight: 0.0870 chunk 91 optimal weight: 0.8980 chunk 173 optimal weight: 0.0980 chunk 152 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.208965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166414 restraints weight = 20873.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.168651 restraints weight = 14426.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170025 restraints weight = 10900.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171163 restraints weight = 7967.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.171608 restraints weight = 7190.290| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 16161 Z= 0.117 Angle : 0.602 8.807 21948 Z= 0.315 Chirality : 0.041 0.182 2568 Planarity : 0.004 0.042 2766 Dihedral : 5.185 57.405 2215 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.84 % Allowed : 26.19 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 2031 helix: 1.27 (0.28), residues: 396 sheet: -0.70 (0.22), residues: 543 loop : -1.50 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 507 TYR 0.024 0.001 TYR C 38 PHE 0.013 0.001 PHE F 137 TRP 0.067 0.002 TRP A 36 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00289 (16131) covalent geometry : angle 0.59747 (21888) SS BOND : bond 0.00601 ( 30) SS BOND : angle 1.53257 ( 60) hydrogen bonds : bond 0.02993 ( 601) hydrogen bonds : angle 4.73372 ( 1650) ********************** 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 321 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 251 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 97 MET cc_start: 0.5796 (mmm) cc_final: 0.5584 (mmm) REVERT: B 148 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8185 (pp) REVERT: B 171 LEU cc_start: 0.8312 (tp) cc_final: 0.7868 (tp) REVERT: B 370 MET cc_start: 0.7703 (tmm) cc_final: 0.6193 (tmm) REVERT: B 399 LYS cc_start: 0.7353 (mtpt) cc_final: 0.6947 (mtpt) REVERT: B 488 PHE cc_start: 0.7148 (t80) cc_final: 0.6748 (t80) REVERT: A 65 LYS cc_start: 0.7665 (tptp) cc_final: 0.7385 (ttpt) REVERT: A 87 ARG cc_start: 0.7228 (ptt180) cc_final: 0.6446 (mmt90) REVERT: A 118 GLN cc_start: 0.7606 (mm-40) cc_final: 0.6905 (mm-40) REVERT: C 100 LYS cc_start: 0.6962 (mmmm) cc_final: 0.6577 (mmmm) REVERT: F 93 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8434 (tt) REVERT: F 148 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8043 (pp) REVERT: F 251 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7222 (mtm) REVERT: F 274 MET cc_start: 0.7731 (ttm) cc_final: 0.7501 (ttp) REVERT: F 310 ASP cc_start: 0.7505 (t70) cc_final: 0.7135 (t70) REVERT: F 391 TYR cc_start: 0.8497 (t80) cc_final: 0.7932 (t80) REVERT: F 441 TYR cc_start: 0.8615 (t80) cc_final: 0.8342 (t80) REVERT: D 39 GLN cc_start: 0.8626 (pp30) cc_final: 0.8229 (pp30) REVERT: D 65 LYS cc_start: 0.7657 (tptp) cc_final: 0.7381 (ttpt) REVERT: D 87 ARG cc_start: 0.7173 (ptt180) cc_final: 0.6380 (mmt90) REVERT: D 98 ARG cc_start: 0.8511 (ttt-90) cc_final: 0.7342 (ttt90) REVERT: G 176 LYS cc_start: 0.8456 (pttt) cc_final: 0.7900 (pttp) REVERT: G 232 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: G 264 MET cc_start: 0.6492 (mtm) cc_final: 0.6180 (mmm) REVERT: G 370 MET cc_start: 0.7156 (tmm) cc_final: 0.6609 (tmm) REVERT: E 3 GLN cc_start: 0.6700 (tt0) cc_final: 0.6478 (tt0) REVERT: E 18 LEU cc_start: 0.7530 (tp) cc_final: 0.7108 (pp) REVERT: E 65 LYS cc_start: 0.7902 (tptp) cc_final: 0.7558 (ttpp) outliers start: 70 outliers final: 56 residues processed: 299 average time/residue: 0.1274 time to fit residues: 57.5755 Evaluate side-chains 299 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 237 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 144 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 174 optimal weight: 0.0670 chunk 137 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** D 82 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 = 0.4205 r_free = 0.4205 target = 0.195190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152565 restraints weight = 21004.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152968 restraints weight = 15368.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154398 restraints weight = 11859.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155914 restraints weight = 8777.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155918 restraints weight = 7578.679| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16161 Z= 0.170 Angle : 0.645 8.843 21948 Z= 0.341 Chirality : 0.043 0.175 2568 Planarity : 0.004 0.082 2766 Dihedral : 5.339 57.843 2215 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.17 % Allowed : 26.03 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.19), residues: 2031 helix: 1.24 (0.27), residues: 390 sheet: -0.77 (0.22), residues: 561 loop : -1.60 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG F 507 TYR 0.027 0.002 TYR C 38 PHE 0.016 0.001 PHE F 137 TRP 0.093 0.003 TRP A 36 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00420 (16131) covalent geometry : angle 0.63964 (21888) SS BOND : bond 0.00647 ( 30) SS BOND : angle 1.75513 ( 60) hydrogen bonds : bond 0.03456 ( 601) hydrogen bonds : angle 4.86368 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.43 seconds wall clock time: 44 minutes 18.71 seconds (2658.71 seconds total)