Starting phenix.real_space_refine on Thu Sep 18 12:30:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5h3o_6656/09_2025/5h3o_6656.cif Found real_map, /net/cci-nas-00/data/ceres_data/5h3o_6656/09_2025/5h3o_6656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5h3o_6656/09_2025/5h3o_6656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5h3o_6656/09_2025/5h3o_6656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5h3o_6656/09_2025/5h3o_6656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5h3o_6656/09_2025/5h3o_6656.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 96 5.16 5 Na 3 4.78 5 C 11008 2.51 5 N 2852 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16958 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4215 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "C" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "D" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' NA': 2, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' NA': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.23 Number of scatterers: 16958 At special positions: 0 Unit cell: (109.56, 109.56, 135.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 4 15.00 Na 3 11.00 O 2995 8.00 N 2852 7.00 C 11008 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: 1.29 Conformation dependent library (CDL) restraints added in 498.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 16 sheets defined 60.7% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 118 through 145 removed outlier: 5.415A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 224 Processing helix chain 'A' and resid 237 through 247 removed outlier: 4.179A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 4.077A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.531A pdb=" N ILE A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 4.112A pdb=" N VAL A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 334 removed outlier: 3.747A pdb=" N PHE A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 385 through 417 removed outlier: 3.987A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.795A pdb=" N THR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 458 removed outlier: 3.704A pdb=" N GLU A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 472 through 490 removed outlier: 4.775A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.636A pdb=" N CYS A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 559 through 564 removed outlier: 4.214A pdb=" N ILE A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 600 Processing helix chain 'A' and resid 602 through 619 removed outlier: 3.749A pdb=" N ARG A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS A 619 " --> pdb=" O GLU A 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 118 through 145 removed outlier: 5.404A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 224 Processing helix chain 'B' and resid 237 through 247 removed outlier: 4.181A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 257 removed outlier: 4.076A pdb=" N ARG B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 276 through 285 removed outlier: 3.549A pdb=" N ILE B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 4.121A pdb=" N VAL B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 334 removed outlier: 3.721A pdb=" N PHE B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 385 through 417 removed outlier: 3.995A pdb=" N ALA B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.793A pdb=" N THR B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 458 removed outlier: 3.711A pdb=" N GLU B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 458 " --> pdb=" O TYR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 490 removed outlier: 4.772A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 497 removed outlier: 3.628A pdb=" N CYS B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 559 through 564 removed outlier: 4.233A pdb=" N ILE B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 600 Processing helix chain 'B' and resid 602 through 619 removed outlier: 3.739A pdb=" N ARG B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 118 through 145 removed outlier: 5.395A pdb=" N ILE C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 224 Processing helix chain 'C' and resid 237 through 247 removed outlier: 4.171A pdb=" N THR C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 removed outlier: 4.069A pdb=" N ARG C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 276 through 285 removed outlier: 3.539A pdb=" N ILE C 285 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 4.103A pdb=" N VAL C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 299 " --> pdb=" O GLU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 334 removed outlier: 3.726A pdb=" N PHE C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 417 removed outlier: 3.999A pdb=" N ALA C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 438 removed outlier: 3.781A pdb=" N THR C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 458 removed outlier: 3.697A pdb=" N GLU C 445 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 458 " --> pdb=" O TYR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 472 through 490 removed outlier: 4.764A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 497 removed outlier: 3.645A pdb=" N CYS C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'C' and resid 559 through 564 removed outlier: 4.218A pdb=" N ILE C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 600 Processing helix chain 'C' and resid 602 through 618 removed outlier: 3.756A pdb=" N ARG C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 118 through 145 removed outlier: 5.429A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 224 Processing helix chain 'D' and resid 237 through 247 removed outlier: 4.184A pdb=" N THR D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 257 removed outlier: 4.054A pdb=" N ARG D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.527A pdb=" N ILE D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 4.112A pdb=" N VAL D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 334 removed outlier: 3.731A pdb=" N PHE D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 312 " --> pdb=" O ARG D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 375 Processing helix chain 'D' and resid 385 through 417 removed outlier: 4.005A pdb=" N ALA D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 438 removed outlier: 3.799A pdb=" N THR D 422 " --> pdb=" O SER D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 458 removed outlier: 3.691A pdb=" N GLU D 445 " --> pdb=" O SER D 441 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 472 through 490 removed outlier: 4.779A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N THR D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 497 removed outlier: 3.607A pdb=" N CYS D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 559 through 564 removed outlier: 4.228A pdb=" N ILE D 563 " --> pdb=" O GLY D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 600 Processing helix chain 'D' and resid 602 through 619 removed outlier: 3.754A pdb=" N ARG D 606 " --> pdb=" O TYR D 602 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS D 619 " --> pdb=" O GLU D 615 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.687A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 510 through 514 removed outlier: 6.586A pdb=" N ASP A 586 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 552 removed outlier: 4.136A pdb=" N ASN A 578 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AA6, first strand: chain 'B' and resid 228 through 229 removed outlier: 3.686A pdb=" N LEU B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 510 through 514 removed outlier: 6.603A pdb=" N ASP B 586 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 550 through 552 removed outlier: 4.166A pdb=" N ASN B 578 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AB1, first strand: chain 'C' and resid 228 through 229 removed outlier: 3.692A pdb=" N LEU C 232 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 510 through 514 removed outlier: 6.587A pdb=" N ASP C 586 " --> pdb=" O LYS C 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 550 through 552 removed outlier: 4.142A pdb=" N ASN C 578 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB5, first strand: chain 'D' and resid 228 through 229 removed outlier: 3.677A pdb=" N LEU D 232 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 510 through 514 removed outlier: 6.611A pdb=" N ASP D 586 " --> pdb=" O LYS D 534 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 550 through 552 removed outlier: 4.140A pdb=" N ASN D 578 " --> pdb=" O VAL D 541 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4780 1.33 - 1.46: 3786 1.46 - 1.58: 8635 1.58 - 1.70: 18 1.70 - 1.83: 156 Bond restraints: 17375 Sorted by residual: bond pdb=" CA ILE A 268 " pdb=" CB ILE A 268 " ideal model delta sigma weight residual 1.537 1.628 -0.091 1.29e-02 6.01e+03 4.95e+01 bond pdb=" CA ILE C 268 " pdb=" CB ILE C 268 " ideal model delta sigma weight residual 1.537 1.626 -0.089 1.29e-02 6.01e+03 4.71e+01 bond pdb=" CA ILE D 268 " pdb=" CB ILE D 268 " ideal model delta sigma weight residual 1.537 1.626 -0.088 1.29e-02 6.01e+03 4.70e+01 bond pdb=" CA ILE B 268 " pdb=" CB ILE B 268 " ideal model delta sigma weight residual 1.537 1.622 -0.085 1.29e-02 6.01e+03 4.37e+01 bond pdb=" C PRO B 277 " pdb=" N ILE B 278 " ideal model delta sigma weight residual 1.335 1.272 0.063 1.10e-02 8.26e+03 3.29e+01 ... (remaining 17370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21481 2.36 - 4.72: 1736 4.72 - 7.08: 252 7.08 - 9.44: 92 9.44 - 11.81: 25 Bond angle restraints: 23586 Sorted by residual: angle pdb=" N SER A 155 " pdb=" CA SER A 155 " pdb=" C SER A 155 " ideal model delta sigma weight residual 111.28 121.73 -10.45 1.09e+00 8.42e-01 9.20e+01 angle pdb=" N SER C 155 " pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 111.28 121.69 -10.41 1.09e+00 8.42e-01 9.12e+01 angle pdb=" N SER B 155 " pdb=" CA SER B 155 " pdb=" C SER B 155 " ideal model delta sigma weight residual 111.28 121.65 -10.37 1.09e+00 8.42e-01 9.05e+01 angle pdb=" N SER D 155 " pdb=" CA SER D 155 " pdb=" C SER D 155 " ideal model delta sigma weight residual 111.28 121.61 -10.33 1.09e+00 8.42e-01 8.99e+01 angle pdb=" N ILE B 377 " pdb=" CA ILE B 377 " pdb=" C ILE B 377 " ideal model delta sigma weight residual 111.45 102.65 8.80 9.30e-01 1.16e+00 8.96e+01 ... (remaining 23581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.99: 9652 26.99 - 53.99: 573 53.99 - 80.98: 78 80.98 - 107.98: 12 107.98 - 134.97: 16 Dihedral angle restraints: 10331 sinusoidal: 4312 harmonic: 6019 Sorted by residual: dihedral pdb=" C LEU A 346 " pdb=" N LEU A 346 " pdb=" CA LEU A 346 " pdb=" CB LEU A 346 " ideal model delta harmonic sigma weight residual -122.60 -152.85 30.25 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" N LEU A 346 " pdb=" C LEU A 346 " pdb=" CA LEU A 346 " pdb=" CB LEU A 346 " ideal model delta harmonic sigma weight residual 122.80 151.82 -29.02 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C LEU D 346 " pdb=" N LEU D 346 " pdb=" CA LEU D 346 " pdb=" CB LEU D 346 " ideal model delta harmonic sigma weight residual -122.60 -151.48 28.88 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 10328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 2596 0.261 - 0.523: 8 0.523 - 0.784: 4 0.784 - 1.046: 0 1.046 - 1.307: 4 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CA LEU A 346 " pdb=" N LEU A 346 " pdb=" C LEU A 346 " pdb=" CB LEU A 346 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.27e+01 chirality pdb=" CA LEU D 346 " pdb=" N LEU D 346 " pdb=" C LEU D 346 " pdb=" CB LEU D 346 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.94e+01 chirality pdb=" CA LEU B 346 " pdb=" N LEU B 346 " pdb=" C LEU B 346 " pdb=" CB LEU B 346 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.70e+01 ... (remaining 2609 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 347 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASN D 347 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN D 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS D 348 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 347 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C ASN A 347 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 348 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 347 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C ASN C 347 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN C 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS C 348 " -0.014 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2869 2.77 - 3.30: 18001 3.30 - 3.83: 27304 3.83 - 4.37: 33569 4.37 - 4.90: 53991 Nonbonded interactions: 135734 Sorted by model distance: nonbonded pdb=" O GLY A 572 " pdb=" N ARG A 574 " model vdw 2.235 3.120 nonbonded pdb=" O GLY B 572 " pdb=" N ARG B 574 " model vdw 2.236 3.120 nonbonded pdb=" O GLY C 572 " pdb=" N ARG C 574 " model vdw 2.239 3.120 nonbonded pdb=" O GLY D 572 " pdb=" N ARG D 574 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG A 537 " pdb=" OE1 GLN B 230 " model vdw 2.243 3.120 ... (remaining 135729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 106 through 801) selection = (chain 'B' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 801)) selection = (chain 'C' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 801)) selection = (chain 'D' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.200 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.011 0.102 17375 Z= 0.650 Angle : 1.503 11.805 23586 Z= 0.970 Chirality : 0.083 1.307 2612 Planarity : 0.006 0.051 2904 Dihedral : 17.481 134.972 6467 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.98 % Favored : 93.43 % Rotamer: Outliers : 6.55 % Allowed : 15.85 % Favored : 77.60 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: -3.19 (0.16), residues: 2024 helix: -2.41 (0.12), residues: 1072 sheet: -0.98 (0.47), residues: 120 loop : -1.63 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 142 TYR 0.021 0.003 TYR D 262 PHE 0.026 0.003 PHE B 403 TRP 0.023 0.003 TRP D 266 HIS 0.009 0.002 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.01066 (17375) covalent geometry : angle 1.50309 (23586) hydrogen bonds : bond 0.15745 ( 915) hydrogen bonds : angle 8.44554 ( 2589) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 545 time to evaluate : 0.503 Fit side-chains REVERT: A 112 TYR cc_start: 0.7449 (t80) cc_final: 0.7124 (t80) REVERT: A 119 ASP cc_start: 0.7889 (t0) cc_final: 0.7273 (t0) REVERT: A 123 TYR cc_start: 0.8477 (m-80) cc_final: 0.8186 (m-80) REVERT: A 158 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.7590 (ptp-110) REVERT: A 180 MET cc_start: 0.8284 (pmm) cc_final: 0.8016 (ptp) REVERT: A 238 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7302 (mp0) REVERT: A 291 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8043 (tpt170) REVERT: A 295 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8134 (mm-30) REVERT: A 303 MET cc_start: 0.8084 (ptp) cc_final: 0.7073 (mmm) REVERT: A 375 THR cc_start: 0.8784 (p) cc_final: 0.8568 (p) REVERT: A 397 MET cc_start: 0.8613 (mmm) cc_final: 0.8186 (mtm) REVERT: A 413 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8422 (mtt) REVERT: A 432 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8618 (mtmm) REVERT: A 460 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6755 (pp30) REVERT: A 467 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8765 (m) REVERT: A 535 ARG cc_start: 0.8682 (ptp90) cc_final: 0.8448 (ttp80) REVERT: A 578 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8703 (p0) REVERT: B 119 ASP cc_start: 0.7768 (t0) cc_final: 0.7146 (t0) REVERT: B 123 TYR cc_start: 0.8453 (m-80) cc_final: 0.8140 (m-80) REVERT: B 153 SER cc_start: 0.8665 (p) cc_final: 0.8346 (m) REVERT: B 180 MET cc_start: 0.8307 (pmm) cc_final: 0.8040 (ptp) REVERT: B 234 VAL cc_start: 0.8625 (t) cc_final: 0.8424 (t) REVERT: B 291 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8062 (tpt170) REVERT: B 295 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8014 (mm-30) REVERT: B 331 SER cc_start: 0.8642 (t) cc_final: 0.8342 (p) REVERT: B 354 ASP cc_start: 0.8228 (m-30) cc_final: 0.7915 (t0) REVERT: B 397 MET cc_start: 0.8645 (mmm) cc_final: 0.8136 (mtm) REVERT: B 423 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: B 427 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8936 (mmmt) REVERT: B 432 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8614 (mtmm) REVERT: B 460 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6610 (pp30) REVERT: B 467 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8799 (m) REVERT: B 535 ARG cc_start: 0.8683 (ptp90) cc_final: 0.8289 (ptp90) REVERT: B 543 ASP cc_start: 0.6564 (m-30) cc_final: 0.6345 (m-30) REVERT: B 578 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8639 (p0) REVERT: C 119 ASP cc_start: 0.7760 (t0) cc_final: 0.7096 (t0) REVERT: C 123 TYR cc_start: 0.8426 (m-80) cc_final: 0.8096 (m-80) REVERT: C 153 SER cc_start: 0.8696 (p) cc_final: 0.8369 (m) REVERT: C 180 MET cc_start: 0.8309 (pmm) cc_final: 0.8015 (ptp) REVERT: C 218 ASP cc_start: 0.8268 (t70) cc_final: 0.7998 (t70) REVERT: C 291 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8033 (tpt170) REVERT: C 303 MET cc_start: 0.8106 (ptp) cc_final: 0.7031 (mmm) REVERT: C 331 SER cc_start: 0.8646 (t) cc_final: 0.8352 (p) REVERT: C 354 ASP cc_start: 0.8298 (m-30) cc_final: 0.7912 (t0) REVERT: C 432 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8610 (mtmm) REVERT: C 460 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6577 (pp30) REVERT: C 467 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8800 (m) REVERT: C 535 ARG cc_start: 0.8679 (ptp90) cc_final: 0.8464 (ttp80) REVERT: C 543 ASP cc_start: 0.6514 (m-30) cc_final: 0.6302 (m-30) REVERT: C 578 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8701 (p0) REVERT: D 119 ASP cc_start: 0.7809 (t0) cc_final: 0.7178 (t0) REVERT: D 123 TYR cc_start: 0.8476 (m-80) cc_final: 0.8154 (m-80) REVERT: D 153 SER cc_start: 0.8725 (p) cc_final: 0.8431 (m) REVERT: D 234 VAL cc_start: 0.8652 (t) cc_final: 0.8446 (t) REVERT: D 291 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8059 (tpt170) REVERT: D 295 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8118 (mm-30) REVERT: D 303 MET cc_start: 0.8080 (ptp) cc_final: 0.7078 (mmm) REVERT: D 331 SER cc_start: 0.8639 (t) cc_final: 0.8338 (p) REVERT: D 342 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8920 (p) REVERT: D 354 ASP cc_start: 0.8273 (m-30) cc_final: 0.7890 (t0) REVERT: D 375 THR cc_start: 0.8705 (p) cc_final: 0.8500 (p) REVERT: D 432 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8630 (mtmm) REVERT: D 460 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6576 (pp30) REVERT: D 467 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8841 (m) REVERT: D 535 ARG cc_start: 0.8691 (ptp90) cc_final: 0.8145 (ptp90) REVERT: D 578 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8677 (p0) outliers start: 121 outliers final: 37 residues processed: 637 average time/residue: 0.1433 time to fit residues: 132.8383 Evaluate side-chains 447 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 391 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 TRP Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 273 TRP Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 578 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0870 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 175 ASN A 323 ASN A 416 ASN B 143 GLN B 175 ASN B 323 ASN B 416 ASN C 143 GLN C 175 ASN C 323 ASN C 416 ASN C 466 GLN D 143 GLN D 175 ASN D 323 ASN D 416 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114848 restraints weight = 25281.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119088 restraints weight = 12914.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120972 restraints weight = 8850.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122408 restraints weight = 7337.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122923 restraints weight = 6460.624| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17375 Z= 0.129 Angle : 0.658 11.905 23586 Z= 0.336 Chirality : 0.045 0.193 2612 Planarity : 0.004 0.032 2904 Dihedral : 14.684 153.824 2528 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.22 % Allowed : 22.73 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: -0.17 (0.18), residues: 2024 helix: 0.49 (0.15), residues: 1096 sheet: -0.67 (0.47), residues: 120 loop : -0.74 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.017 0.001 TYR D 223 PHE 0.010 0.001 PHE C 206 TRP 0.010 0.001 TRP C 322 HIS 0.002 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00279 (17375) covalent geometry : angle 0.65763 (23586) hydrogen bonds : bond 0.03994 ( 915) hydrogen bonds : angle 4.88867 ( 2589) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 488 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7337 (t80) cc_final: 0.6858 (t80) REVERT: A 158 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7209 (ptp-110) REVERT: A 238 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6865 (mp0) REVERT: A 288 LYS cc_start: 0.8361 (tttt) cc_final: 0.7857 (ttmm) REVERT: A 303 MET cc_start: 0.7197 (ptp) cc_final: 0.6536 (mmm) REVERT: A 331 SER cc_start: 0.8852 (t) cc_final: 0.8590 (p) REVERT: A 342 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8536 (p) REVERT: A 397 MET cc_start: 0.7952 (mmm) cc_final: 0.7390 (mtp) REVERT: A 423 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7479 (tm-30) REVERT: A 436 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6662 (mm-30) REVERT: A 460 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6467 (pp30) REVERT: A 535 ARG cc_start: 0.8337 (ptp90) cc_final: 0.7898 (ttp80) REVERT: A 594 ASP cc_start: 0.8296 (m-30) cc_final: 0.7968 (m-30) REVERT: B 288 LYS cc_start: 0.8060 (tttt) cc_final: 0.7701 (ttmm) REVERT: B 303 MET cc_start: 0.7218 (ptp) cc_final: 0.6542 (mmm) REVERT: B 397 MET cc_start: 0.7964 (mmm) cc_final: 0.7409 (mtp) REVERT: B 436 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 460 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6384 (pp30) REVERT: B 492 ARG cc_start: 0.7390 (mmm160) cc_final: 0.6767 (mmm-85) REVERT: B 535 ARG cc_start: 0.8393 (ptp90) cc_final: 0.7962 (ttp80) REVERT: B 594 ASP cc_start: 0.8290 (m-30) cc_final: 0.7961 (m-30) REVERT: C 228 MET cc_start: 0.7275 (ttm) cc_final: 0.6991 (tpp) REVERT: C 291 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7107 (tpp-160) REVERT: C 303 MET cc_start: 0.7197 (ptp) cc_final: 0.6506 (mmm) REVERT: C 397 MET cc_start: 0.7879 (mmt) cc_final: 0.7445 (mtm) REVERT: C 423 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 436 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6652 (mm-30) REVERT: C 460 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6462 (pp30) REVERT: C 471 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8638 (mp) REVERT: C 492 ARG cc_start: 0.7323 (mmm160) cc_final: 0.6839 (mmm-85) REVERT: C 535 ARG cc_start: 0.8401 (ptp90) cc_final: 0.7915 (ttp80) REVERT: C 594 ASP cc_start: 0.8305 (m-30) cc_final: 0.7977 (m-30) REVERT: D 303 MET cc_start: 0.7249 (ptp) cc_final: 0.6578 (mmm) REVERT: D 331 SER cc_start: 0.8932 (t) cc_final: 0.8564 (p) REVERT: D 342 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8547 (p) REVERT: D 397 MET cc_start: 0.7857 (mmt) cc_final: 0.7409 (mtm) REVERT: D 423 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7454 (tm-30) REVERT: D 436 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6650 (mm-30) REVERT: D 460 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6380 (pp30) REVERT: D 535 ARG cc_start: 0.8394 (ptp90) cc_final: 0.7866 (ttp80) REVERT: D 594 ASP cc_start: 0.8319 (m-30) cc_final: 0.7980 (m-30) outliers start: 78 outliers final: 34 residues processed: 525 average time/residue: 0.1346 time to fit residues: 105.5190 Evaluate side-chains 426 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 384 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 502 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 169 GLN A 416 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 476 GLN B 143 GLN B 416 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 476 GLN C 143 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN D 143 GLN D 416 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 GLN D 476 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.155820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115934 restraints weight = 25747.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116735 restraints weight = 14388.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116871 restraints weight = 10895.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117749 restraints weight = 10753.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117651 restraints weight = 9752.403| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17375 Z= 0.173 Angle : 0.654 9.769 23586 Z= 0.330 Chirality : 0.045 0.186 2612 Planarity : 0.004 0.039 2904 Dihedral : 13.766 154.622 2453 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.49 % Allowed : 22.24 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 0.59 (0.19), residues: 2024 helix: 1.20 (0.16), residues: 1072 sheet: -0.49 (0.48), residues: 120 loop : -0.47 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 283 TYR 0.025 0.001 TYR A 223 PHE 0.011 0.002 PHE D 328 TRP 0.012 0.001 TRP B 124 HIS 0.001 0.000 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00397 (17375) covalent geometry : angle 0.65424 (23586) hydrogen bonds : bond 0.03858 ( 915) hydrogen bonds : angle 4.47061 ( 2589) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 401 time to evaluate : 0.635 Fit side-chains REVERT: A 238 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7022 (mp0) REVERT: A 303 MET cc_start: 0.7553 (ptp) cc_final: 0.6876 (mmm) REVERT: A 436 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6568 (mm-30) REVERT: A 460 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6488 (pp30) REVERT: A 561 LEU cc_start: 0.8249 (mt) cc_final: 0.8045 (mm) REVERT: A 594 ASP cc_start: 0.8247 (m-30) cc_final: 0.7883 (m-30) REVERT: B 218 ASP cc_start: 0.8084 (t70) cc_final: 0.7835 (t70) REVERT: B 303 MET cc_start: 0.7501 (ptp) cc_final: 0.6694 (mmm) REVERT: B 423 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 436 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6564 (mm-30) REVERT: B 460 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6301 (pp30) REVERT: B 478 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: B 561 LEU cc_start: 0.8225 (mt) cc_final: 0.7722 (mt) REVERT: B 594 ASP cc_start: 0.8294 (m-30) cc_final: 0.7956 (m-30) REVERT: C 291 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7153 (tpt170) REVERT: C 303 MET cc_start: 0.7517 (ptp) cc_final: 0.6694 (mmm) REVERT: C 397 MET cc_start: 0.7736 (mmt) cc_final: 0.7256 (mtm) REVERT: C 436 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6538 (mm-30) REVERT: C 460 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6325 (pp30) REVERT: C 471 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8718 (mp) REVERT: C 478 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 594 ASP cc_start: 0.8269 (m-30) cc_final: 0.7919 (m-30) REVERT: D 137 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9037 (mt) REVERT: D 176 MET cc_start: 0.7899 (ttp) cc_final: 0.7667 (ttp) REVERT: D 303 MET cc_start: 0.7593 (ptp) cc_final: 0.7036 (mmm) REVERT: D 397 MET cc_start: 0.7730 (mmt) cc_final: 0.7262 (mtm) REVERT: D 436 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6504 (mm-30) REVERT: D 460 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6307 (pp30) REVERT: D 478 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: D 561 LEU cc_start: 0.8225 (mt) cc_final: 0.7724 (mt) REVERT: D 594 ASP cc_start: 0.8256 (m-30) cc_final: 0.7903 (m-30) outliers start: 120 outliers final: 59 residues processed: 473 average time/residue: 0.1252 time to fit residues: 91.4293 Evaluate side-chains 430 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 361 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 185 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 272 ASN A 416 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 272 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 272 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN D 272 ASN D 416 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117116 restraints weight = 25566.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117675 restraints weight = 14739.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118821 restraints weight = 10866.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119593 restraints weight = 10318.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119310 restraints weight = 9133.355| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17375 Z= 0.146 Angle : 0.611 9.931 23586 Z= 0.311 Chirality : 0.044 0.188 2612 Planarity : 0.004 0.043 2904 Dihedral : 13.534 155.357 2452 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.11 % Allowed : 24.24 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 0.99 (0.19), residues: 2024 helix: 1.56 (0.16), residues: 1076 sheet: -0.52 (0.50), residues: 120 loop : -0.30 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 580 TYR 0.021 0.001 TYR A 223 PHE 0.011 0.001 PHE A 206 TRP 0.011 0.001 TRP C 124 HIS 0.001 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00337 (17375) covalent geometry : angle 0.61075 (23586) hydrogen bonds : bond 0.03561 ( 915) hydrogen bonds : angle 4.18180 ( 2589) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 374 time to evaluate : 0.540 Fit side-chains REVERT: A 176 MET cc_start: 0.7638 (ttp) cc_final: 0.7283 (ttp) REVERT: A 229 ASP cc_start: 0.8112 (m-30) cc_final: 0.7757 (m-30) REVERT: A 303 MET cc_start: 0.7668 (ptp) cc_final: 0.7004 (mmm) REVERT: A 436 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 445 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 460 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6387 (pp30) REVERT: A 594 ASP cc_start: 0.8277 (m-30) cc_final: 0.8003 (m-30) REVERT: B 176 MET cc_start: 0.7746 (ttp) cc_final: 0.7477 (ttp) REVERT: B 218 ASP cc_start: 0.8058 (t70) cc_final: 0.7835 (t70) REVERT: B 227 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8268 (p90) REVERT: B 228 MET cc_start: 0.7410 (tpp) cc_final: 0.7209 (tpp) REVERT: B 303 MET cc_start: 0.7641 (ptp) cc_final: 0.7004 (mmm) REVERT: B 423 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 436 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6599 (mm-30) REVERT: B 460 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6362 (pp30) REVERT: B 478 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: B 594 ASP cc_start: 0.8293 (m-30) cc_final: 0.8018 (m-30) REVERT: C 176 MET cc_start: 0.7657 (ttp) cc_final: 0.7297 (ttp) REVERT: C 227 TYR cc_start: 0.8617 (p90) cc_final: 0.8345 (p90) REVERT: C 291 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7116 (tpp-160) REVERT: C 303 MET cc_start: 0.7572 (ptp) cc_final: 0.7013 (mmm) REVERT: C 397 MET cc_start: 0.7698 (mmt) cc_final: 0.7311 (mtm) REVERT: C 436 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6618 (mm-30) REVERT: C 445 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7942 (tm-30) REVERT: C 460 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6288 (pp30) REVERT: C 471 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8703 (mp) REVERT: C 478 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: C 561 LEU cc_start: 0.8523 (mm) cc_final: 0.8265 (mm) REVERT: C 594 ASP cc_start: 0.8305 (m-30) cc_final: 0.8037 (m-30) REVERT: D 176 MET cc_start: 0.7901 (ttp) cc_final: 0.7502 (ttp) REVERT: D 212 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: D 227 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8186 (p90) REVERT: D 248 LYS cc_start: 0.8234 (mttp) cc_final: 0.7718 (mmtt) REVERT: D 303 MET cc_start: 0.7660 (ptp) cc_final: 0.7003 (mmm) REVERT: D 397 MET cc_start: 0.7717 (mmt) cc_final: 0.7356 (mtm) REVERT: D 429 ASP cc_start: 0.7824 (m-30) cc_final: 0.7562 (m-30) REVERT: D 436 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6758 (mm-30) REVERT: D 445 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 460 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6368 (pp30) REVERT: D 478 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: D 594 ASP cc_start: 0.8310 (m-30) cc_final: 0.8055 (m-30) outliers start: 113 outliers final: 71 residues processed: 441 average time/residue: 0.1144 time to fit residues: 79.0332 Evaluate side-chains 435 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 352 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 416 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN D 143 GLN D 416 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118507 restraints weight = 25469.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120644 restraints weight = 15843.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120637 restraints weight = 11813.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121339 restraints weight = 11103.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121466 restraints weight = 9817.112| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17375 Z= 0.146 Angle : 0.604 9.932 23586 Z= 0.304 Chirality : 0.044 0.190 2612 Planarity : 0.004 0.043 2904 Dihedral : 13.373 155.215 2452 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.93 % Allowed : 23.48 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 1.11 (0.19), residues: 2024 helix: 1.65 (0.16), residues: 1072 sheet: -0.42 (0.51), residues: 120 loop : -0.23 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 580 TYR 0.020 0.001 TYR A 223 PHE 0.011 0.001 PHE C 328 TRP 0.012 0.001 TRP B 124 HIS 0.002 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00338 (17375) covalent geometry : angle 0.60410 (23586) hydrogen bonds : bond 0.03469 ( 915) hydrogen bonds : angle 4.10245 ( 2589) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 367 time to evaluate : 0.675 Fit side-chains REVERT: A 176 MET cc_start: 0.7601 (ttp) cc_final: 0.7292 (ttp) REVERT: A 227 TYR cc_start: 0.8401 (p90) cc_final: 0.7945 (p90) REVERT: A 303 MET cc_start: 0.7699 (ptp) cc_final: 0.7061 (mmm) REVERT: A 436 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6782 (mm-30) REVERT: A 445 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 460 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6502 (pp30) REVERT: A 594 ASP cc_start: 0.8226 (m-30) cc_final: 0.7983 (m-30) REVERT: A 620 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6403 (t0) REVERT: B 176 MET cc_start: 0.7730 (ttp) cc_final: 0.7257 (ttp) REVERT: B 227 TYR cc_start: 0.8573 (p90) cc_final: 0.8201 (p90) REVERT: B 248 LYS cc_start: 0.8222 (mttp) cc_final: 0.7981 (mttm) REVERT: B 303 MET cc_start: 0.7640 (ptp) cc_final: 0.6972 (mmm) REVERT: B 397 MET cc_start: 0.7909 (mmm) cc_final: 0.7506 (mtp) REVERT: B 423 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 436 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6879 (mm-30) REVERT: B 445 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 460 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6409 (pp30) REVERT: B 478 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: B 594 ASP cc_start: 0.8189 (m-30) cc_final: 0.7924 (m-30) REVERT: B 620 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6513 (t0) REVERT: C 176 MET cc_start: 0.7536 (ttp) cc_final: 0.7216 (ttp) REVERT: C 227 TYR cc_start: 0.8501 (p90) cc_final: 0.8170 (p90) REVERT: C 248 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7385 (mttm) REVERT: C 291 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7190 (tpp-160) REVERT: C 303 MET cc_start: 0.7678 (ptp) cc_final: 0.7017 (mmm) REVERT: C 397 MET cc_start: 0.7783 (mmt) cc_final: 0.7400 (mtm) REVERT: C 436 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6640 (mm-30) REVERT: C 445 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 460 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6318 (pp30) REVERT: C 471 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8708 (mp) REVERT: C 478 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: C 561 LEU cc_start: 0.8629 (mm) cc_final: 0.8306 (mm) REVERT: C 580 ARG cc_start: 0.8695 (ttp-110) cc_final: 0.8375 (ttp80) REVERT: C 594 ASP cc_start: 0.8270 (m-30) cc_final: 0.8010 (m-30) REVERT: D 227 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8169 (p90) REVERT: D 248 LYS cc_start: 0.8124 (mttp) cc_final: 0.7738 (mmtt) REVERT: D 303 MET cc_start: 0.7652 (ptp) cc_final: 0.6975 (mmm) REVERT: D 342 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8758 (m) REVERT: D 397 MET cc_start: 0.7774 (mmt) cc_final: 0.7418 (mtm) REVERT: D 429 ASP cc_start: 0.7790 (m-30) cc_final: 0.7568 (m-30) REVERT: D 436 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6831 (mm-30) REVERT: D 445 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 460 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.6382 (pp30) REVERT: D 478 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: D 580 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8377 (ttp80) REVERT: D 594 ASP cc_start: 0.8192 (m-30) cc_final: 0.7936 (m-30) REVERT: D 620 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6514 (t0) outliers start: 128 outliers final: 80 residues processed: 447 average time/residue: 0.1284 time to fit residues: 88.1000 Evaluate side-chains 449 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 355 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 620 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 31 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 154 optimal weight: 0.2980 chunk 55 optimal weight: 0.0670 chunk 166 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 416 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 416 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN D 416 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.162888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123725 restraints weight = 25550.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124757 restraints weight = 14101.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124668 restraints weight = 10805.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125704 restraints weight = 10418.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125694 restraints weight = 9409.315| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17375 Z= 0.096 Angle : 0.567 10.813 23586 Z= 0.279 Chirality : 0.042 0.184 2612 Planarity : 0.003 0.043 2904 Dihedral : 13.050 151.749 2452 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.06 % Allowed : 26.89 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 1.36 (0.19), residues: 2024 helix: 1.79 (0.16), residues: 1100 sheet: -0.27 (0.54), residues: 120 loop : -0.09 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 580 TYR 0.025 0.001 TYR B 262 PHE 0.009 0.001 PHE B 558 TRP 0.009 0.001 TRP C 369 HIS 0.001 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00208 (17375) covalent geometry : angle 0.56719 (23586) hydrogen bonds : bond 0.02910 ( 915) hydrogen bonds : angle 3.84994 ( 2589) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 415 time to evaluate : 0.639 Fit side-chains REVERT: A 176 MET cc_start: 0.7447 (ttp) cc_final: 0.7123 (ttp) REVERT: A 202 MET cc_start: 0.7482 (mmm) cc_final: 0.7171 (mmm) REVERT: A 212 ASP cc_start: 0.8557 (m-30) cc_final: 0.8118 (m-30) REVERT: A 227 TYR cc_start: 0.8357 (p90) cc_final: 0.7917 (p90) REVERT: A 238 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6806 (mp0) REVERT: A 291 ARG cc_start: 0.6787 (tpt170) cc_final: 0.6178 (tpp-160) REVERT: A 303 MET cc_start: 0.7226 (ptp) cc_final: 0.6785 (mmm) REVERT: A 416 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7349 (t0) REVERT: A 429 ASP cc_start: 0.7858 (m-30) cc_final: 0.7510 (m-30) REVERT: A 436 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6833 (mm-30) REVERT: A 445 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 460 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6365 (pp30) REVERT: B 158 ARG cc_start: 0.7721 (ptp-170) cc_final: 0.7462 (ptp-170) REVERT: B 176 MET cc_start: 0.7621 (ttp) cc_final: 0.7200 (ttp) REVERT: B 202 MET cc_start: 0.7510 (mmm) cc_final: 0.7179 (mmm) REVERT: B 227 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7872 (p90) REVERT: B 248 LYS cc_start: 0.8120 (mttp) cc_final: 0.7721 (mmtt) REVERT: B 303 MET cc_start: 0.7212 (ptp) cc_final: 0.6871 (mmm) REVERT: B 397 MET cc_start: 0.7679 (mmm) cc_final: 0.7446 (mtp) REVERT: B 429 ASP cc_start: 0.7817 (m-30) cc_final: 0.7476 (m-30) REVERT: B 436 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6798 (mm-30) REVERT: B 445 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7496 (tm-30) REVERT: B 460 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6237 (pp30) REVERT: B 478 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: B 594 ASP cc_start: 0.8112 (m-30) cc_final: 0.7907 (m-30) REVERT: C 176 MET cc_start: 0.7446 (ttp) cc_final: 0.7099 (ttp) REVERT: C 202 MET cc_start: 0.7499 (mmm) cc_final: 0.7181 (mmm) REVERT: C 227 TYR cc_start: 0.8501 (p90) cc_final: 0.7925 (p90) REVERT: C 291 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7119 (tpp-160) REVERT: C 303 MET cc_start: 0.7211 (ptp) cc_final: 0.6881 (mmm) REVERT: C 429 ASP cc_start: 0.7819 (m-30) cc_final: 0.7462 (m-30) REVERT: C 436 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6829 (mm-30) REVERT: C 445 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7526 (tm-30) REVERT: C 460 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6274 (pp30) REVERT: C 471 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 478 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: C 554 GLU cc_start: 0.8023 (pt0) cc_final: 0.7738 (tt0) REVERT: C 561 LEU cc_start: 0.8711 (mm) cc_final: 0.8374 (mm) REVERT: C 580 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.8148 (ttp80) REVERT: D 176 MET cc_start: 0.6968 (ttp) cc_final: 0.6761 (ptt) REVERT: D 202 MET cc_start: 0.7490 (mmm) cc_final: 0.7176 (mmm) REVERT: D 227 TYR cc_start: 0.8457 (p90) cc_final: 0.7892 (p90) REVERT: D 248 LYS cc_start: 0.8117 (mttp) cc_final: 0.7694 (mmtt) REVERT: D 303 MET cc_start: 0.7226 (ptp) cc_final: 0.6885 (mmm) REVERT: D 342 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8599 (m) REVERT: D 416 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7288 (t0) REVERT: D 429 ASP cc_start: 0.7872 (m-30) cc_final: 0.7530 (m-30) REVERT: D 436 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6764 (mm-30) REVERT: D 445 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7506 (tm-30) REVERT: D 460 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6285 (pp30) REVERT: D 478 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: D 580 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.8136 (ttp80) REVERT: D 594 ASP cc_start: 0.8106 (m-30) cc_final: 0.7905 (m-30) outliers start: 75 outliers final: 46 residues processed: 449 average time/residue: 0.1216 time to fit residues: 84.8583 Evaluate side-chains 420 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 361 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 579 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 169 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 161 optimal weight: 0.4980 chunk 135 optimal weight: 0.0670 chunk 191 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN B 143 GLN B 416 ASN B 425 GLN C 143 GLN C 425 GLN D 143 GLN D 425 GLN D 539 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.159993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116651 restraints weight = 25415.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120669 restraints weight = 13186.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122735 restraints weight = 9105.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124050 restraints weight = 7489.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124858 restraints weight = 6550.704| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17375 Z= 0.127 Angle : 0.616 10.221 23586 Z= 0.304 Chirality : 0.043 0.178 2612 Planarity : 0.004 0.059 2904 Dihedral : 13.118 154.532 2450 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.98 % Allowed : 27.16 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 1.24 (0.19), residues: 2024 helix: 1.67 (0.16), residues: 1100 sheet: -0.30 (0.54), residues: 120 loop : -0.11 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.020 0.001 TYR C 262 PHE 0.008 0.001 PHE B 328 TRP 0.010 0.001 TRP A 124 HIS 0.001 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00295 (17375) covalent geometry : angle 0.61606 (23586) hydrogen bonds : bond 0.03248 ( 915) hydrogen bonds : angle 3.99204 ( 2589) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 353 time to evaluate : 0.626 Fit side-chains REVERT: A 112 TYR cc_start: 0.7499 (t80) cc_final: 0.7098 (t80) REVERT: A 158 ARG cc_start: 0.7889 (ptp-170) cc_final: 0.7580 (ptp-110) REVERT: A 176 MET cc_start: 0.7433 (ttp) cc_final: 0.7109 (ttp) REVERT: A 227 TYR cc_start: 0.8432 (p90) cc_final: 0.7982 (p90) REVERT: A 238 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6834 (mp0) REVERT: A 248 LYS cc_start: 0.8193 (mttp) cc_final: 0.7914 (mttm) REVERT: A 303 MET cc_start: 0.7560 (ptp) cc_final: 0.6911 (mmm) REVERT: A 425 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7519 (mm-40) REVERT: A 429 ASP cc_start: 0.7880 (m-30) cc_final: 0.7490 (m-30) REVERT: A 436 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 445 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 460 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6365 (pp30) REVERT: A 478 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: A 594 ASP cc_start: 0.8032 (m-30) cc_final: 0.7771 (m-30) REVERT: B 227 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7979 (p90) REVERT: B 248 LYS cc_start: 0.8090 (mttp) cc_final: 0.7723 (mmtt) REVERT: B 303 MET cc_start: 0.7542 (ptp) cc_final: 0.6876 (mmm) REVERT: B 416 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7608 (t0) REVERT: B 425 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: B 429 ASP cc_start: 0.7847 (m-30) cc_final: 0.7504 (m-30) REVERT: B 436 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6818 (mm-30) REVERT: B 445 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 460 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6350 (pp30) REVERT: B 478 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: B 481 MET cc_start: 0.7873 (mmm) cc_final: 0.7655 (mmm) REVERT: B 535 ARG cc_start: 0.8357 (ptp90) cc_final: 0.7779 (ttp80) REVERT: B 594 ASP cc_start: 0.8162 (m-30) cc_final: 0.7896 (m-30) REVERT: B 620 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6582 (t0) REVERT: C 176 MET cc_start: 0.7392 (ttp) cc_final: 0.7069 (ttp) REVERT: C 227 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7909 (p90) REVERT: C 229 ASP cc_start: 0.6834 (m-30) cc_final: 0.6201 (m-30) REVERT: C 291 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7046 (tpp-160) REVERT: C 303 MET cc_start: 0.7305 (ptp) cc_final: 0.6785 (mmm) REVERT: C 425 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7576 (mm-40) REVERT: C 429 ASP cc_start: 0.7843 (m-30) cc_final: 0.7512 (m-30) REVERT: C 436 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6850 (mm-30) REVERT: C 445 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 460 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6291 (pp30) REVERT: C 471 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8650 (mp) REVERT: C 478 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: C 481 MET cc_start: 0.7764 (mmm) cc_final: 0.7558 (mmm) REVERT: C 561 LEU cc_start: 0.8710 (mm) cc_final: 0.8353 (mm) REVERT: C 580 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.8024 (ttp80) REVERT: D 176 MET cc_start: 0.7342 (ttp) cc_final: 0.6971 (ptt) REVERT: D 212 ASP cc_start: 0.8720 (m-30) cc_final: 0.8382 (m-30) REVERT: D 227 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7946 (p90) REVERT: D 248 LYS cc_start: 0.8086 (mttp) cc_final: 0.7694 (mmtt) REVERT: D 303 MET cc_start: 0.7559 (ptp) cc_final: 0.6897 (mmm) REVERT: D 342 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8757 (p) REVERT: D 425 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7569 (mm-40) REVERT: D 429 ASP cc_start: 0.7907 (m-30) cc_final: 0.7591 (m-30) REVERT: D 436 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6805 (mm-30) REVERT: D 445 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 460 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6300 (pp30) REVERT: D 478 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: D 594 ASP cc_start: 0.8213 (m-30) cc_final: 0.7955 (m-30) REVERT: D 620 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6579 (t0) outliers start: 92 outliers final: 55 residues processed: 402 average time/residue: 0.1183 time to fit residues: 74.3311 Evaluate side-chains 415 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 339 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 620 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 79 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN A 425 GLN B 143 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.158385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118716 restraints weight = 25390.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119361 restraints weight = 14342.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120240 restraints weight = 10866.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121066 restraints weight = 10652.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120771 restraints weight = 9248.121| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17375 Z= 0.164 Angle : 0.650 9.923 23586 Z= 0.321 Chirality : 0.044 0.179 2612 Planarity : 0.004 0.047 2904 Dihedral : 13.205 155.651 2450 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.90 % Allowed : 25.87 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 1.03 (0.19), residues: 2024 helix: 1.50 (0.15), residues: 1100 sheet: -0.70 (0.52), residues: 128 loop : -0.12 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 580 TYR 0.023 0.001 TYR C 262 PHE 0.010 0.001 PHE C 328 TRP 0.013 0.001 TRP A 124 HIS 0.002 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00384 (17375) covalent geometry : angle 0.65013 (23586) hydrogen bonds : bond 0.03559 ( 915) hydrogen bonds : angle 4.13056 ( 2589) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 345 time to evaluate : 0.523 Fit side-chains REVERT: A 112 TYR cc_start: 0.7477 (t80) cc_final: 0.7103 (t80) REVERT: A 158 ARG cc_start: 0.7934 (ptp-170) cc_final: 0.7577 (ptp-110) REVERT: A 176 MET cc_start: 0.7550 (ttp) cc_final: 0.7293 (ttp) REVERT: A 202 MET cc_start: 0.7450 (mmm) cc_final: 0.7148 (mmm) REVERT: A 227 TYR cc_start: 0.8456 (p90) cc_final: 0.8002 (p90) REVERT: A 238 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6867 (mp0) REVERT: A 248 LYS cc_start: 0.8235 (mttp) cc_final: 0.7955 (mttm) REVERT: A 303 MET cc_start: 0.7605 (ptp) cc_final: 0.6929 (mmm) REVERT: A 425 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7648 (mm-40) REVERT: A 429 ASP cc_start: 0.7842 (m-30) cc_final: 0.7498 (m-30) REVERT: A 436 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 445 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 460 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6379 (pp30) REVERT: A 478 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: A 594 ASP cc_start: 0.8173 (m-30) cc_final: 0.7908 (m-30) REVERT: A 620 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6608 (t0) REVERT: B 132 TYR cc_start: 0.8709 (t80) cc_final: 0.8405 (t80) REVERT: B 202 MET cc_start: 0.7422 (mmm) cc_final: 0.7130 (mmm) REVERT: B 227 TYR cc_start: 0.8462 (p90) cc_final: 0.7981 (p90) REVERT: B 248 LYS cc_start: 0.8106 (mttp) cc_final: 0.7739 (mmtt) REVERT: B 303 MET cc_start: 0.7573 (ptp) cc_final: 0.6902 (mmm) REVERT: B 429 ASP cc_start: 0.7946 (m-30) cc_final: 0.7600 (m-30) REVERT: B 436 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6834 (mm-30) REVERT: B 445 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 460 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.6408 (pp30) REVERT: B 478 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: B 594 ASP cc_start: 0.8204 (m-30) cc_final: 0.7957 (m-30) REVERT: B 620 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6644 (t0) REVERT: C 176 MET cc_start: 0.7528 (ttp) cc_final: 0.7284 (ttp) REVERT: C 202 MET cc_start: 0.7426 (mmm) cc_final: 0.7134 (mmm) REVERT: C 227 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7877 (p90) REVERT: C 248 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7638 (mmtm) REVERT: C 291 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7177 (tpp-160) REVERT: C 303 MET cc_start: 0.7613 (ptp) cc_final: 0.6911 (mmm) REVERT: C 425 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7617 (mm-40) REVERT: C 429 ASP cc_start: 0.7905 (m-30) cc_final: 0.7569 (m-30) REVERT: C 436 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6858 (mm-30) REVERT: C 445 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7662 (tm-30) REVERT: C 460 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6323 (pp30) REVERT: C 471 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8706 (mp) REVERT: C 478 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: C 481 MET cc_start: 0.7809 (mmm) cc_final: 0.7607 (mmm) REVERT: C 561 LEU cc_start: 0.8678 (mm) cc_final: 0.8311 (mm) REVERT: C 620 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6696 (t0) REVERT: D 176 MET cc_start: 0.7443 (ttp) cc_final: 0.7157 (ttp) REVERT: D 202 MET cc_start: 0.7429 (mmm) cc_final: 0.7137 (mmm) REVERT: D 227 TYR cc_start: 0.8422 (p90) cc_final: 0.7897 (p90) REVERT: D 248 LYS cc_start: 0.8108 (mttp) cc_final: 0.7720 (mmtt) REVERT: D 303 MET cc_start: 0.7681 (ptp) cc_final: 0.6983 (mmm) REVERT: D 425 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7550 (mm-40) REVERT: D 429 ASP cc_start: 0.7882 (m-30) cc_final: 0.7568 (m-30) REVERT: D 436 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6804 (mm-30) REVERT: D 445 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7595 (tm-30) REVERT: D 460 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6373 (pp30) REVERT: D 478 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: D 580 ARG cc_start: 0.8450 (ttp-110) cc_final: 0.7942 (ttp80) REVERT: D 594 ASP cc_start: 0.8204 (m-30) cc_final: 0.7967 (m-30) REVERT: D 612 LYS cc_start: 0.8303 (mttt) cc_final: 0.8043 (ttpp) REVERT: D 620 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6638 (t0) outliers start: 109 outliers final: 71 residues processed: 415 average time/residue: 0.1243 time to fit residues: 79.8467 Evaluate side-chains 418 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 329 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 620 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.161355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121641 restraints weight = 25287.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122834 restraints weight = 14340.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122766 restraints weight = 10613.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123432 restraints weight = 10658.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124023 restraints weight = 9495.152| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17375 Z= 0.113 Angle : 0.631 10.420 23586 Z= 0.309 Chirality : 0.043 0.178 2612 Planarity : 0.004 0.047 2904 Dihedral : 13.050 153.950 2449 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.00 % Allowed : 27.87 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 1.14 (0.19), residues: 2024 helix: 1.61 (0.16), residues: 1100 sheet: -0.69 (0.52), residues: 128 loop : -0.11 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 580 TYR 0.022 0.001 TYR B 262 PHE 0.009 0.001 PHE D 424 TRP 0.011 0.001 TRP A 124 HIS 0.001 0.000 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00260 (17375) covalent geometry : angle 0.63106 (23586) hydrogen bonds : bond 0.03207 ( 915) hydrogen bonds : angle 4.06755 ( 2589) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 353 time to evaluate : 0.505 Fit side-chains REVERT: A 112 TYR cc_start: 0.7473 (t80) cc_final: 0.7099 (t80) REVERT: A 158 ARG cc_start: 0.7853 (ptp-170) cc_final: 0.7523 (ptp-110) REVERT: A 176 MET cc_start: 0.7482 (ttp) cc_final: 0.7201 (ttp) REVERT: A 202 MET cc_start: 0.7433 (mmm) cc_final: 0.7129 (mmm) REVERT: A 227 TYR cc_start: 0.8416 (p90) cc_final: 0.7989 (p90) REVERT: A 229 ASP cc_start: 0.7247 (m-30) cc_final: 0.6741 (m-30) REVERT: A 238 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6843 (mp0) REVERT: A 248 LYS cc_start: 0.8243 (mttp) cc_final: 0.7964 (mttm) REVERT: A 291 ARG cc_start: 0.6821 (tpt170) cc_final: 0.6187 (tpp-160) REVERT: A 303 MET cc_start: 0.7560 (ptp) cc_final: 0.6887 (mmm) REVERT: A 347 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7791 (p0) REVERT: A 416 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7144 (t0) REVERT: A 429 ASP cc_start: 0.7840 (m-30) cc_final: 0.7495 (m-30) REVERT: A 436 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6804 (mm-30) REVERT: A 445 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 460 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6477 (pp30) REVERT: A 478 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: A 594 ASP cc_start: 0.8114 (m-30) cc_final: 0.7832 (m-30) REVERT: A 620 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6522 (t0) REVERT: B 132 TYR cc_start: 0.8636 (t80) cc_final: 0.8357 (t80) REVERT: B 202 MET cc_start: 0.7391 (mmm) cc_final: 0.7090 (mmm) REVERT: B 227 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7997 (p90) REVERT: B 229 ASP cc_start: 0.7258 (m-30) cc_final: 0.6726 (m-30) REVERT: B 248 LYS cc_start: 0.8102 (mttp) cc_final: 0.7757 (mmtt) REVERT: B 303 MET cc_start: 0.7524 (ptp) cc_final: 0.6875 (mmm) REVERT: B 397 MET cc_start: 0.7802 (mmm) cc_final: 0.7517 (mtp) REVERT: B 429 ASP cc_start: 0.7823 (m-30) cc_final: 0.7498 (m-30) REVERT: B 436 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6765 (mm-30) REVERT: B 445 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 460 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6376 (pp30) REVERT: B 478 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: B 554 GLU cc_start: 0.8227 (pp20) cc_final: 0.8025 (pp20) REVERT: B 594 ASP cc_start: 0.8173 (m-30) cc_final: 0.7912 (m-30) REVERT: C 176 MET cc_start: 0.7445 (ttp) cc_final: 0.7163 (ttp) REVERT: C 202 MET cc_start: 0.7407 (mmm) cc_final: 0.7104 (mmm) REVERT: C 227 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7857 (p90) REVERT: C 248 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7597 (mmtm) REVERT: C 291 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7188 (tpp-160) REVERT: C 303 MET cc_start: 0.7284 (ptp) cc_final: 0.6751 (mmm) REVERT: C 429 ASP cc_start: 0.7834 (m-30) cc_final: 0.7495 (m-30) REVERT: C 436 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6800 (mm-30) REVERT: C 445 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 460 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6357 (pp30) REVERT: C 471 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8607 (mp) REVERT: C 478 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: C 561 LEU cc_start: 0.8725 (mm) cc_final: 0.8385 (mm) REVERT: C 580 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8089 (ttp80) REVERT: D 176 MET cc_start: 0.7074 (ttp) cc_final: 0.6761 (ttp) REVERT: D 202 MET cc_start: 0.7407 (mmm) cc_final: 0.7115 (mmm) REVERT: D 227 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7932 (p90) REVERT: D 229 ASP cc_start: 0.7297 (m-30) cc_final: 0.6721 (m-30) REVERT: D 248 LYS cc_start: 0.8092 (mttp) cc_final: 0.7718 (mmtt) REVERT: D 303 MET cc_start: 0.7286 (ptp) cc_final: 0.6760 (mmm) REVERT: D 429 ASP cc_start: 0.7879 (m-30) cc_final: 0.7532 (m-30) REVERT: D 436 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6756 (mm-30) REVERT: D 445 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7548 (tm-30) REVERT: D 460 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6369 (pp30) REVERT: D 478 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: D 580 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.7998 (ttp80) REVERT: D 594 ASP cc_start: 0.8165 (m-30) cc_final: 0.7922 (m-30) REVERT: D 612 LYS cc_start: 0.8164 (mttt) cc_final: 0.7925 (ttpp) outliers start: 74 outliers final: 44 residues processed: 391 average time/residue: 0.1238 time to fit residues: 74.9172 Evaluate side-chains 401 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 341 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 199 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 196 optimal weight: 0.0770 chunk 154 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 425 GLN B 416 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 143 GLN D 425 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.163119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123745 restraints weight = 25396.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124624 restraints weight = 14236.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124518 restraints weight = 10572.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125203 restraints weight = 10736.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125594 restraints weight = 9535.332| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17375 Z= 0.105 Angle : 0.638 12.109 23586 Z= 0.309 Chirality : 0.043 0.190 2612 Planarity : 0.004 0.045 2904 Dihedral : 12.911 153.224 2449 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.57 % Allowed : 28.63 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 1.19 (0.19), residues: 2024 helix: 1.70 (0.16), residues: 1100 sheet: -0.74 (0.52), residues: 128 loop : -0.14 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 580 TYR 0.026 0.001 TYR D 123 PHE 0.009 0.001 PHE D 558 TRP 0.011 0.001 TRP A 124 HIS 0.001 0.000 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.00237 (17375) covalent geometry : angle 0.63791 (23586) hydrogen bonds : bond 0.03100 ( 915) hydrogen bonds : angle 4.05615 ( 2589) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 366 time to evaluate : 0.672 Fit side-chains REVERT: A 158 ARG cc_start: 0.7857 (ptp-170) cc_final: 0.7542 (ptp-110) REVERT: A 176 MET cc_start: 0.7478 (ttp) cc_final: 0.7182 (ttp) REVERT: A 202 MET cc_start: 0.7489 (mmm) cc_final: 0.7170 (mmm) REVERT: A 227 TYR cc_start: 0.8422 (p90) cc_final: 0.8067 (p90) REVERT: A 229 ASP cc_start: 0.6911 (m-30) cc_final: 0.6448 (m-30) REVERT: A 238 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6885 (mp0) REVERT: A 248 LYS cc_start: 0.8181 (mttp) cc_final: 0.7918 (mttm) REVERT: A 303 MET cc_start: 0.7131 (ptp) cc_final: 0.6856 (mmm) REVERT: A 347 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7964 (p0) REVERT: A 425 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7571 (tp40) REVERT: A 429 ASP cc_start: 0.7819 (m-30) cc_final: 0.7475 (m-30) REVERT: A 436 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6868 (mm-30) REVERT: A 445 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 460 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6359 (pp30) REVERT: A 478 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: A 594 ASP cc_start: 0.7858 (m-30) cc_final: 0.7534 (m-30) REVERT: B 202 MET cc_start: 0.7451 (mmm) cc_final: 0.7150 (mmm) REVERT: B 206 PHE cc_start: 0.8677 (t80) cc_final: 0.8333 (t80) REVERT: B 212 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: B 227 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8039 (p90) REVERT: B 229 ASP cc_start: 0.7143 (m-30) cc_final: 0.6572 (m-30) REVERT: B 248 LYS cc_start: 0.8090 (mttp) cc_final: 0.7755 (mmtt) REVERT: B 264 LEU cc_start: 0.6488 (mt) cc_final: 0.5856 (tt) REVERT: B 303 MET cc_start: 0.7098 (ptp) cc_final: 0.6821 (mmm) REVERT: B 397 MET cc_start: 0.7778 (mmm) cc_final: 0.7496 (mtp) REVERT: B 416 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7216 (t0) REVERT: B 429 ASP cc_start: 0.7784 (m-30) cc_final: 0.7436 (m-30) REVERT: B 436 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6843 (mm-30) REVERT: B 445 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 451 TRP cc_start: 0.8672 (t60) cc_final: 0.8374 (t60) REVERT: B 460 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6357 (pp30) REVERT: B 478 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 554 GLU cc_start: 0.8139 (pp20) cc_final: 0.7931 (pp20) REVERT: B 594 ASP cc_start: 0.8169 (m-30) cc_final: 0.7884 (m-30) REVERT: B 620 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6502 (t0) REVERT: C 112 TYR cc_start: 0.7465 (t80) cc_final: 0.7231 (t80) REVERT: C 176 MET cc_start: 0.7449 (ttp) cc_final: 0.7166 (ttp) REVERT: C 202 MET cc_start: 0.7466 (mmm) cc_final: 0.7172 (mmm) REVERT: C 206 PHE cc_start: 0.8676 (t80) cc_final: 0.8392 (t80) REVERT: C 227 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7949 (p90) REVERT: C 248 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7559 (mmtm) REVERT: C 283 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7694 (mmt90) REVERT: C 291 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7187 (tpp-160) REVERT: C 303 MET cc_start: 0.7101 (ptp) cc_final: 0.6832 (mmm) REVERT: C 425 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7957 (mm-40) REVERT: C 436 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6764 (mm-30) REVERT: C 445 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7562 (tm-30) REVERT: C 451 TRP cc_start: 0.8697 (t60) cc_final: 0.8364 (t60) REVERT: C 460 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6179 (pp30) REVERT: C 471 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (mp) REVERT: C 478 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 561 LEU cc_start: 0.8704 (mm) cc_final: 0.8354 (mm) REVERT: C 580 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.8044 (ttp80) REVERT: D 112 TYR cc_start: 0.7244 (t80) cc_final: 0.7037 (t80) REVERT: D 176 MET cc_start: 0.7008 (ttp) cc_final: 0.5919 (mtt) REVERT: D 202 MET cc_start: 0.7466 (mmm) cc_final: 0.7140 (mmm) REVERT: D 206 PHE cc_start: 0.8670 (t80) cc_final: 0.8343 (t80) REVERT: D 225 MET cc_start: 0.7715 (mmm) cc_final: 0.7286 (mmm) REVERT: D 227 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.8003 (p90) REVERT: D 248 LYS cc_start: 0.8081 (mttp) cc_final: 0.7722 (mmtt) REVERT: D 303 MET cc_start: 0.7081 (ptp) cc_final: 0.6846 (mmm) REVERT: D 425 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7602 (tp40) REVERT: D 429 ASP cc_start: 0.7877 (m-30) cc_final: 0.7547 (m-30) REVERT: D 436 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6834 (mm-30) REVERT: D 445 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7490 (tm-30) REVERT: D 460 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6347 (pp30) REVERT: D 478 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: D 535 ARG cc_start: 0.8294 (ptp90) cc_final: 0.7908 (ttp80) REVERT: D 554 GLU cc_start: 0.8178 (pp20) cc_final: 0.7768 (pp20) REVERT: D 580 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.7934 (ttp80) REVERT: D 594 ASP cc_start: 0.8137 (m-30) cc_final: 0.7870 (m-30) REVERT: D 612 LYS cc_start: 0.8177 (mttt) cc_final: 0.7926 (ttpp) outliers start: 66 outliers final: 42 residues processed: 402 average time/residue: 0.1251 time to fit residues: 77.7465 Evaluate side-chains 406 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 344 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 478 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN B 416 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.163903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125080 restraints weight = 25379.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127282 restraints weight = 15605.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.127935 restraints weight = 10845.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128656 restraints weight = 10416.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128525 restraints weight = 8842.977| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 17375 Z= 0.279 Angle : 1.227 59.200 23586 Z= 0.719 Chirality : 0.044 0.377 2612 Planarity : 0.004 0.082 2904 Dihedral : 12.913 153.207 2449 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.68 % Allowed : 28.46 % Favored : 67.86 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 13.33 % 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 aren not related in a simple way. whole: 1.13 (0.19), residues: 2024 helix: 1.63 (0.16), residues: 1100 sheet: -0.74 (0.52), residues: 128 loop : -0.15 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 580 TYR 0.018 0.001 TYR A 262 PHE 0.009 0.001 PHE D 558 TRP 0.011 0.001 TRP A 124 HIS 0.001 0.000 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.00566 (17375) covalent geometry : angle 1.22710 (23586) hydrogen bonds : bond 0.03124 ( 915) hydrogen bonds : angle 4.09167 ( 2589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.04 seconds wall clock time: 53 minutes 14.79 seconds (3194.79 seconds total)