Starting phenix.real_space_refine on Sat Jul 4 11:08:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q12_13752/07_2026/7q12_13752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q12_13752/07_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_13752/07_2026/7q12_13752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q12_13752/07_2026/7q12_13752.map" model { file = "/net/cci-nas-00/data/ceres_data/7q12_13752/07_2026/7q12_13752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q12_13752/07_2026/7q12_13752.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7q12_13752/07_2026/7q12_13752.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q12_13752/07_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-6108/lib/python3.11/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: 7.02, per 1000 atoms: 0.35 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: 1.72 Conformation dependent library (CDL) restraints added in 1.6 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: 0.50 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: 3.30 Time building geometry restraints manager: 2.23 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 - 17.85: 10852 17.85 - 35.71: 1116 35.71 - 53.56: 216 53.56 - 71.42: 28 71.42 - 89.27: 16 Dihedral angle restraints: 12228 sinusoidal: 4956 harmonic: 7272 Sorted by residual: dihedral pdb=" CA ASN D 228 " pdb=" C ASN D 228 " pdb=" N VAL D 229 " pdb=" CA VAL D 229 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN A 228 " pdb=" C ASN A 228 " pdb=" N VAL A 229 " pdb=" CA VAL A 229 " ideal model delta harmonic sigma weight residual -180.00 -163.52 -16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN C 228 " pdb=" C ASN C 228 " pdb=" N VAL C 229 " pdb=" CA VAL C 229 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 12225 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: 0.06 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: 0.010 Normalize map: mean=0, sd=1: 2.560 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.520 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 14.571 89.273 7556 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/Z covalent geometry : bond 0.00299 / 0.14 (20772) covalent geometry : angle 0.58120 / 0.28 (28144) hydrogen bonds : bond 0.17756 / 11.88 ( 967) hydrogen bonds : angle 6.48904 / 4.63 ( 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 : 0.685 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: 0.1360 time to fit residues: 63.9769 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 : 0.810 ------------------------------------------------------------------------------- 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... A 587 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 ASN D 587 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.135283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095175 restraints weight = 112278.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.096345 restraints weight = 48569.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096996 restraints weight = 32879.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097711 restraints weight = 26469.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097965 restraints weight = 23465.698| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1160 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 : 0.591 7.860 28144 Z= 0.301 Chirality : 0.045 0.291 3008 Planarity : 0.003 0.040 3616 Dihedral : 3.573 15.652 2776 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.12 % Allowed : 8.85 % Favored : 90.04 % 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: 0.27 (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 0.011 0.001 TYR B 212 PHE 0.034 0.002 PHE D 400 TRP 0.010 0.001 TRP F 325 HIS 0.012 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (20772) covalent geometry : angle 0.59139 / 0.30 (28144) hydrogen bonds : bond 0.05021 / 3.26 ( 967) hydrogen bonds : angle 5.04643 / 3.62 ( 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 292 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.978 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. 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: 0.9392 (p90) cc_final: 0.8723 (p90) REVERT: A 271 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8598 (mmmt) REVERT: A 606 MET cc_start: 0.8745 (ttm) cc_final: 0.8509 (ttp) REVERT: F 342 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7936 (mttm) REVERT: B 271 LYS cc_start: 0.8973 (mmpt) cc_final: 0.8585 (mmmt) REVERT: C 240 HIS cc_start: 0.9359 (p90) cc_final: 0.9134 (p90) REVERT: C 271 LYS cc_start: 0.8913 (mmpt) cc_final: 0.8501 (mmmt) REVERT: D 271 LYS cc_start: 0.8986 (mmpt) cc_final: 0.8577 (mmmt) outliers start: 24 outliers final: 5 residues processed: 281 average time/residue: 0.1432 time to fit residues: 63.3354 Evaluate side-chains 244 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 239 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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: 0.4980 chunk 189 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 HIS A 178 HIS A 291 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 B 178 HIS B 291 HIS ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 291 HIS D 174 HIS D 178 HIS D 291 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091793 restraints weight = 113780.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.093052 restraints weight = 46379.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093545 restraints weight = 35632.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.094215 restraints weight = 27404.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.095073 restraints weight = 23694.986| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 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 = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1629 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= 0.171 Angle : 0.607 11.688 28144 Z= 0.309 Chirality : 0.044 0.283 3008 Planarity : 0.003 0.034 3616 Dihedral : 3.645 17.083 2776 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.40 % Allowed : 12.06 % Favored : 86.55 % 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: 0.24 (0.17), residues: 2480 helix: 1.09 (0.15), residues: 1260 sheet: -0.23 (0.36), residues: 192 loop : -0.90 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 241 TYR 0.009 0.001 TYR B 548 PHE 0.035 0.002 PHE C 400 TRP 0.007 0.001 TRP B 182 HIS 0.013 0.002 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (20772) covalent geometry : angle 0.60694 / 0.31 (28144) hydrogen bonds : bond 0.04712 / 3.04 ( 967) hydrogen bonds : angle 4.88954 / 3.50 ( 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 273 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.799 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. 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.9219 (p90) cc_final: 0.8925 (p90) REVERT: A 271 LYS cc_start: 0.8937 (mmpt) cc_final: 0.8559 (mmmt) REVERT: A 606 MET cc_start: 0.8801 (ttm) cc_final: 0.8555 (ttp) REVERT: F 342 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7954 (mttm) REVERT: B 271 LYS cc_start: 0.8909 (mmpt) cc_final: 0.8544 (mmmt) REVERT: C 240 HIS cc_start: 0.9346 (p90) cc_final: 0.9104 (p90) REVERT: C 271 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8454 (mmmt) REVERT: D 271 LYS cc_start: 0.8920 (mmpt) cc_final: 0.8526 (mmmt) outliers start: 30 outliers final: 20 residues processed: 259 average time/residue: 0.1390 time to fit residues: 57.1239 Evaluate side-chains 253 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 532 SER 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 332 TYR Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 231 LYS 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 344 GLU 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: 0.4980 chunk 179 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 chunk 47 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 C 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.133922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095133 restraints weight = 103700.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094630 restraints weight = 45452.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.096414 restraints weight = 33168.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096556 restraints weight = 24707.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098022 restraints weight = 21426.486| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20772 Z= 0.113 Angle : 0.570 8.880 28144 Z= 0.285 Chirality : 0.043 0.341 3008 Planarity : 0.003 0.031 3616 Dihedral : 3.563 18.995 2776 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.40 % Allowed : 11.82 % Favored : 86.78 % 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: 0.29 (0.17), residues: 2480 helix: 1.13 (0.15), residues: 1264 sheet: -0.30 (0.37), residues: 192 loop : -0.85 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 386 TYR 0.008 0.001 TYR C 212 PHE 0.027 0.001 PHE C 400 TRP 0.008 0.001 TRP B 182 HIS 0.011 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (20772) covalent geometry : angle 0.56998 / 0.28 (28144) hydrogen bonds : bond 0.04031 / 2.59 ( 967) hydrogen bonds : angle 4.63308 / 3.31 ( 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 284 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.793 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 240 HIS cc_start: 0.9229 (p90) cc_final: 0.8972 (p90) REVERT: A 269 LEU cc_start: 0.8774 (tp) cc_final: 0.8547 (tp) REVERT: A 271 LYS cc_start: 0.8823 (mmpt) cc_final: 0.8464 (mmmt) REVERT: F 342 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7778 (mttm) REVERT: B 271 LYS cc_start: 0.8780 (mmpt) cc_final: 0.8434 (mmmt) REVERT: C 240 HIS cc_start: 0.9328 (p90) cc_final: 0.9107 (p90) REVERT: C 269 LEU cc_start: 0.8717 (tp) cc_final: 0.8496 (tp) REVERT: C 271 LYS cc_start: 0.8765 (mmpt) cc_final: 0.8375 (mmmt) REVERT: C 423 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8586 (tm-30) REVERT: D 269 LEU cc_start: 0.8756 (tp) cc_final: 0.8501 (tp) REVERT: D 271 LYS cc_start: 0.8796 (mmpt) cc_final: 0.8438 (mmmt) REVERT: D 423 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8574 (tm-30) outliers start: 30 outliers final: 17 residues processed: 273 average time/residue: 0.1398 time to fit residues: 60.7739 Evaluate side-chains 258 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 352 LEU Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 174 HIS 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 174 HIS Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 174 HIS 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: 1.9990 chunk 24 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 174 HIS C 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.131003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091905 restraints weight = 120091.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091324 restraints weight = 51121.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092354 restraints weight = 40513.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092839 restraints weight = 29533.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093640 restraints weight = 25099.172| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20772 Z= 0.181 Angle : 0.609 8.543 28144 Z= 0.310 Chirality : 0.044 0.289 3008 Planarity : 0.004 0.030 3616 Dihedral : 3.683 18.522 2776 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.58 % Allowed : 13.13 % Favored : 85.29 % 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: 0.08 (0.17), residues: 2480 helix: 1.01 (0.15), residues: 1264 sheet: -0.52 (0.36), residues: 192 loop : -1.00 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 461 TYR 0.028 0.001 TYR H 332 PHE 0.026 0.002 PHE C 400 TRP 0.007 0.001 TRP B 182 HIS 0.012 0.002 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (20772) covalent geometry : angle 0.60908 / 0.31 (28144) hydrogen bonds : bond 0.04415 / 2.86 ( 967) hydrogen bonds : angle 4.70680 / 3.37 ( 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 280 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.789 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. 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 240 HIS cc_start: 0.9291 (p90) cc_final: 0.8952 (p90) REVERT: A 269 LEU cc_start: 0.8784 (tp) cc_final: 0.8547 (tp) REVERT: A 271 LYS cc_start: 0.8855 (mmpt) cc_final: 0.8483 (mmmt) REVERT: F 342 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7921 (mmtt) REVERT: B 271 LYS cc_start: 0.8817 (mmpt) cc_final: 0.8468 (mmmt) REVERT: C 240 HIS cc_start: 0.9345 (p90) cc_final: 0.8740 (p90) REVERT: C 269 LEU cc_start: 0.8727 (tp) cc_final: 0.8451 (tp) REVERT: C 271 LYS cc_start: 0.8821 (mmpt) cc_final: 0.8426 (mmmt) REVERT: C 423 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8661 (tm-30) REVERT: D 269 LEU cc_start: 0.8743 (tp) cc_final: 0.8493 (tp) REVERT: D 271 LYS cc_start: 0.8836 (mmpt) cc_final: 0.8469 (mmmt) REVERT: D 423 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8665 (tm-30) outliers start: 34 outliers final: 24 residues processed: 264 average time/residue: 0.1336 time to fit residues: 56.1876 Evaluate side-chains 256 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 345 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 175 VAL 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 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 421 ASP 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: 4.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 174 HIS C 174 HIS ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.130572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092265 restraints weight = 93691.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091280 restraints weight = 42889.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.092679 restraints weight = 35119.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092732 restraints weight = 27014.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093696 restraints weight = 23386.360| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20772 Z= 0.179 Angle : 0.631 10.957 28144 Z= 0.318 Chirality : 0.045 0.362 3008 Planarity : 0.003 0.029 3616 Dihedral : 3.798 19.242 2776 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.72 % Allowed : 13.87 % Favored : 84.40 % 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: -0.16 (0.17), residues: 2480 helix: 0.87 (0.15), residues: 1268 sheet: -0.94 (0.35), residues: 192 loop : -1.16 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 236 TYR 0.015 0.001 TYR H 332 PHE 0.030 0.002 PHE B 165 TRP 0.008 0.001 TRP D 129 HIS 0.012 0.002 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (20772) covalent geometry : angle 0.63055 / 0.32 (28144) hydrogen bonds : bond 0.04412 / 2.84 ( 967) hydrogen bonds : angle 4.70779 / 3.36 ( 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 286 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.671 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. revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.9281 (p90) cc_final: 0.8897 (p90) REVERT: A 269 LEU cc_start: 0.8706 (tp) cc_final: 0.8497 (tp) REVERT: A 271 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8456 (mmmt) REVERT: F 342 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7876 (mmtt) REVERT: B 271 LYS cc_start: 0.8780 (mmpt) cc_final: 0.8441 (mmmt) REVERT: B 423 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8497 (tm-30) REVERT: C 240 HIS cc_start: 0.9307 (p90) cc_final: 0.8720 (p90) REVERT: C 269 LEU cc_start: 0.8678 (tp) cc_final: 0.8436 (tp) REVERT: C 271 LYS cc_start: 0.8826 (mmpt) cc_final: 0.8447 (mmmt) REVERT: C 423 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8525 (tm-30) REVERT: D 269 LEU cc_start: 0.8676 (tp) cc_final: 0.8442 (tp) REVERT: D 271 LYS cc_start: 0.8790 (mmpt) cc_final: 0.8435 (mmmt) REVERT: D 423 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8536 (tm-30) outliers start: 37 outliers final: 24 residues processed: 270 average time/residue: 0.1321 time to fit residues: 57.4535 Evaluate side-chains 265 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 HIS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 344 GLU 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 174 HIS 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 174 HIS Chi-restraints excluded: chain D residue 235 GLU 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 421 ASP 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: 3.9990 chunk 11 optimal weight: 0.8980 chunk 233 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 174 HIS C 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.131949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091338 restraints weight = 106300.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091714 restraints weight = 44468.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092742 restraints weight = 30547.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093500 restraints weight = 22772.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093627 restraints weight = 19815.236| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20772 Z= 0.126 Angle : 0.615 12.218 28144 Z= 0.305 Chirality : 0.044 0.375 3008 Planarity : 0.003 0.028 3616 Dihedral : 3.730 19.468 2776 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.40 % Allowed : 14.15 % Favored : 84.45 % 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: -0.08 (0.17), residues: 2480 helix: 0.96 (0.15), residues: 1268 sheet: -0.94 (0.35), residues: 192 loop : -1.14 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 241 TYR 0.016 0.001 TYR H 332 PHE 0.022 0.001 PHE C 400 TRP 0.007 0.001 TRP D 129 HIS 0.012 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (20772) covalent geometry : angle 0.61478 / 0.30 (28144) hydrogen bonds : bond 0.04076 / 2.62 ( 967) hydrogen bonds : angle 4.56043 / 3.25 ( 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 283 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.810 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. 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 TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 240 HIS cc_start: 0.9240 (p90) cc_final: 0.8917 (p90) REVERT: A 269 LEU cc_start: 0.8757 (tp) cc_final: 0.8542 (tp) REVERT: A 271 LYS cc_start: 0.8831 (mmpt) cc_final: 0.8467 (mmmt) REVERT: A 423 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8551 (tm-30) REVERT: F 342 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7866 (mmtt) REVERT: H 342 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7866 (mmtt) REVERT: B 146 ARG cc_start: 0.8842 (ppt170) cc_final: 0.8053 (ttp80) REVERT: B 244 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8820 (ppp) REVERT: B 271 LYS cc_start: 0.8800 (mmpt) cc_final: 0.8454 (mmmt) REVERT: B 423 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8597 (tm-30) REVERT: C 146 ARG cc_start: 0.8863 (ppt170) cc_final: 0.8056 (ttp80) REVERT: C 269 LEU cc_start: 0.8700 (tp) cc_final: 0.8461 (tp) REVERT: C 271 LYS cc_start: 0.8836 (mmpt) cc_final: 0.8439 (mmmt) REVERT: C 423 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8576 (tm-30) REVERT: D 146 ARG cc_start: 0.8772 (ppt170) cc_final: 0.8000 (ttp80) REVERT: D 269 LEU cc_start: 0.8724 (tp) cc_final: 0.8484 (tp) REVERT: D 271 LYS cc_start: 0.8803 (mmpt) cc_final: 0.8434 (mmmt) REVERT: D 423 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8611 (tm-30) outliers start: 30 outliers final: 22 residues processed: 270 average time/residue: 0.1432 time to fit residues: 61.3341 Evaluate side-chains 264 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 421 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 174 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 76 optimal weight: 9.9990 chunk 171 optimal weight: 0.5980 chunk 211 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 228 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 174 HIS C 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.132316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.093342 restraints weight = 113917.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092680 restraints weight = 47848.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093646 restraints weight = 37421.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094772 restraints weight = 26850.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.095028 restraints weight = 22821.156| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2317 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= 0.122 Angle : 0.618 12.628 28144 Z= 0.303 Chirality : 0.044 0.381 3008 Planarity : 0.003 0.029 3616 Dihedral : 3.704 19.623 2776 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.77 % Allowed : 13.92 % 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: -0.07 (0.17), residues: 2480 helix: 0.99 (0.15), residues: 1268 sheet: -0.95 (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 192 TYR 0.010 0.001 TYR H 332 PHE 0.025 0.001 PHE B 165 TRP 0.007 0.001 TRP B 182 HIS 0.012 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (20772) covalent geometry : angle 0.61840 / 0.30 (28144) hydrogen bonds : bond 0.03953 / 2.54 ( 967) hydrogen bonds : angle 4.50351 / 3.21 ( 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 284 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.708 Fit side-chains 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 TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 240 HIS cc_start: 0.9229 (p90) cc_final: 0.8902 (p90) REVERT: A 269 LEU cc_start: 0.8789 (tp) cc_final: 0.8544 (tp) REVERT: A 271 LYS cc_start: 0.8830 (mmpt) cc_final: 0.8474 (mmmt) REVERT: A 423 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8561 (tm-30) REVERT: F 342 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7903 (mmtt) REVERT: H 342 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7853 (mmtt) REVERT: B 146 ARG cc_start: 0.8786 (ppt170) cc_final: 0.8024 (ttp80) REVERT: B 244 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8821 (ppp) REVERT: B 269 LEU cc_start: 0.8663 (tp) cc_final: 0.8382 (tp) REVERT: B 271 LYS cc_start: 0.8787 (mmpt) cc_final: 0.8442 (mmmt) REVERT: B 423 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8578 (tm-30) REVERT: C 146 ARG cc_start: 0.8819 (ppt170) cc_final: 0.8044 (ttp80) REVERT: C 269 LEU cc_start: 0.8702 (tp) cc_final: 0.8429 (tp) REVERT: C 271 LYS cc_start: 0.8801 (mmpt) cc_final: 0.8417 (mmmt) REVERT: C 423 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8564 (tm-30) REVERT: D 146 ARG cc_start: 0.8791 (ppt170) cc_final: 0.8029 (ttp80) REVERT: D 269 LEU cc_start: 0.8770 (tp) cc_final: 0.8490 (tp) REVERT: D 271 LYS cc_start: 0.8804 (mmpt) cc_final: 0.8453 (mmmt) REVERT: D 423 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8587 (tm-30) outliers start: 38 outliers final: 23 residues processed: 266 average time/residue: 0.1350 time to fit residues: 57.2134 Evaluate side-chains 265 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 421 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 448 MET 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 231 LYS 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 448 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS ** 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** D 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.131623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092530 restraints weight = 115979.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091927 restraints weight = 47943.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093073 restraints weight = 37490.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093618 restraints weight = 27589.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.094172 restraints weight = 23410.768| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20772 Z= 0.140 Angle : 0.639 12.617 28144 Z= 0.315 Chirality : 0.045 0.382 3008 Planarity : 0.003 0.030 3616 Dihedral : 3.750 19.246 2776 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.26 % Allowed : 14.29 % Favored : 84.45 % 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: -0.13 (0.17), residues: 2480 helix: 0.98 (0.15), residues: 1268 sheet: -1.04 (0.35), residues: 192 loop : -1.23 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 192 TYR 0.011 0.001 TYR H 332 PHE 0.021 0.001 PHE C 400 TRP 0.007 0.001 TRP D 129 HIS 0.012 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (20772) covalent geometry : angle 0.63942 / 0.31 (28144) hydrogen bonds : bond 0.04010 / 2.58 ( 967) hydrogen bonds : angle 4.52541 / 3.23 ( 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 271 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.845 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 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: A 146 ARG cc_start: 0.8890 (ppt170) cc_final: 0.8107 (ttp80) REVERT: A 269 LEU cc_start: 0.8762 (tp) cc_final: 0.8541 (tp) REVERT: A 271 LYS cc_start: 0.8830 (mmpt) cc_final: 0.8464 (mmmt) REVERT: A 423 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8555 (tm-30) REVERT: F 342 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7865 (mmtt) REVERT: B 146 ARG cc_start: 0.8794 (ppt170) cc_final: 0.8033 (ttp80) REVERT: B 244 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8841 (ppp) REVERT: B 269 LEU cc_start: 0.8640 (tp) cc_final: 0.8416 (tp) REVERT: B 271 LYS cc_start: 0.8801 (mmpt) cc_final: 0.8453 (mmmt) REVERT: B 423 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8614 (tm-30) REVERT: C 146 ARG cc_start: 0.8899 (ppt170) cc_final: 0.8137 (ttp80) REVERT: C 269 LEU cc_start: 0.8688 (tp) cc_final: 0.8436 (tp) REVERT: C 271 LYS cc_start: 0.8811 (mmpt) cc_final: 0.8420 (mmmt) REVERT: C 423 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8572 (tm-30) REVERT: D 146 ARG cc_start: 0.8815 (ppt170) cc_final: 0.8067 (ttp80) REVERT: D 269 LEU cc_start: 0.8765 (tp) cc_final: 0.8517 (tp) REVERT: D 271 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8461 (mmmt) REVERT: D 423 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8606 (tm-30) outliers start: 27 outliers final: 25 residues processed: 257 average time/residue: 0.1454 time to fit residues: 59.5009 Evaluate side-chains 267 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 421 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain G residue 332 TYR 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 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 448 MET 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 231 LYS 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 448 MET 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: 1.9990 chunk 174 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4059 r_free = 0.4059 target = 0.131600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091247 restraints weight = 101367.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091596 restraints weight = 43097.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.092608 restraints weight = 29716.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093351 restraints weight = 22536.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093464 restraints weight = 19541.473| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20772 Z= 0.137 Angle : 0.644 13.174 28144 Z= 0.314 Chirality : 0.045 0.373 3008 Planarity : 0.003 0.030 3616 Dihedral : 3.763 19.404 2776 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.40 % Allowed : 14.39 % Favored : 84.22 % 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: -0.15 (0.17), residues: 2480 helix: 0.97 (0.15), residues: 1268 sheet: -1.08 (0.35), residues: 192 loop : -1.24 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 236 TYR 0.014 0.001 TYR H 332 PHE 0.021 0.001 PHE B 165 TRP 0.008 0.001 TRP A 129 HIS 0.013 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (20772) covalent geometry : angle 0.64402 / 0.31 (28144) hydrogen bonds : bond 0.03966 / 2.55 ( 967) hydrogen bonds : angle 4.51106 / 3.22 ( 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 273 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.743 Fit side-chains revert: symmetry clash 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 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: 0.8757 (tp) cc_final: 0.8536 (tp) REVERT: A 271 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8445 (mmmt) REVERT: A 423 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8533 (tm-30) REVERT: F 342 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7927 (mmtt) REVERT: B 146 ARG cc_start: 0.8847 (ppt170) cc_final: 0.8065 (ttp80) REVERT: B 244 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8848 (ppp) REVERT: B 269 LEU cc_start: 0.8634 (tp) cc_final: 0.8380 (tp) REVERT: B 271 LYS cc_start: 0.8811 (mmpt) cc_final: 0.8458 (mmmt) REVERT: B 423 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 146 ARG cc_start: 0.8874 (ppt170) cc_final: 0.8087 (ttp80) REVERT: C 269 LEU cc_start: 0.8712 (tp) cc_final: 0.8469 (tp) REVERT: C 271 LYS cc_start: 0.8812 (mmpt) cc_final: 0.8418 (mmmt) REVERT: C 423 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8560 (tm-30) REVERT: D 146 ARG cc_start: 0.8879 (ppt170) cc_final: 0.8130 (ttp80) REVERT: D 269 LEU cc_start: 0.8771 (tp) cc_final: 0.8512 (tp) REVERT: D 271 LYS cc_start: 0.8816 (mmpt) cc_final: 0.8451 (mmmt) REVERT: D 423 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8584 (tm-30) outliers start: 30 outliers final: 26 residues processed: 259 average time/residue: 0.1371 time to fit residues: 56.7457 Evaluate side-chains 268 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 421 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain G residue 321 ARG Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain G residue 345 LEU 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 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 448 MET 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 231 LYS 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 448 MET 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: 0.7980 chunk 167 optimal weight: 0.7980 chunk 236 optimal weight: 0.0670 chunk 110 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 202 optimal weight: 0.3980 chunk 52 optimal weight: 0.0870 chunk 134 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4084 r_free = 0.4084 target = 0.133574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093056 restraints weight = 102617.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093717 restraints weight = 41744.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.094993 restraints weight = 27751.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095557 restraints weight = 21151.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095710 restraints weight = 18735.144| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20772 Z= 0.112 Angle : 0.634 13.418 28144 Z= 0.307 Chirality : 0.044 0.359 3008 Planarity : 0.003 0.030 3616 Dihedral : 3.708 20.256 2776 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.88 % Allowed : 14.76 % Favored : 84.36 % 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: -0.05 (0.17), residues: 2480 helix: 1.05 (0.15), residues: 1272 sheet: -0.99 (0.35), residues: 192 loop : -1.21 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 321 TYR 0.012 0.001 TYR H 332 PHE 0.019 0.001 PHE C 400 TRP 0.009 0.001 TRP D 512 HIS 0.013 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (20772) covalent geometry : angle 0.63372 / 0.31 (28144) hydrogen bonds : bond 0.03649 / 2.34 ( 967) hydrogen bonds : angle 4.40928 / 3.15 ( 2825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.78 seconds wall clock time: 62 minutes 27.70 seconds (3747.70 seconds total)