Starting phenix.real_space_refine on Wed Nov 19 03:11:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8a_20686/11_2025/6u8a_20686.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8a_20686/11_2025/6u8a_20686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u8a_20686/11_2025/6u8a_20686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8a_20686/11_2025/6u8a_20686.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8a_20686/11_2025/6u8a_20686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8a_20686/11_2025/6u8a_20686.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13172 2.51 5 N 3324 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} 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: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.09, per 1000 atoms: 0.25 Number of scatterers: 20032 At special positions: 0 Unit cell: (126.14, 126.14, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3420 8.00 N 3324 7.00 C 13172 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: 1.68 Conformation dependent library (CDL) restraints added in 809.6 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 61.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 718 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.619A pdb=" N THR C 112 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 145 Processing helix chain 'C' and resid 166 through 174 removed outlier: 4.037A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.329A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.837A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 533 through 559 removed outlier: 3.705A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.623A pdb=" N PHE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 6.661A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 6.659A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6137 1.34 - 1.46: 5115 1.46 - 1.58: 9112 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 20544 Sorted by residual: bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T A1002 " pdb=" O02 P0T A1002 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T D1001 " pdb=" O02 P0T D1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C11 P0T A1001 " pdb=" O01 P0T A1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.41e+00 ... (remaining 20539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 26945 2.34 - 4.67: 796 4.67 - 7.01: 83 7.01 - 9.34: 36 9.34 - 11.68: 16 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N ILE D 529 " pdb=" CA ILE D 529 " pdb=" C ILE D 529 " ideal model delta sigma weight residual 111.91 108.09 3.82 8.90e-01 1.26e+00 1.84e+01 angle pdb=" N ILE B 529 " pdb=" CA ILE B 529 " pdb=" C ILE B 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.83e+01 angle pdb=" N ILE C 529 " pdb=" CA ILE C 529 " pdb=" C ILE C 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 122.80 -11.68 3.00e+00 1.11e-01 1.52e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 10837 19.27 - 38.53: 1023 38.53 - 57.80: 196 57.80 - 77.07: 32 77.07 - 96.33: 12 Dihedral angle restraints: 12100 sinusoidal: 4880 harmonic: 7220 Sorted by residual: dihedral pdb=" CA ASN C 655 " pdb=" C ASN C 655 " pdb=" N SER C 656 " pdb=" CA SER C 656 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN A 655 " pdb=" C ASN A 655 " pdb=" N SER A 656 " pdb=" CA SER A 656 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN B 655 " pdb=" C ASN B 655 " pdb=" N SER B 656 " pdb=" CA SER B 656 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1999 0.045 - 0.090: 861 0.090 - 0.135: 212 0.135 - 0.180: 68 0.180 - 0.225: 8 Chirality restraints: 3148 Sorted by residual: chirality pdb=" C03 P0T A1002 " pdb=" C04 P0T A1002 " pdb=" C05 P0T A1002 " pdb=" C10 P0T A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T C1001 " pdb=" C04 P0T C1001 " pdb=" C05 P0T C1001 " pdb=" C10 P0T C1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C05 P0T A1001 " pdb=" C10 P0T A1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3145 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 137 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO A 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO D 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 138 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6104 2.82 - 3.34: 17959 3.34 - 3.86: 33559 3.86 - 4.38: 37894 4.38 - 4.90: 66133 Nonbonded interactions: 161649 Sorted by model distance: nonbonded pdb=" O GLU C 90 " pdb=" OG1 THR C 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU D 90 " pdb=" OG1 THR D 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU A 90 " pdb=" OG1 THR A 93 " model vdw 2.297 3.040 nonbonded pdb=" O GLU B 90 " pdb=" OG1 THR B 93 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 529 " pdb=" ND2 ASN B 639 " model vdw 2.302 3.120 ... (remaining 161644 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 32 through 719) selection = chain 'B' selection = (chain 'C' and resid 32 through 719) selection = (chain 'D' and resid 32 through 719) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.790 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.008 0.065 20544 Z= 0.343 Angle : 0.966 11.681 27876 Z= 0.497 Chirality : 0.054 0.225 3148 Planarity : 0.007 0.067 3420 Dihedral : 15.898 96.335 7428 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.37 % Allowed : 8.94 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.12), residues: 2428 helix: -2.38 (0.09), residues: 1460 sheet: -2.79 (0.43), residues: 92 loop : -2.72 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 392 TYR 0.013 0.002 TYR D 111 PHE 0.019 0.003 PHE B 161 TRP 0.019 0.002 TRP D 333 HIS 0.006 0.002 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00806 (20544) covalent geometry : angle 0.96569 (27876) hydrogen bonds : bond 0.14053 ( 1072) hydrogen bonds : angle 6.14329 ( 3108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 405 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7255 (mm) cc_final: 0.6675 (pp) REVERT: A 113 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6692 (mt-10) REVERT: A 173 GLU cc_start: 0.8400 (tp30) cc_final: 0.8199 (tp30) REVERT: A 541 LEU cc_start: 0.9104 (tp) cc_final: 0.8896 (tp) REVERT: B 255 MET cc_start: 0.8120 (mmm) cc_final: 0.7901 (mmm) REVERT: B 372 MET cc_start: 0.9125 (mtt) cc_final: 0.8904 (mtt) REVERT: B 383 GLN cc_start: 0.7898 (tp40) cc_final: 0.7601 (tt0) REVERT: B 404 MET cc_start: 0.8670 (mmp) cc_final: 0.8460 (mmt) REVERT: B 541 LEU cc_start: 0.9052 (tp) cc_final: 0.8787 (tp) REVERT: B 640 MET cc_start: 0.8412 (ttp) cc_final: 0.8069 (ttp) REVERT: C 113 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7061 (mt-10) REVERT: C 235 GLN cc_start: 0.7661 (mt0) cc_final: 0.7436 (mt0) REVERT: C 255 MET cc_start: 0.8176 (mmm) cc_final: 0.7930 (mmt) REVERT: C 464 TRP cc_start: 0.6065 (m100) cc_final: 0.5830 (m100) REVERT: D 113 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7087 (mt-10) REVERT: D 255 MET cc_start: 0.8169 (mmm) cc_final: 0.7959 (mmt) REVERT: D 305 GLU cc_start: 0.7603 (tt0) cc_final: 0.7064 (mt-10) REVERT: D 464 TRP cc_start: 0.6079 (m100) cc_final: 0.5859 (m100) REVERT: D 473 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7528 (mp0) REVERT: D 528 MET cc_start: 0.8073 (ttt) cc_final: 0.7568 (ttt) REVERT: D 536 ASP cc_start: 0.7392 (t70) cc_final: 0.7189 (t0) outliers start: 8 outliers final: 0 residues processed: 405 average time/residue: 0.1383 time to fit residues: 87.9789 Evaluate side-chains 271 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 186 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 316 GLN B 163 GLN B 186 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 316 GLN C 186 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 316 GLN D 186 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 316 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129015 restraints weight = 26943.600| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.79 r_work: 0.3322 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20544 Z= 0.099 Angle : 0.508 7.622 27876 Z= 0.259 Chirality : 0.036 0.192 3148 Planarity : 0.005 0.063 3420 Dihedral : 6.767 54.909 2772 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.09 % Allowed : 13.04 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.16), residues: 2428 helix: 0.06 (0.13), residues: 1452 sheet: -2.16 (0.47), residues: 92 loop : -1.84 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 706 TYR 0.015 0.001 TYR D 455 PHE 0.017 0.001 PHE C 467 TRP 0.014 0.001 TRP A 715 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00210 (20544) covalent geometry : angle 0.50760 (27876) hydrogen bonds : bond 0.03327 ( 1072) hydrogen bonds : angle 4.06329 ( 3108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 381 time to evaluate : 0.603 Fit side-chains REVERT: A 92 LEU cc_start: 0.7324 (mm) cc_final: 0.6429 (pp) REVERT: A 178 GLN cc_start: 0.7859 (mt0) cc_final: 0.7447 (mp10) REVERT: A 454 TRP cc_start: 0.8135 (t-100) cc_final: 0.7845 (t60) REVERT: B 305 GLU cc_start: 0.8150 (tt0) cc_final: 0.7842 (mt-10) REVERT: B 318 GLU cc_start: 0.7276 (tt0) cc_final: 0.7010 (tt0) REVERT: B 324 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 372 MET cc_start: 0.9119 (mtt) cc_final: 0.8911 (mtt) REVERT: B 383 GLN cc_start: 0.8353 (tp40) cc_final: 0.8131 (tp40) REVERT: B 455 TYR cc_start: 0.9131 (t80) cc_final: 0.8865 (t80) REVERT: B 645 MET cc_start: 0.8258 (tmm) cc_final: 0.7818 (tmm) REVERT: B 687 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7610 (mtm110) REVERT: C 111 TYR cc_start: 0.6013 (m-80) cc_final: 0.5596 (m-80) REVERT: C 113 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7338 (mt-10) REVERT: C 118 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8124 (tttt) REVERT: C 235 GLN cc_start: 0.7700 (mt0) cc_final: 0.7489 (mt0) REVERT: C 305 GLU cc_start: 0.8223 (tt0) cc_final: 0.7900 (mt-10) REVERT: C 454 TRP cc_start: 0.8208 (t-100) cc_final: 0.7944 (t60) REVERT: C 455 TYR cc_start: 0.9218 (t80) cc_final: 0.8982 (t80) REVERT: C 457 TRP cc_start: 0.8275 (t-100) cc_final: 0.8057 (t-100) REVERT: C 473 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8070 (mp0) REVERT: D 111 TYR cc_start: 0.6154 (m-80) cc_final: 0.5794 (m-80) REVERT: D 113 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7269 (mt-10) REVERT: D 118 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8025 (tttt) REVERT: D 235 GLN cc_start: 0.7706 (mt0) cc_final: 0.7472 (mt0) REVERT: D 255 MET cc_start: 0.8809 (mmm) cc_final: 0.8427 (mmt) REVERT: D 305 GLU cc_start: 0.8028 (tt0) cc_final: 0.7514 (mt-10) REVERT: D 358 GLU cc_start: 0.8217 (tt0) cc_final: 0.7793 (tt0) REVERT: D 454 TRP cc_start: 0.8109 (t-100) cc_final: 0.7884 (t60) outliers start: 45 outliers final: 19 residues processed: 408 average time/residue: 0.1317 time to fit residues: 86.4982 Evaluate side-chains 318 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 299 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 316 GLN Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 234 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 487 GLN B 414 GLN B 487 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 487 GLN D 163 GLN D 414 GLN D 487 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126525 restraints weight = 26984.327| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.80 r_work: 0.3303 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20544 Z= 0.099 Angle : 0.514 9.779 27876 Z= 0.250 Chirality : 0.036 0.193 3148 Planarity : 0.004 0.058 3420 Dihedral : 6.329 54.466 2772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.40 % Allowed : 16.15 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2428 helix: 0.99 (0.13), residues: 1472 sheet: -1.81 (0.49), residues: 92 loop : -1.69 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 687 TYR 0.012 0.001 TYR D 455 PHE 0.017 0.001 PHE D 467 TRP 0.008 0.001 TRP A 715 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00221 (20544) covalent geometry : angle 0.51429 (27876) hydrogen bonds : bond 0.03085 ( 1072) hydrogen bonds : angle 3.78977 ( 3108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 328 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7327 (mm) cc_final: 0.6347 (pp) REVERT: A 178 GLN cc_start: 0.7886 (mt0) cc_final: 0.7519 (mp10) REVERT: A 269 HIS cc_start: 0.7937 (t70) cc_final: 0.7546 (t70) REVERT: A 454 TRP cc_start: 0.8162 (t-100) cc_final: 0.7837 (t60) REVERT: A 647 GLU cc_start: 0.8954 (tt0) cc_final: 0.8606 (mt-10) REVERT: A 670 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7604 (tp30) REVERT: B 305 GLU cc_start: 0.8118 (tt0) cc_final: 0.7740 (mt-10) REVERT: B 324 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 383 GLN cc_start: 0.8392 (tp40) cc_final: 0.8170 (tp40) REVERT: B 455 TYR cc_start: 0.9184 (t80) cc_final: 0.8891 (t80) REVERT: B 645 MET cc_start: 0.8353 (tmm) cc_final: 0.7689 (tmm) REVERT: B 687 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7707 (mtm110) REVERT: C 111 TYR cc_start: 0.5865 (m-80) cc_final: 0.5468 (m-80) REVERT: C 113 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7109 (mt-10) REVERT: C 118 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8168 (ttpt) REVERT: C 178 GLN cc_start: 0.7879 (mt0) cc_final: 0.7499 (mp10) REVERT: C 235 GLN cc_start: 0.7752 (mt0) cc_final: 0.7538 (mt0) REVERT: C 305 GLU cc_start: 0.8178 (tt0) cc_final: 0.7819 (mt-10) REVERT: C 454 TRP cc_start: 0.8223 (t-100) cc_final: 0.7919 (t60) REVERT: C 455 TYR cc_start: 0.9198 (t80) cc_final: 0.8909 (t80) REVERT: D 111 TYR cc_start: 0.5923 (m-80) cc_final: 0.5590 (m-80) REVERT: D 113 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7125 (mt-10) REVERT: D 118 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8028 (ttpt) REVERT: D 178 GLN cc_start: 0.7916 (mt0) cc_final: 0.7537 (mp10) REVERT: D 235 GLN cc_start: 0.7741 (mt0) cc_final: 0.7512 (mt0) REVERT: D 269 HIS cc_start: 0.7870 (t70) cc_final: 0.7585 (t70) REVERT: D 454 TRP cc_start: 0.8133 (t-100) cc_final: 0.7903 (t60) REVERT: D 457 TRP cc_start: 0.8251 (t-100) cc_final: 0.7988 (t-100) outliers start: 30 outliers final: 16 residues processed: 347 average time/residue: 0.1329 time to fit residues: 73.8258 Evaluate side-chains 302 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 286 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123884 restraints weight = 27090.192| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.82 r_work: 0.3270 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20544 Z= 0.120 Angle : 0.513 7.399 27876 Z= 0.254 Chirality : 0.036 0.171 3148 Planarity : 0.004 0.054 3420 Dihedral : 6.268 54.114 2772 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.47 % Allowed : 16.76 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2428 helix: 1.44 (0.14), residues: 1472 sheet: -1.62 (0.49), residues: 92 loop : -1.47 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 706 TYR 0.013 0.001 TYR D 455 PHE 0.019 0.001 PHE A 467 TRP 0.011 0.001 TRP B 715 HIS 0.006 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00281 (20544) covalent geometry : angle 0.51306 (27876) hydrogen bonds : bond 0.03150 ( 1072) hydrogen bonds : angle 3.70148 ( 3108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7241 (mm) cc_final: 0.6290 (pp) REVERT: A 178 GLN cc_start: 0.7986 (mt0) cc_final: 0.7569 (mp10) REVERT: A 269 HIS cc_start: 0.8020 (t70) cc_final: 0.7680 (t70) REVERT: A 457 TRP cc_start: 0.8234 (t-100) cc_final: 0.8009 (t-100) REVERT: A 545 LEU cc_start: 0.9460 (mm) cc_final: 0.9246 (mt) REVERT: A 647 GLU cc_start: 0.8950 (tt0) cc_final: 0.8507 (mt-10) REVERT: B 39 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.5712 (p90) REVERT: B 305 GLU cc_start: 0.8205 (tt0) cc_final: 0.7805 (mt-10) REVERT: B 383 GLN cc_start: 0.8397 (tp40) cc_final: 0.7958 (tt0) REVERT: B 634 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7436 (m-80) REVERT: B 645 MET cc_start: 0.8443 (tmm) cc_final: 0.7703 (tmm) REVERT: C 111 TYR cc_start: 0.5541 (m-80) cc_final: 0.5309 (m-80) REVERT: C 178 GLN cc_start: 0.8000 (mt0) cc_final: 0.7592 (mp10) REVERT: C 235 GLN cc_start: 0.7782 (mt0) cc_final: 0.7538 (mt0) REVERT: C 305 GLU cc_start: 0.8224 (tt0) cc_final: 0.7794 (mt-10) REVERT: D 111 TYR cc_start: 0.5960 (m-80) cc_final: 0.5518 (m-80) REVERT: D 178 GLN cc_start: 0.8102 (mt0) cc_final: 0.7652 (mp10) REVERT: D 454 TRP cc_start: 0.8198 (t-100) cc_final: 0.7924 (t60) REVERT: D 528 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8244 (ptp) REVERT: D 670 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7660 (tp30) outliers start: 53 outliers final: 23 residues processed: 348 average time/residue: 0.1381 time to fit residues: 77.1353 Evaluate side-chains 300 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 195 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.0170 chunk 215 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 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 = 0.3771 r_free = 0.3771 target = 0.155394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127412 restraints weight = 26870.456| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.83 r_work: 0.3286 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20544 Z= 0.101 Angle : 0.496 7.593 27876 Z= 0.245 Chirality : 0.036 0.165 3148 Planarity : 0.003 0.052 3420 Dihedral : 6.021 54.872 2772 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.47 % Allowed : 17.50 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2428 helix: 1.71 (0.14), residues: 1476 sheet: -1.55 (0.50), residues: 92 loop : -1.30 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 197 TYR 0.014 0.001 TYR C 455 PHE 0.020 0.001 PHE C 467 TRP 0.012 0.001 TRP A 715 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00231 (20544) covalent geometry : angle 0.49630 (27876) hydrogen bonds : bond 0.02983 ( 1072) hydrogen bonds : angle 3.61884 ( 3108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.5940 (p90) REVERT: A 92 LEU cc_start: 0.7014 (mm) cc_final: 0.6133 (pp) REVERT: A 178 GLN cc_start: 0.8086 (mt0) cc_final: 0.7693 (mp10) REVERT: A 647 GLU cc_start: 0.8915 (tt0) cc_final: 0.8453 (mt-10) REVERT: A 670 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7570 (tp30) REVERT: B 269 HIS cc_start: 0.8039 (t70) cc_final: 0.7702 (t70) REVERT: B 277 MET cc_start: 0.7506 (mmp) cc_final: 0.7236 (mmp) REVERT: B 383 GLN cc_start: 0.8305 (tp40) cc_final: 0.7923 (tt0) REVERT: B 545 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9237 (mt) REVERT: B 634 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: B 645 MET cc_start: 0.8387 (tmm) cc_final: 0.7583 (tmm) REVERT: C 39 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.5590 (p90) REVERT: C 235 GLN cc_start: 0.7778 (mt0) cc_final: 0.7539 (mt0) REVERT: C 269 HIS cc_start: 0.8014 (t70) cc_final: 0.7743 (t70) REVERT: D 111 TYR cc_start: 0.5733 (m-80) cc_final: 0.5335 (m-80) REVERT: D 178 GLN cc_start: 0.7994 (mt0) cc_final: 0.7584 (mp10) REVERT: D 255 MET cc_start: 0.8602 (mmt) cc_final: 0.8248 (mmm) REVERT: D 305 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7813 (mt-10) REVERT: D 670 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7596 (tp30) outliers start: 53 outliers final: 31 residues processed: 337 average time/residue: 0.1337 time to fit residues: 72.3566 Evaluate side-chains 302 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 223 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 185 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 222 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 = 0.3774 r_free = 0.3774 target = 0.155682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127905 restraints weight = 26880.659| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.84 r_work: 0.3298 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20544 Z= 0.095 Angle : 0.485 7.448 27876 Z= 0.240 Chirality : 0.036 0.159 3148 Planarity : 0.003 0.049 3420 Dihedral : 5.930 56.629 2772 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.65 % Allowed : 18.11 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 2428 helix: 1.99 (0.14), residues: 1452 sheet: -2.43 (0.45), residues: 112 loop : -1.18 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.013 0.001 TYR C 455 PHE 0.021 0.001 PHE D 467 TRP 0.015 0.001 TRP D 715 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00214 (20544) covalent geometry : angle 0.48531 (27876) hydrogen bonds : bond 0.02891 ( 1072) hydrogen bonds : angle 3.54564 ( 3108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 292 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.5894 (p90) REVERT: A 92 LEU cc_start: 0.7116 (mm) cc_final: 0.6207 (pp) REVERT: A 178 GLN cc_start: 0.8047 (mt0) cc_final: 0.7638 (mp10) REVERT: A 647 GLU cc_start: 0.8892 (tt0) cc_final: 0.8397 (mt-10) REVERT: A 670 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7589 (tp30) REVERT: B 39 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.5611 (p90) REVERT: B 277 MET cc_start: 0.7452 (mmp) cc_final: 0.7140 (mmp) REVERT: B 383 GLN cc_start: 0.8294 (tp40) cc_final: 0.7921 (tt0) REVERT: B 634 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: B 645 MET cc_start: 0.8329 (tmm) cc_final: 0.8098 (ttm) REVERT: C 39 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.5580 (p90) REVERT: C 178 GLN cc_start: 0.8097 (mt0) cc_final: 0.7701 (mp10) REVERT: C 235 GLN cc_start: 0.7770 (mt0) cc_final: 0.7538 (mt0) REVERT: C 269 HIS cc_start: 0.7999 (t70) cc_final: 0.7722 (t70) REVERT: C 528 MET cc_start: 0.8483 (ptm) cc_final: 0.8168 (ttp) REVERT: D 92 LEU cc_start: 0.7707 (mt) cc_final: 0.6213 (pp) REVERT: D 178 GLN cc_start: 0.8048 (mt0) cc_final: 0.7625 (mp10) REVERT: D 235 GLN cc_start: 0.7761 (mt0) cc_final: 0.7517 (mt0) REVERT: D 670 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7650 (tp30) outliers start: 57 outliers final: 33 residues processed: 333 average time/residue: 0.1308 time to fit residues: 70.3256 Evaluate side-chains 300 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 144 optimal weight: 0.0270 chunk 59 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 0.0970 chunk 240 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 236 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127657 restraints weight = 26967.034| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.81 r_work: 0.3310 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20544 Z= 0.091 Angle : 0.505 11.376 27876 Z= 0.241 Chirality : 0.036 0.153 3148 Planarity : 0.003 0.047 3420 Dihedral : 5.825 57.860 2772 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.33 % Allowed : 18.81 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.18), residues: 2428 helix: 2.13 (0.14), residues: 1452 sheet: -2.42 (0.45), residues: 112 loop : -1.10 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.012 0.001 TYR B 455 PHE 0.022 0.001 PHE A 467 TRP 0.018 0.001 TRP A 715 HIS 0.007 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00204 (20544) covalent geometry : angle 0.50479 (27876) hydrogen bonds : bond 0.02838 ( 1072) hydrogen bonds : angle 3.48707 ( 3108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8179 (tt0) cc_final: 0.7363 (tp40) REVERT: A 178 GLN cc_start: 0.8040 (mt0) cc_final: 0.7664 (mp10) REVERT: A 235 GLN cc_start: 0.7815 (mt0) cc_final: 0.7573 (mt0) REVERT: A 528 MET cc_start: 0.8464 (ptm) cc_final: 0.8180 (ttp) REVERT: A 647 GLU cc_start: 0.8890 (tt0) cc_final: 0.8344 (mt-10) REVERT: A 670 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7615 (tp30) REVERT: B 277 MET cc_start: 0.7465 (mmp) cc_final: 0.7155 (mmp) REVERT: B 383 GLN cc_start: 0.8236 (tp40) cc_final: 0.7875 (tt0) REVERT: B 634 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: C 39 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.5501 (p90) REVERT: C 178 GLN cc_start: 0.8083 (mt0) cc_final: 0.7691 (mp10) REVERT: C 235 GLN cc_start: 0.7731 (mt0) cc_final: 0.7515 (mt0) REVERT: C 269 HIS cc_start: 0.7972 (t70) cc_final: 0.7712 (t70) REVERT: C 528 MET cc_start: 0.8477 (ptm) cc_final: 0.8169 (ttp) REVERT: D 39 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.5641 (p90) REVERT: D 92 LEU cc_start: 0.7702 (mt) cc_final: 0.6165 (pp) REVERT: D 178 GLN cc_start: 0.8031 (mt0) cc_final: 0.7580 (mp10) REVERT: D 235 GLN cc_start: 0.7751 (mt0) cc_final: 0.7510 (mt0) REVERT: D 457 TRP cc_start: 0.8641 (t-100) cc_final: 0.7746 (t-100) REVERT: D 528 MET cc_start: 0.8792 (ptp) cc_final: 0.8375 (ptp) REVERT: D 670 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7623 (tp30) outliers start: 50 outliers final: 32 residues processed: 330 average time/residue: 0.1328 time to fit residues: 70.4102 Evaluate side-chains 300 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 115 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125926 restraints weight = 27071.566| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.83 r_work: 0.3291 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20544 Z= 0.106 Angle : 0.526 10.582 27876 Z= 0.252 Chirality : 0.036 0.153 3148 Planarity : 0.003 0.046 3420 Dihedral : 5.896 59.305 2772 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.28 % Allowed : 19.60 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.18), residues: 2428 helix: 2.19 (0.14), residues: 1452 sheet: -2.41 (0.44), residues: 112 loop : -1.07 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 197 TYR 0.013 0.001 TYR C 455 PHE 0.023 0.001 PHE A 467 TRP 0.022 0.001 TRP A 715 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00247 (20544) covalent geometry : angle 0.52631 (27876) hydrogen bonds : bond 0.02935 ( 1072) hydrogen bonds : angle 3.50044 ( 3108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.5857 (p90) REVERT: A 92 LEU cc_start: 0.7075 (mm) cc_final: 0.6222 (pp) REVERT: A 178 GLN cc_start: 0.8054 (mt0) cc_final: 0.7659 (mp10) REVERT: A 528 MET cc_start: 0.8515 (ptm) cc_final: 0.8231 (ttp) REVERT: A 647 GLU cc_start: 0.8896 (tt0) cc_final: 0.8327 (mt-10) REVERT: A 670 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7658 (tp30) REVERT: B 39 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.5599 (p90) REVERT: B 178 GLN cc_start: 0.8076 (mt0) cc_final: 0.7657 (mp10) REVERT: B 277 MET cc_start: 0.7475 (mmp) cc_final: 0.7170 (mmp) REVERT: B 383 GLN cc_start: 0.8336 (tp40) cc_final: 0.7989 (tt0) REVERT: B 519 PHE cc_start: 0.7956 (m-10) cc_final: 0.7683 (m-10) REVERT: C 39 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.5504 (p90) REVERT: C 92 LEU cc_start: 0.7600 (mt) cc_final: 0.6175 (pp) REVERT: C 178 GLN cc_start: 0.8020 (mt0) cc_final: 0.7593 (mp10) REVERT: C 235 GLN cc_start: 0.7789 (mt0) cc_final: 0.7540 (mt0) REVERT: C 269 HIS cc_start: 0.8067 (t70) cc_final: 0.7789 (t70) REVERT: C 528 MET cc_start: 0.8438 (ptm) cc_final: 0.8162 (ttp) REVERT: C 634 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: D 39 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.5598 (p90) REVERT: D 92 LEU cc_start: 0.7722 (mt) cc_final: 0.6207 (pp) REVERT: D 178 GLN cc_start: 0.8040 (mt0) cc_final: 0.7598 (mp10) REVERT: D 473 GLU cc_start: 0.8387 (mp0) cc_final: 0.8055 (mm-30) REVERT: D 528 MET cc_start: 0.8831 (ptp) cc_final: 0.8428 (ptp) REVERT: D 670 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7655 (tp30) outliers start: 49 outliers final: 31 residues processed: 319 average time/residue: 0.1335 time to fit residues: 68.3223 Evaluate side-chains 306 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN C 127 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120099 restraints weight = 27144.783| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.97 r_work: 0.3199 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20544 Z= 0.215 Angle : 0.639 11.280 27876 Z= 0.308 Chirality : 0.041 0.190 3148 Planarity : 0.004 0.043 3420 Dihedral : 6.872 62.842 2772 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.14 % Allowed : 19.93 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2428 helix: 1.72 (0.13), residues: 1468 sheet: -2.54 (0.45), residues: 112 loop : -1.34 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 197 TYR 0.016 0.002 TYR B 455 PHE 0.023 0.002 PHE B 394 TRP 0.027 0.001 TRP A 715 HIS 0.007 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00515 (20544) covalent geometry : angle 0.63900 (27876) hydrogen bonds : bond 0.03702 ( 1072) hydrogen bonds : angle 3.85362 ( 3108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.5552 (p90) REVERT: A 92 LEU cc_start: 0.7573 (mm) cc_final: 0.6591 (pp) REVERT: A 537 LEU cc_start: 0.7955 (mt) cc_final: 0.7334 (mt) REVERT: A 670 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7706 (tp30) REVERT: B 39 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.5921 (p90) REVERT: B 383 GLN cc_start: 0.8340 (tp40) cc_final: 0.8056 (tt0) REVERT: B 634 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: C 39 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.5891 (p90) REVERT: C 634 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: D 39 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.5381 (p90) REVERT: D 92 LEU cc_start: 0.7709 (mt) cc_final: 0.6320 (pp) REVERT: D 670 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7796 (tp30) outliers start: 46 outliers final: 30 residues processed: 303 average time/residue: 0.1304 time to fit residues: 64.0967 Evaluate side-chains 290 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 224 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125818 restraints weight = 27137.229| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.84 r_work: 0.3265 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20544 Z= 0.123 Angle : 0.563 9.587 27876 Z= 0.271 Chirality : 0.037 0.202 3148 Planarity : 0.003 0.045 3420 Dihedral : 6.200 58.568 2772 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.68 % Allowed : 20.72 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2428 helix: 2.02 (0.14), residues: 1444 sheet: -2.52 (0.44), residues: 112 loop : -1.06 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.015 0.001 TYR C 455 PHE 0.023 0.001 PHE B 467 TRP 0.041 0.001 TRP D 715 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00297 (20544) covalent geometry : angle 0.56268 (27876) hydrogen bonds : bond 0.03174 ( 1072) hydrogen bonds : angle 3.65017 ( 3108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.5515 (p90) REVERT: A 92 LEU cc_start: 0.7358 (mm) cc_final: 0.6458 (pp) REVERT: A 305 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8047 (tt0) REVERT: A 519 PHE cc_start: 0.8189 (m-10) cc_final: 0.7981 (m-10) REVERT: A 528 MET cc_start: 0.8465 (ptm) cc_final: 0.8233 (ttp) REVERT: A 647 GLU cc_start: 0.8907 (tt0) cc_final: 0.8329 (mt-10) REVERT: A 670 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7640 (tp30) REVERT: B 39 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.5790 (p90) REVERT: B 305 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7972 (tt0) REVERT: B 383 GLN cc_start: 0.8323 (tp40) cc_final: 0.8015 (tt0) REVERT: B 634 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: C 39 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.5712 (p90) REVERT: C 92 LEU cc_start: 0.7627 (mt) cc_final: 0.6263 (pp) REVERT: C 305 GLU cc_start: 0.8200 (mt-10) cc_final: 0.8000 (tt0) REVERT: C 634 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: D 39 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.5357 (p90) REVERT: D 92 LEU cc_start: 0.7651 (mt) cc_final: 0.6266 (pp) REVERT: D 670 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7694 (tp30) outliers start: 36 outliers final: 29 residues processed: 301 average time/residue: 0.1260 time to fit residues: 61.7118 Evaluate side-chains 299 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 95 optimal weight: 1.9990 chunk 228 optimal weight: 0.3980 chunk 125 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122567 restraints weight = 27342.251| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.93 r_work: 0.3224 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20544 Z= 0.168 Angle : 0.605 10.319 27876 Z= 0.291 Chirality : 0.039 0.176 3148 Planarity : 0.004 0.045 3420 Dihedral : 6.570 59.861 2772 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.05 % Allowed : 20.62 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2428 helix: 1.95 (0.14), residues: 1444 sheet: -2.53 (0.44), residues: 112 loop : -1.06 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.016 0.001 TYR A 455 PHE 0.021 0.001 PHE A 405 TRP 0.037 0.001 TRP D 715 HIS 0.005 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00408 (20544) covalent geometry : angle 0.60450 (27876) hydrogen bonds : bond 0.03403 ( 1072) hydrogen bonds : angle 3.74208 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4708.07 seconds wall clock time: 81 minutes 28.17 seconds (4888.17 seconds total)