Starting phenix.real_space_refine on Thu Mar 5 07:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q12_13752/03_2026/7q12_13752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q12_13752/03_2026/7q12_13752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q12_13752/03_2026/7q12_13752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q12_13752/03_2026/7q12_13752.map" model { file = "/net/cci-nas-00/data/ceres_data/7q12_13752/03_2026/7q12_13752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q12_13752/03_2026/7q12_13752.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 108 5.16 5 C 12956 2.51 5 N 3504 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20244 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 4866 Chain: "E" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 4866 Chain: "C" Number of atoms: 4774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 4866 Chain: "D" Number of atoms: 4774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 4866 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.57, per 1000 atoms: 0.37 Number of scatterers: 20244 At special positions: 0 Unit cell: (131.406, 127.062, 131.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 4 15.00 O 3672 8.00 N 3504 7.00 C 12956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.49 Conformation dependent library (CDL) restraints added in 1.5 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 54.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.256A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 4.075A pdb=" N VAL A 73 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 97 removed outlier: 3.528A pdb=" N ASP A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 145 through 169 Processing helix chain 'A' and resid 185 through 194 removed outlier: 4.110A pdb=" N CYS A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.725A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.923A pdb=" N LEU A 224 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 291 through 312 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 376 through 411 Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 532 through 540 Processing helix chain 'A' and resid 559 through 577 removed outlier: 3.646A pdb=" N GLN A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 591 removed outlier: 3.650A pdb=" N ARG A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.934A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 5.256A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 removed outlier: 4.364A pdb=" N GLU E 323 " --> pdb=" O GLU E 320 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 324 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 346 removed outlier: 4.400A pdb=" N LYS E 344 " --> pdb=" O ASN E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.364A pdb=" N GLU F 323 " --> pdb=" O GLU F 320 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 324 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 346 removed outlier: 4.400A pdb=" N LYS F 344 " --> pdb=" O ASN F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'G' and resid 318 through 326 removed outlier: 4.365A pdb=" N GLU G 323 " --> pdb=" O GLU G 320 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG G 324 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 346 removed outlier: 4.400A pdb=" N LYS G 344 " --> pdb=" O ASN G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 349 No H-bonds generated for 'chain 'G' and resid 347 through 349' Processing helix chain 'H' and resid 318 through 326 removed outlier: 4.364A pdb=" N GLU H 323 " --> pdb=" O GLU H 320 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG H 324 " --> pdb=" O ARG H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 346 removed outlier: 4.400A pdb=" N LYS H 344 " --> pdb=" O ASN H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 349 No H-bonds generated for 'chain 'H' and resid 347 through 349' Processing helix chain 'B' and resid 42 through 59 removed outlier: 4.255A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 4.074A pdb=" N VAL B 73 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 97 removed outlier: 3.529A pdb=" N ASP B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 145 through 169 Processing helix chain 'B' and resid 185 through 194 removed outlier: 4.111A pdb=" N CYS B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 190 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.726A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.924A pdb=" N LEU B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 291 through 312 removed outlier: 3.500A pdb=" N PHE B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 376 through 411 Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 514 through 523 Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 559 through 577 removed outlier: 3.645A pdb=" N GLN B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 591 removed outlier: 3.650A pdb=" N ARG B 591 " --> pdb=" O ASN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.934A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 617 removed outlier: 5.257A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.255A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 removed outlier: 4.075A pdb=" N VAL C 73 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 97 removed outlier: 3.528A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 145 through 169 Processing helix chain 'C' and resid 185 through 194 removed outlier: 4.109A pdb=" N CYS C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.725A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.923A pdb=" N LEU C 224 " --> pdb=" O TYR C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 291 through 312 Processing helix chain 'C' and resid 319 through 321 No H-bonds generated for 'chain 'C' and resid 319 through 321' Processing helix chain 'C' and resid 338 through 354 Processing helix chain 'C' and resid 376 through 411 Processing helix chain 'C' and resid 423 through 436 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'C' and resid 514 through 523 Processing helix chain 'C' and resid 532 through 540 Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.647A pdb=" N GLN C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 591 removed outlier: 3.650A pdb=" N ARG C 591 " --> pdb=" O ASN C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 597 removed outlier: 3.934A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 617 removed outlier: 5.256A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.257A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 removed outlier: 4.075A pdb=" N VAL D 73 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 97 removed outlier: 3.529A pdb=" N ASP D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 145 through 169 Processing helix chain 'D' and resid 185 through 194 removed outlier: 4.110A pdb=" N CYS D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 removed outlier: 3.725A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.923A pdb=" N LEU D 224 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 291 through 312 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 338 through 354 Processing helix chain 'D' and resid 376 through 411 Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 514 through 523 Processing helix chain 'D' and resid 532 through 540 Processing helix chain 'D' and resid 559 through 577 removed outlier: 3.646A pdb=" N GLN D 577 " --> pdb=" O SER D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 591 removed outlier: 3.650A pdb=" N ARG D 591 " --> pdb=" O ASN D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 597 removed outlier: 3.934A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 617 removed outlier: 5.256A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 5.880A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE A 30 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL A 254 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.309A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N LEU A 502 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.981A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 5.880A pdb=" N GLU B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL B 254 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 200 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR B 256 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE B 202 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.309A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N LEU B 502 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.981A pdb=" N ASN B 447 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 79 removed outlier: 5.880A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL C 254 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 276 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 477 removed outlier: 6.308A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE C 365 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE C 326 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 375 removed outlier: 3.980A pdb=" N ASN C 447 " --> pdb=" O ASN C 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 79 removed outlier: 5.880A pdb=" N GLU D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE D 30 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N VAL D 254 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 473 through 477 removed outlier: 6.309A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N LEU D 502 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 372 through 375 removed outlier: 3.981A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2825 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: 3.70 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6568 1.34 - 1.46: 5178 1.46 - 1.58: 8858 1.58 - 1.70: 4 1.70 - 1.81: 164 Bond restraints: 20772 Sorted by residual: bond pdb=" O6 G6P B 801 " pdb=" P G6P B 801 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O6 G6P A 801 " pdb=" P G6P A 801 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O6 G6P D 801 " pdb=" P G6P D 801 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O6 G6P C 801 " pdb=" P G6P C 801 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C2 G6P C 801 " pdb=" C3 G6P C 801 " ideal model delta sigma weight residual 1.523 1.461 0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 20767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 27579 1.67 - 3.34: 418 3.34 - 5.01: 80 5.01 - 6.68: 63 6.68 - 8.35: 4 Bond angle restraints: 28144 Sorted by residual: angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 111.88 107.82 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N ILE D 238 " pdb=" CA ILE D 238 " pdb=" C ILE D 238 " ideal model delta sigma weight residual 111.88 107.82 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N ILE C 238 " pdb=" CA ILE C 238 " pdb=" C ILE C 238 " ideal model delta sigma weight residual 111.88 107.83 4.05 1.06e+00 8.90e-01 1.46e+01 angle pdb=" N ILE B 238 " pdb=" CA ILE B 238 " pdb=" C ILE B 238 " ideal model delta sigma weight residual 111.88 107.83 4.05 1.06e+00 8.90e-01 1.46e+01 angle pdb=" C THR A 136 " pdb=" N CYS A 137 " pdb=" CA CYS A 137 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 ... (remaining 28139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.43: 11776 28.43 - 56.86: 448 56.86 - 85.29: 36 85.29 - 113.72: 32 113.72 - 142.15: 24 Dihedral angle restraints: 12316 sinusoidal: 5044 harmonic: 7272 Sorted by residual: dihedral pdb=" C3 G6P B 801 " pdb=" C1 G6P B 801 " pdb=" C2 G6P B 801 " pdb=" O1 G6P B 801 " ideal model delta sinusoidal sigma weight residual 74.65 -67.50 142.15 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C3 G6P A 801 " pdb=" C1 G6P A 801 " pdb=" C2 G6P A 801 " pdb=" O1 G6P A 801 " ideal model delta sinusoidal sigma weight residual 74.65 -67.49 142.14 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C3 G6P D 801 " pdb=" C1 G6P D 801 " pdb=" C2 G6P D 801 " pdb=" O1 G6P D 801 " ideal model delta sinusoidal sigma weight residual 74.65 -67.46 142.11 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 12313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.016: 2992 1.016 - 2.033: 0 2.033 - 3.049: 0 3.049 - 4.065: 0 4.065 - 5.081: 16 Chirality restraints: 3008 Sorted by residual: chirality pdb=" C5 G6P B 801 " pdb=" C4 G6P B 801 " pdb=" C6 G6P B 801 " pdb=" O5 G6P B 801 " both_signs ideal model delta sigma weight residual False -2.51 2.57 -5.08 2.00e-01 2.50e+01 6.46e+02 chirality pdb=" C5 G6P C 801 " pdb=" C4 G6P C 801 " pdb=" C6 G6P C 801 " pdb=" O5 G6P C 801 " both_signs ideal model delta sigma weight residual False -2.51 2.57 -5.08 2.00e-01 2.50e+01 6.46e+02 chirality pdb=" C5 G6P A 801 " pdb=" C4 G6P A 801 " pdb=" C6 G6P A 801 " pdb=" O5 G6P A 801 " both_signs ideal model delta sigma weight residual False -2.51 2.57 -5.08 2.00e-01 2.50e+01 6.45e+02 ... (remaining 3005 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 141 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO C 142 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 141 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 142 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 141 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO B 142 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.025 5.00e-02 4.00e+02 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4041 2.77 - 3.30: 19887 3.30 - 3.84: 33727 3.84 - 4.37: 38429 4.37 - 4.90: 65797 Nonbonded interactions: 161881 Sorted by model distance: nonbonded pdb=" OD2 ASP A 317 " pdb=" OG SER A 469 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP D 317 " pdb=" OG SER D 469 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP C 317 " pdb=" OG SER C 469 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP B 317 " pdb=" OG SER B 469 " model vdw 2.241 3.040 nonbonded pdb=" O PHE D 165 " pdb=" OG SER D 169 " model vdw 2.250 3.040 ... (remaining 161876 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.820 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.840 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 0.076 20772 Z= 0.144 Angle : 0.581 8.352 28144 Z= 0.283 Chirality : 0.351 5.081 3008 Planarity : 0.003 0.045 3616 Dihedral : 17.596 142.147 7644 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2480 helix: 0.95 (0.15), residues: 1240 sheet: 0.37 (0.37), residues: 216 loop : -0.79 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 371 TYR 0.006 0.001 TYR C 221 PHE 0.008 0.001 PHE C 425 TRP 0.008 0.001 TRP F 325 HIS 0.002 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00299 (20772) covalent geometry : angle 0.58120 (28144) hydrogen bonds : bond 0.17756 ( 967) hydrogen bonds : angle 6.48904 ( 2825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.519 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.8840 (ppt170) cc_final: 0.8491 (ppt170) REVERT: A 209 LEU cc_start: 0.7621 (tt) cc_final: 0.7218 (tp) REVERT: A 244 MET cc_start: 0.9180 (pmm) cc_final: 0.8955 (pmm) REVERT: A 271 LYS cc_start: 0.9053 (mmpt) cc_final: 0.8726 (mmmt) REVERT: A 306 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7161 (mp0) REVERT: B 146 ARG cc_start: 0.8884 (ppt170) cc_final: 0.8562 (ppt170) REVERT: B 209 LEU cc_start: 0.7436 (tt) cc_final: 0.6990 (tp) REVERT: B 244 MET cc_start: 0.9151 (pmm) cc_final: 0.8907 (pmm) REVERT: B 271 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8693 (mmmt) REVERT: B 306 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7121 (mp0) REVERT: C 146 ARG cc_start: 0.8904 (ppt170) cc_final: 0.8554 (ppt170) REVERT: C 209 LEU cc_start: 0.7503 (tt) cc_final: 0.7081 (tp) REVERT: C 240 HIS cc_start: 0.9308 (p90) cc_final: 0.8639 (p90) REVERT: C 244 MET cc_start: 0.9151 (pmm) cc_final: 0.8897 (pmm) REVERT: C 271 LYS cc_start: 0.8995 (mmpt) cc_final: 0.8625 (mmmt) REVERT: C 306 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7145 (mp0) REVERT: D 146 ARG cc_start: 0.8765 (ppt170) cc_final: 0.8404 (ppt170) REVERT: D 209 LEU cc_start: 0.7456 (tt) cc_final: 0.7018 (tp) REVERT: D 244 MET cc_start: 0.9120 (pmm) cc_final: 0.8872 (pmm) REVERT: D 271 LYS cc_start: 0.9057 (mmpt) cc_final: 0.8714 (mmmt) REVERT: D 306 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7069 (mp0) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1373 time to fit residues: 64.1344 Evaluate side-chains 227 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 40.0000 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 587 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS B 587 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS C 587 ASN D 291 HIS D 587 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.134994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.094279 restraints weight = 112171.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095590 restraints weight = 47554.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096616 restraints weight = 31219.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.096797 restraints weight = 27723.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097791 restraints weight = 23302.650| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20772 Z= 0.128 Angle : 0.612 8.099 28144 Z= 0.307 Chirality : 0.045 0.275 3008 Planarity : 0.003 0.043 3616 Dihedral : 7.317 59.228 2864 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.12 % Allowed : 9.12 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2480 helix: 1.21 (0.15), residues: 1260 sheet: 0.24 (0.39), residues: 192 loop : -0.77 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 192 TYR 0.010 0.001 TYR B 212 PHE 0.035 0.002 PHE D 400 TRP 0.011 0.001 TRP F 325 HIS 0.013 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00267 (20772) covalent geometry : angle 0.61221 (28144) hydrogen bonds : bond 0.04805 ( 967) hydrogen bonds : angle 5.00669 ( 2825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.9396 (p90) cc_final: 0.8735 (p90) REVERT: A 271 LYS cc_start: 0.8994 (mmpt) cc_final: 0.8588 (mmmt) REVERT: A 606 MET cc_start: 0.8747 (ttm) cc_final: 0.8516 (ttp) REVERT: F 342 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7893 (mttm) REVERT: B 250 HIS cc_start: 0.8742 (t-170) cc_final: 0.8473 (t-170) REVERT: B 271 LYS cc_start: 0.8966 (mmpt) cc_final: 0.8574 (mmmt) REVERT: C 240 HIS cc_start: 0.9353 (p90) cc_final: 0.9120 (p90) REVERT: C 271 LYS cc_start: 0.8905 (mmpt) cc_final: 0.8490 (mmmt) REVERT: D 271 LYS cc_start: 0.8982 (mmpt) cc_final: 0.8569 (mmmt) outliers start: 24 outliers final: 5 residues processed: 283 average time/residue: 0.1372 time to fit residues: 61.0214 Evaluate side-chains 243 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 238 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain B residue 29 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 115 optimal weight: 2.9990 chunk 237 optimal weight: 0.3980 chunk 189 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 85 optimal weight: 0.0060 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS C 178 HIS ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS D 240 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.134217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.095645 restraints weight = 125920.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.095432 restraints weight = 50365.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097470 restraints weight = 34296.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.097503 restraints weight = 25779.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.098274 restraints weight = 22361.955| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20772 Z= 0.123 Angle : 0.578 10.471 28144 Z= 0.290 Chirality : 0.043 0.307 3008 Planarity : 0.003 0.035 3616 Dihedral : 4.862 58.362 2864 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.26 % Allowed : 11.73 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2480 helix: 1.18 (0.15), residues: 1264 sheet: 0.03 (0.37), residues: 192 loop : -0.76 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 241 TYR 0.010 0.001 TYR B 212 PHE 0.033 0.001 PHE C 400 TRP 0.012 0.001 TRP C 134 HIS 0.012 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00265 (20772) covalent geometry : angle 0.57812 (28144) hydrogen bonds : bond 0.04307 ( 967) hydrogen bonds : angle 4.73244 ( 2825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.9211 (p-80) cc_final: 0.8991 (p90) REVERT: A 271 LYS cc_start: 0.8845 (mmpt) cc_final: 0.8503 (mmmt) REVERT: A 606 MET cc_start: 0.8758 (ttm) cc_final: 0.8533 (ttp) REVERT: F 342 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7903 (mttm) REVERT: B 250 HIS cc_start: 0.8610 (t-170) cc_final: 0.8385 (t-170) REVERT: B 271 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8469 (mmmt) REVERT: C 240 HIS cc_start: 0.9325 (p90) cc_final: 0.9094 (p90) REVERT: C 271 LYS cc_start: 0.8800 (mmpt) cc_final: 0.8424 (mmmt) REVERT: D 271 LYS cc_start: 0.8817 (mmpt) cc_final: 0.8456 (mmmt) outliers start: 27 outliers final: 16 residues processed: 265 average time/residue: 0.1358 time to fit residues: 57.0585 Evaluate side-chains 243 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 178 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 0.0170 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS A 178 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS D 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.134097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096123 restraints weight = 106250.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.095633 restraints weight = 46591.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097456 restraints weight = 34145.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097345 restraints weight = 26046.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.099886 restraints weight = 22090.750| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20772 Z= 0.115 Angle : 0.568 8.379 28144 Z= 0.284 Chirality : 0.043 0.325 3008 Planarity : 0.003 0.033 3616 Dihedral : 4.565 57.378 2864 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.21 % Allowed : 11.59 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2480 helix: 1.20 (0.15), residues: 1264 sheet: -0.15 (0.37), residues: 192 loop : -0.77 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 321 TYR 0.008 0.001 TYR B 212 PHE 0.028 0.002 PHE B 165 TRP 0.009 0.001 TRP D 134 HIS 0.011 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00254 (20772) covalent geometry : angle 0.56795 (28144) hydrogen bonds : bond 0.04007 ( 967) hydrogen bonds : angle 4.59999 ( 2825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8739 (tp) cc_final: 0.8524 (tp) REVERT: A 271 LYS cc_start: 0.8806 (mmpt) cc_final: 0.8449 (mmmt) REVERT: F 342 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7828 (mttm) REVERT: B 240 HIS cc_start: 0.9370 (p90) cc_final: 0.9161 (p90) REVERT: B 250 HIS cc_start: 0.8659 (t-170) cc_final: 0.8425 (t-170) REVERT: B 271 LYS cc_start: 0.8752 (mmpt) cc_final: 0.8414 (mmmt) REVERT: C 240 HIS cc_start: 0.9310 (p90) cc_final: 0.9097 (p90) REVERT: C 269 LEU cc_start: 0.8673 (tp) cc_final: 0.8453 (tp) REVERT: C 271 LYS cc_start: 0.8796 (mmpt) cc_final: 0.8418 (mmmt) REVERT: C 423 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8501 (tm-30) REVERT: D 269 LEU cc_start: 0.8718 (tp) cc_final: 0.8442 (tp) REVERT: D 271 LYS cc_start: 0.8765 (mmpt) cc_final: 0.8415 (mmmt) outliers start: 26 outliers final: 12 residues processed: 263 average time/residue: 0.1345 time to fit residues: 55.9772 Evaluate side-chains 244 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.130457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.090534 restraints weight = 121464.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090527 restraints weight = 49690.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091868 restraints weight = 36056.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.092280 restraints weight = 27147.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092866 restraints weight = 23132.277| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20772 Z= 0.204 Angle : 0.630 8.299 28144 Z= 0.323 Chirality : 0.045 0.283 3008 Planarity : 0.004 0.031 3616 Dihedral : 4.853 59.739 2864 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.54 % Allowed : 13.04 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2480 helix: 1.02 (0.15), residues: 1260 sheet: -0.51 (0.36), residues: 192 loop : -1.00 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 586 TYR 0.027 0.001 TYR H 332 PHE 0.027 0.002 PHE C 400 TRP 0.008 0.001 TRP B 598 HIS 0.012 0.002 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00473 (20772) covalent geometry : angle 0.62953 (28144) hydrogen bonds : bond 0.04630 ( 967) hydrogen bonds : angle 4.79452 ( 2825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8767 (tp) cc_final: 0.8548 (tp) REVERT: A 271 LYS cc_start: 0.8858 (mmpt) cc_final: 0.8490 (mmmt) REVERT: B 271 LYS cc_start: 0.8827 (mmpt) cc_final: 0.8470 (mmmt) REVERT: C 240 HIS cc_start: 0.9360 (p90) cc_final: 0.8766 (p90) REVERT: C 269 LEU cc_start: 0.8714 (tp) cc_final: 0.8451 (tp) REVERT: C 271 LYS cc_start: 0.8807 (mmpt) cc_final: 0.8419 (mmmt) REVERT: C 423 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8644 (tm-30) REVERT: D 269 LEU cc_start: 0.8704 (tp) cc_final: 0.8456 (tp) REVERT: D 271 LYS cc_start: 0.8838 (mmpt) cc_final: 0.8477 (mmmt) outliers start: 33 outliers final: 24 residues processed: 259 average time/residue: 0.1273 time to fit residues: 53.1462 Evaluate side-chains 247 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 86 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 100 optimal weight: 0.0270 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.131372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092812 restraints weight = 95742.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091913 restraints weight = 42761.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093565 restraints weight = 32708.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093692 restraints weight = 25018.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095115 restraints weight = 21911.815| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20772 Z= 0.148 Angle : 0.611 11.431 28144 Z= 0.307 Chirality : 0.044 0.360 3008 Planarity : 0.003 0.030 3616 Dihedral : 4.730 56.780 2864 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.30 % Allowed : 14.20 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2480 helix: 0.94 (0.15), residues: 1268 sheet: -0.64 (0.36), residues: 192 loop : -1.06 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 558 TYR 0.017 0.001 TYR H 332 PHE 0.028 0.001 PHE B 165 TRP 0.008 0.001 TRP C 182 HIS 0.012 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00339 (20772) covalent geometry : angle 0.61131 (28144) hydrogen bonds : bond 0.04234 ( 967) hydrogen bonds : angle 4.63876 ( 2825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8745 (tp) cc_final: 0.8534 (tp) REVERT: A 271 LYS cc_start: 0.8811 (mmpt) cc_final: 0.8440 (mmmt) REVERT: F 342 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7891 (mmtt) REVERT: B 271 LYS cc_start: 0.8811 (mmpt) cc_final: 0.8463 (mmmt) REVERT: B 423 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8519 (tp30) REVERT: C 240 HIS cc_start: 0.9299 (p90) cc_final: 0.8739 (p90) REVERT: C 269 LEU cc_start: 0.8693 (tp) cc_final: 0.8469 (tp) REVERT: C 271 LYS cc_start: 0.8830 (mmpt) cc_final: 0.8452 (mmmt) REVERT: C 423 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8494 (tm-30) REVERT: D 146 ARG cc_start: 0.8775 (ppt170) cc_final: 0.7959 (ttp80) REVERT: D 269 LEU cc_start: 0.8685 (tp) cc_final: 0.8457 (tp) REVERT: D 271 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8432 (mmmt) REVERT: D 423 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8513 (tm-30) outliers start: 28 outliers final: 22 residues processed: 254 average time/residue: 0.1373 time to fit residues: 55.8874 Evaluate side-chains 255 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 14 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 190 optimal weight: 0.0070 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS ** D 138 ASN ** 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 = 0.4045 r_free = 0.4045 target = 0.130565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090230 restraints weight = 107787.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090661 restraints weight = 45738.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091841 restraints weight = 31019.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092365 restraints weight = 23505.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092549 restraints weight = 20610.956| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20772 Z= 0.164 Angle : 0.639 12.554 28144 Z= 0.318 Chirality : 0.045 0.373 3008 Planarity : 0.003 0.030 3616 Dihedral : 4.862 59.067 2864 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.49 % Allowed : 14.20 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.17), residues: 2480 helix: 0.92 (0.15), residues: 1268 sheet: -0.90 (0.35), residues: 192 loop : -1.16 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 586 TYR 0.017 0.001 TYR E 332 PHE 0.023 0.001 PHE C 400 TRP 0.008 0.001 TRP D 129 HIS 0.014 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00378 (20772) covalent geometry : angle 0.63934 (28144) hydrogen bonds : bond 0.04271 ( 967) hydrogen bonds : angle 4.64775 ( 2825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8762 (tp) cc_final: 0.8550 (tp) REVERT: A 271 LYS cc_start: 0.8844 (mmpt) cc_final: 0.8477 (mmmt) REVERT: E 342 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7885 (mmtt) REVERT: F 342 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7815 (mmtt) REVERT: H 342 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7855 (mmtt) REVERT: B 269 LEU cc_start: 0.8657 (tp) cc_final: 0.8364 (tp) REVERT: B 271 LYS cc_start: 0.8804 (mmpt) cc_final: 0.8454 (mmmt) REVERT: B 423 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8637 (tm-30) REVERT: C 269 LEU cc_start: 0.8675 (tp) cc_final: 0.8444 (tp) REVERT: C 271 LYS cc_start: 0.8814 (mmpt) cc_final: 0.8421 (mmmt) REVERT: C 423 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8605 (tm-30) REVERT: D 269 LEU cc_start: 0.8715 (tp) cc_final: 0.8495 (tp) REVERT: D 271 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8432 (mmmt) REVERT: D 423 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8602 (tm-30) outliers start: 32 outliers final: 24 residues processed: 263 average time/residue: 0.1314 time to fit residues: 54.9615 Evaluate side-chains 267 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 76 optimal weight: 7.9990 chunk 171 optimal weight: 0.0070 chunk 211 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.132299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092107 restraints weight = 115146.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092835 restraints weight = 46270.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093884 restraints weight = 31516.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094323 restraints weight = 23868.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094564 restraints weight = 20687.377| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20772 Z= 0.118 Angle : 0.623 13.976 28144 Z= 0.304 Chirality : 0.044 0.369 3008 Planarity : 0.003 0.029 3616 Dihedral : 4.718 57.358 2864 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.35 % Allowed : 14.15 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2480 helix: 1.01 (0.15), residues: 1268 sheet: -0.87 (0.35), residues: 192 loop : -1.14 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 192 TYR 0.023 0.001 TYR G 332 PHE 0.023 0.001 PHE B 165 TRP 0.008 0.001 TRP D 129 HIS 0.014 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00262 (20772) covalent geometry : angle 0.62310 (28144) hydrogen bonds : bond 0.03894 ( 967) hydrogen bonds : angle 4.48507 ( 2825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 269 LEU cc_start: 0.8777 (tp) cc_final: 0.8574 (tp) REVERT: A 271 LYS cc_start: 0.8812 (mmpt) cc_final: 0.8464 (mmmt) REVERT: E 342 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7902 (mmtt) REVERT: F 342 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7874 (mmtt) REVERT: H 342 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7868 (mmtt) REVERT: B 146 ARG cc_start: 0.8841 (ppt170) cc_final: 0.8070 (ttp80) REVERT: B 244 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8817 (ppp) REVERT: B 269 LEU cc_start: 0.8677 (tp) cc_final: 0.8403 (tp) REVERT: B 271 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8449 (mmmt) REVERT: B 423 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8603 (tm-30) REVERT: C 146 ARG cc_start: 0.8788 (ppt170) cc_final: 0.8019 (ttp80) REVERT: C 269 LEU cc_start: 0.8731 (tp) cc_final: 0.8456 (tp) REVERT: C 271 LYS cc_start: 0.8776 (mmpt) cc_final: 0.8396 (mmmt) REVERT: C 423 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8573 (tm-30) REVERT: D 146 ARG cc_start: 0.8799 (ppt170) cc_final: 0.8047 (ttp80) REVERT: D 269 LEU cc_start: 0.8734 (tp) cc_final: 0.8503 (tp) REVERT: D 271 LYS cc_start: 0.8788 (mmpt) cc_final: 0.8438 (mmmt) REVERT: D 423 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8601 (tm-30) outliers start: 29 outliers final: 22 residues processed: 269 average time/residue: 0.1411 time to fit residues: 59.7499 Evaluate side-chains 263 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 96 optimal weight: 0.0040 chunk 107 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 246 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.132387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091606 restraints weight = 116753.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092132 restraints weight = 46744.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093638 restraints weight = 30237.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093839 restraints weight = 23081.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095401 restraints weight = 20318.488| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20772 Z= 0.120 Angle : 0.637 14.602 28144 Z= 0.310 Chirality : 0.045 0.366 3008 Planarity : 0.003 0.041 3616 Dihedral : 4.731 58.120 2864 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.40 % Allowed : 14.34 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2480 helix: 1.05 (0.15), residues: 1268 sheet: -0.87 (0.35), residues: 192 loop : -1.15 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 321 TYR 0.010 0.001 TYR B 212 PHE 0.020 0.001 PHE A 227 TRP 0.007 0.001 TRP D 129 HIS 0.013 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00268 (20772) covalent geometry : angle 0.63655 (28144) hydrogen bonds : bond 0.03818 ( 967) hydrogen bonds : angle 4.45308 ( 2825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 146 ARG cc_start: 0.8880 (ppt170) cc_final: 0.8096 (ttp80) REVERT: A 269 LEU cc_start: 0.8800 (tp) cc_final: 0.8547 (tp) REVERT: A 271 LYS cc_start: 0.8811 (mmpt) cc_final: 0.8448 (mmmt) REVERT: E 342 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7925 (mmtt) REVERT: F 342 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7870 (mmtt) REVERT: H 342 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7880 (mmtt) REVERT: B 146 ARG cc_start: 0.8847 (ppt170) cc_final: 0.8072 (ttp80) REVERT: B 244 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8844 (ppp) REVERT: B 423 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8593 (tm-30) REVERT: C 146 ARG cc_start: 0.8788 (ppt170) cc_final: 0.8019 (ttp80) REVERT: C 269 LEU cc_start: 0.8703 (tp) cc_final: 0.8462 (tp) REVERT: C 271 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8386 (mmmt) REVERT: C 423 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8520 (tm-30) REVERT: D 146 ARG cc_start: 0.8876 (ppt170) cc_final: 0.8122 (ttp80) REVERT: D 269 LEU cc_start: 0.8782 (tp) cc_final: 0.8504 (tp) REVERT: D 271 LYS cc_start: 0.8793 (mmpt) cc_final: 0.8428 (mmmt) REVERT: D 423 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8558 (tm-30) outliers start: 30 outliers final: 25 residues processed: 270 average time/residue: 0.1331 time to fit residues: 57.6651 Evaluate side-chains 273 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 225 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 0.0870 chunk 160 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.131728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091598 restraints weight = 102176.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091918 restraints weight = 43154.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093097 restraints weight = 29493.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093734 restraints weight = 22285.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093896 restraints weight = 19514.817| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20772 Z= 0.136 Angle : 0.652 14.630 28144 Z= 0.319 Chirality : 0.046 0.360 3008 Planarity : 0.003 0.041 3616 Dihedral : 4.816 59.740 2864 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.26 % Allowed : 14.80 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2480 helix: 1.04 (0.15), residues: 1264 sheet: -0.99 (0.35), residues: 192 loop : -1.21 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 321 TYR 0.018 0.001 TYR B 239 PHE 0.036 0.001 PHE A 400 TRP 0.008 0.001 TRP D 129 HIS 0.013 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00312 (20772) covalent geometry : angle 0.65173 (28144) hydrogen bonds : bond 0.03911 ( 967) hydrogen bonds : angle 4.46770 ( 2825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 146 ARG cc_start: 0.8929 (ppt170) cc_final: 0.8131 (ttp80) REVERT: A 269 LEU cc_start: 0.8767 (tp) cc_final: 0.8547 (tp) REVERT: A 271 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8458 (mmmt) REVERT: E 342 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7929 (mmtt) REVERT: F 342 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7833 (mmtt) REVERT: H 342 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7872 (mmtt) REVERT: B 146 ARG cc_start: 0.8903 (ppt170) cc_final: 0.8119 (ttp80) REVERT: B 423 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8581 (tm-30) REVERT: C 146 ARG cc_start: 0.8928 (ppt170) cc_final: 0.8125 (ttp80) REVERT: C 269 LEU cc_start: 0.8707 (tp) cc_final: 0.8468 (tp) REVERT: C 271 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8389 (mmmt) REVERT: C 423 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8539 (tm-30) REVERT: D 146 ARG cc_start: 0.8867 (ppt170) cc_final: 0.8112 (ttp80) REVERT: D 269 LEU cc_start: 0.8739 (tp) cc_final: 0.8500 (tp) REVERT: D 271 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8425 (mmmt) REVERT: D 423 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8597 (tm-30) outliers start: 27 outliers final: 24 residues processed: 262 average time/residue: 0.1299 time to fit residues: 54.7400 Evaluate side-chains 269 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 234 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 52 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 18 optimal weight: 0.0070 chunk 242 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.132737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091873 restraints weight = 103633.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093145 restraints weight = 40608.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094322 restraints weight = 27036.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094711 restraints weight = 21336.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094922 restraints weight = 18760.850| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20772 Z= 0.119 Angle : 0.651 14.642 28144 Z= 0.316 Chirality : 0.045 0.362 3008 Planarity : 0.003 0.036 3616 Dihedral : 4.788 59.960 2864 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.21 % Allowed : 14.76 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2480 helix: 1.09 (0.15), residues: 1268 sheet: -0.95 (0.35), residues: 192 loop : -1.17 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 321 TYR 0.017 0.001 TYR B 239 PHE 0.035 0.001 PHE A 400 TRP 0.008 0.001 TRP D 129 HIS 0.013 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00266 (20772) covalent geometry : angle 0.65108 (28144) hydrogen bonds : bond 0.03721 ( 967) hydrogen bonds : angle 4.39235 ( 2825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3415.34 seconds wall clock time: 59 minutes 52.72 seconds (3592.72 seconds total)