Starting phenix.real_space_refine on Sat Feb 7 19:30:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4n_65639/02_2026/9w4n_65639_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4n_65639/02_2026/9w4n_65639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w4n_65639/02_2026/9w4n_65639_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4n_65639/02_2026/9w4n_65639_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w4n_65639/02_2026/9w4n_65639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4n_65639/02_2026/9w4n_65639.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 100 5.16 5 Cl 4 4.86 5 C 11468 2.51 5 N 2832 2.21 5 O 3100 1.98 5 H 17564 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35068 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 8747 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 522} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'ZEI': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 9.99, per 1000 atoms: 0.28 Number of scatterers: 35068 At special positions: 0 Unit cell: (121.83, 121.83, 116.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 100 16.00 O 3100 8.00 N 2832 7.00 C 11468 6.00 H 17564 1.00 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: 2.87 Conformation dependent library (CDL) restraints added in 947.0 milliseconds 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 66.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.654A pdb=" N LYS A 200 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 201 " --> pdb=" O TYR A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 201' Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 213 through 223 removed outlier: 4.251A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.773A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.733A pdb=" N ILE A 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.281A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Processing helix chain 'A' and resid 430 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 531 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.910A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.899A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 4.056A pdb=" N ILE A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.534A pdb=" N THR A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 712 removed outlier: 5.963A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.654A pdb=" N LYS B 200 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 201 " --> pdb=" O TYR B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 201' Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 213 through 223 removed outlier: 4.251A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.773A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.733A pdb=" N ILE B 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.281A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 430 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 531 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.910A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 removed outlier: 3.899A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 removed outlier: 4.056A pdb=" N ILE B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.534A pdb=" N THR B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 712 removed outlier: 5.963A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.654A pdb=" N LYS C 200 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 201 " --> pdb=" O TYR C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 201' Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 213 through 223 removed outlier: 4.251A pdb=" N ASN C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.773A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.733A pdb=" N ILE C 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.281A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 Processing helix chain 'C' and resid 430 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 531 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.910A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 558 removed outlier: 3.899A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 576 removed outlier: 4.056A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 599 Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.534A pdb=" N THR C 633 " --> pdb=" O SER C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 712 removed outlier: 5.963A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.654A pdb=" N LYS D 200 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D 201 " --> pdb=" O TYR D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 197 through 201' Processing helix chain 'D' and resid 203 through 212 Processing helix chain 'D' and resid 213 through 223 removed outlier: 4.251A pdb=" N ASN D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.773A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.733A pdb=" N ILE D 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.281A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 430 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 531 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.910A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 removed outlier: 3.899A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 576 removed outlier: 4.056A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 599 Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.534A pdb=" N THR D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 712 removed outlier: 5.963A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 374 removed outlier: 4.654A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 377 " --> pdb=" O TYR A 374 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 724 through 731 removed outlier: 4.160A pdb=" N VAL A 728 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 730 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS A 735 " --> pdb=" O PHE A 730 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 370 through 374 removed outlier: 4.654A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 377 " --> pdb=" O TYR B 374 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 724 through 731 removed outlier: 4.160A pdb=" N VAL B 728 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 730 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS B 735 " --> pdb=" O PHE B 730 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 370 through 374 removed outlier: 4.654A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 377 " --> pdb=" O TYR C 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 724 through 731 removed outlier: 4.160A pdb=" N VAL C 728 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE C 730 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS C 735 " --> pdb=" O PHE C 730 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 370 through 374 removed outlier: 4.654A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 377 " --> pdb=" O TYR D 374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 724 through 731 removed outlier: 4.160A pdb=" N VAL D 728 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE D 730 " --> pdb=" O LYS D 735 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS D 735 " --> pdb=" O PHE D 730 " (cutoff:3.500A) 1028 hydrogen bonds defined for protein. 3000 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: 7.16 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17104 1.03 - 1.23: 468 1.23 - 1.42: 7716 1.42 - 1.62: 10032 1.62 - 1.81: 168 Bond restraints: 35488 Sorted by residual: bond pdb=" N ASP B 745 " pdb=" H ASP B 745 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" N ASP C 745 " pdb=" H ASP C 745 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" N ASP D 745 " pdb=" H ASP D 745 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" N ASP A 745 " pdb=" H ASP A 745 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" N ILE B 672 " pdb=" H ILE B 672 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 ... (remaining 35483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 62928 1.68 - 3.35: 908 3.35 - 5.03: 92 5.03 - 6.70: 16 6.70 - 8.38: 4 Bond angle restraints: 63948 Sorted by residual: angle pdb=" N ASN A 676 " pdb=" CA ASN A 676 " pdb=" C ASN A 676 " ideal model delta sigma weight residual 111.28 106.55 4.73 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ASN B 676 " pdb=" CA ASN B 676 " pdb=" C ASN B 676 " ideal model delta sigma weight residual 111.28 106.55 4.73 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ASN C 676 " pdb=" CA ASN C 676 " pdb=" C ASN C 676 " ideal model delta sigma weight residual 111.28 106.55 4.73 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ASN D 676 " pdb=" CA ASN D 676 " pdb=" C ASN D 676 " ideal model delta sigma weight residual 111.28 106.55 4.73 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N VAL A 283 " pdb=" CA VAL A 283 " pdb=" C VAL A 283 " ideal model delta sigma weight residual 113.07 107.83 5.24 1.36e+00 5.41e-01 1.49e+01 ... (remaining 63943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 14400 17.61 - 35.21: 1652 35.21 - 52.82: 408 52.82 - 70.43: 152 70.43 - 88.03: 64 Dihedral angle restraints: 16676 sinusoidal: 8824 harmonic: 7852 Sorted by residual: dihedral pdb=" CA PHE C 559 " pdb=" C PHE C 559 " pdb=" N GLN C 560 " pdb=" CA GLN C 560 " ideal model delta harmonic sigma weight residual 180.00 -164.20 -15.80 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CA PHE D 559 " pdb=" C PHE D 559 " pdb=" N GLN D 560 " pdb=" CA GLN D 560 " ideal model delta harmonic sigma weight residual -180.00 -164.20 -15.80 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CA PHE A 559 " pdb=" C PHE A 559 " pdb=" N GLN A 560 " pdb=" CA GLN A 560 " ideal model delta harmonic sigma weight residual -180.00 -164.20 -15.80 0 5.00e+00 4.00e-02 9.98e+00 ... (remaining 16673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1832 0.032 - 0.063: 640 0.063 - 0.095: 168 0.095 - 0.126: 60 0.126 - 0.158: 12 Chirality restraints: 2712 Sorted by residual: chirality pdb=" CA VAL D 283 " pdb=" N VAL D 283 " pdb=" C VAL D 283 " pdb=" CB VAL D 283 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL C 283 " pdb=" N VAL C 283 " pdb=" C VAL C 283 " pdb=" CB VAL C 283 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL A 283 " pdb=" N VAL A 283 " pdb=" C VAL A 283 " pdb=" CB VAL A 283 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2709 not shown) Planarity restraints: 5096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 676 " 0.080 2.00e-02 2.50e+03 7.71e-02 8.93e+01 pdb=" CG ASN B 676 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN B 676 " -0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN B 676 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 676 " -0.108 2.00e-02 2.50e+03 pdb="HD22 ASN B 676 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 676 " -0.080 2.00e-02 2.50e+03 7.71e-02 8.93e+01 pdb=" CG ASN A 676 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN A 676 " 0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN A 676 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 676 " 0.108 2.00e-02 2.50e+03 pdb="HD22 ASN A 676 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 676 " 0.080 2.00e-02 2.50e+03 7.71e-02 8.93e+01 pdb=" CG ASN C 676 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN C 676 " -0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN C 676 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 676 " -0.108 2.00e-02 2.50e+03 pdb="HD22 ASN C 676 " 0.108 2.00e-02 2.50e+03 ... (remaining 5093 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 112 1.89 - 2.56: 33144 2.56 - 3.24: 109952 3.24 - 3.92: 131486 3.92 - 4.60: 209312 Nonbonded interactions: 484006 Sorted by model distance: nonbonded pdb=" OH TYR C 584 " pdb=" HG1 THR C 641 " model vdw 1.208 2.450 nonbonded pdb=" OH TYR D 584 " pdb=" HG1 THR D 641 " model vdw 1.208 2.450 nonbonded pdb=" OH TYR B 584 " pdb=" HG1 THR B 641 " model vdw 1.208 2.450 nonbonded pdb=" OH TYR A 584 " pdb=" HG1 THR A 641 " model vdw 1.208 2.450 nonbonded pdb=" O LEU A 588 " pdb=" HG SER A 592 " model vdw 1.465 2.450 ... (remaining 484001 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.390 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.440 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.004 0.081 17924 Z= 0.225 Angle : 0.623 8.377 24256 Z= 0.368 Chirality : 0.036 0.158 2712 Planarity : 0.003 0.041 3012 Dihedral : 15.764 88.032 6464 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 14.77 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.53 (0.19), residues: 2132 helix: 1.75 (0.15), residues: 1280 sheet: -4.46 (0.41), residues: 92 loop : -1.50 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 743 TYR 0.009 0.001 TYR C 351 PHE 0.010 0.001 PHE A 742 TRP 0.006 0.001 TRP A 697 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00404 (17924) covalent geometry : angle 0.62329 (24256) hydrogen bonds : bond 0.12799 ( 1028) hydrogen bonds : angle 5.72094 ( 3000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7774 (ttm-80) REVERT: A 474 ARG cc_start: 0.7318 (ttp80) cc_final: 0.6586 (tpt170) REVERT: A 478 GLU cc_start: 0.5974 (tp30) cc_final: 0.5714 (tp30) REVERT: B 428 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7776 (ttm-80) REVERT: B 474 ARG cc_start: 0.7320 (ttp80) cc_final: 0.6587 (tpt170) REVERT: B 478 GLU cc_start: 0.5977 (tp30) cc_final: 0.5717 (tp30) REVERT: C 428 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7776 (ttm-80) REVERT: C 474 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6585 (tpt170) REVERT: C 478 GLU cc_start: 0.5975 (tp30) cc_final: 0.5717 (tp30) REVERT: D 428 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7775 (ttm-80) REVERT: D 474 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6584 (tpt170) REVERT: D 478 GLU cc_start: 0.5970 (tp30) cc_final: 0.5713 (tp30) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2778 time to fit residues: 120.1337 Evaluate side-chains 260 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.200882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141144 restraints weight = 60252.048| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.37 r_work: 0.3504 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17924 Z= 0.134 Angle : 0.482 4.527 24256 Z= 0.265 Chirality : 0.033 0.116 2712 Planarity : 0.003 0.039 3012 Dihedral : 6.002 80.950 2388 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.21 % Allowed : 15.19 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.70 (0.18), residues: 2132 helix: 1.87 (0.14), residues: 1312 sheet: -4.51 (0.36), residues: 92 loop : -1.52 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 455 TYR 0.010 0.001 TYR D 309 PHE 0.009 0.001 PHE C 655 TRP 0.006 0.001 TRP B 697 HIS 0.002 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00288 (17924) covalent geometry : angle 0.48240 (24256) hydrogen bonds : bond 0.04525 ( 1028) hydrogen bonds : angle 4.54368 ( 3000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 276 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8500 (ttm170) cc_final: 0.8125 (ttm-80) REVERT: A 478 GLU cc_start: 0.5807 (tp30) cc_final: 0.5410 (tp30) REVERT: B 428 ARG cc_start: 0.8499 (ttm170) cc_final: 0.8126 (ttm-80) REVERT: B 478 GLU cc_start: 0.5800 (tp30) cc_final: 0.5408 (tp30) REVERT: C 428 ARG cc_start: 0.8510 (ttm170) cc_final: 0.8134 (ttm-80) REVERT: C 478 GLU cc_start: 0.5801 (tp30) cc_final: 0.5406 (tp30) REVERT: D 428 ARG cc_start: 0.8501 (ttm170) cc_final: 0.8128 (ttm-80) REVERT: D 478 GLU cc_start: 0.5818 (tp30) cc_final: 0.5400 (tp30) outliers start: 4 outliers final: 4 residues processed: 280 average time/residue: 0.2894 time to fit residues: 126.6611 Evaluate side-chains 272 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 184 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.199732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141620 restraints weight = 59449.030| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.35 r_work: 0.3488 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17924 Z= 0.106 Angle : 0.446 4.439 24256 Z= 0.240 Chirality : 0.033 0.120 2712 Planarity : 0.003 0.036 3012 Dihedral : 5.136 66.367 2388 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.63 % Allowed : 13.71 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2132 helix: 2.17 (0.14), residues: 1312 sheet: -4.27 (0.40), residues: 92 loop : -1.50 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 212 TYR 0.009 0.001 TYR C 351 PHE 0.008 0.001 PHE D 742 TRP 0.007 0.001 TRP B 697 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00228 (17924) covalent geometry : angle 0.44613 (24256) hydrogen bonds : bond 0.04031 ( 1028) hydrogen bonds : angle 4.26441 ( 3000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 280 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8139 (ttm-80) REVERT: A 478 GLU cc_start: 0.5721 (tp30) cc_final: 0.5264 (tp30) REVERT: B 428 ARG cc_start: 0.8500 (ttm170) cc_final: 0.8136 (ttm-80) REVERT: B 478 GLU cc_start: 0.5718 (tp30) cc_final: 0.5281 (tp30) REVERT: C 428 ARG cc_start: 0.8506 (ttm170) cc_final: 0.8141 (ttm-80) REVERT: C 478 GLU cc_start: 0.5724 (tp30) cc_final: 0.5261 (tp30) REVERT: D 428 ARG cc_start: 0.8491 (ttm170) cc_final: 0.8125 (ttm-80) REVERT: D 478 GLU cc_start: 0.5724 (tp30) cc_final: 0.5249 (tp30) outliers start: 12 outliers final: 8 residues processed: 292 average time/residue: 0.2884 time to fit residues: 131.7125 Evaluate side-chains 268 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 260 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.195584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137403 restraints weight = 59605.819| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.30 r_work: 0.3437 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 17924 Z= 0.176 Angle : 0.485 4.473 24256 Z= 0.264 Chirality : 0.034 0.119 2712 Planarity : 0.003 0.037 3012 Dihedral : 4.377 44.083 2388 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.42 % Allowed : 14.98 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.86 (0.18), residues: 2132 helix: 2.01 (0.14), residues: 1320 sheet: -4.08 (0.41), residues: 84 loop : -1.63 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 739 TYR 0.017 0.001 TYR C 309 PHE 0.009 0.001 PHE C 559 TRP 0.005 0.001 TRP B 697 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00403 (17924) covalent geometry : angle 0.48453 (24256) hydrogen bonds : bond 0.04366 ( 1028) hydrogen bonds : angle 4.33172 ( 3000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 268 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8545 (ttm170) cc_final: 0.8162 (ttm-80) REVERT: B 428 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8151 (ttm-80) REVERT: C 428 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8143 (ttm-80) REVERT: D 428 ARG cc_start: 0.8523 (ttm170) cc_final: 0.8138 (ttm-80) outliers start: 8 outliers final: 8 residues processed: 276 average time/residue: 0.2794 time to fit residues: 121.0380 Evaluate side-chains 268 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 260 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 108 optimal weight: 0.0270 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.196362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137915 restraints weight = 59933.823| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.30 r_work: 0.3455 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17924 Z= 0.149 Angle : 0.468 4.290 24256 Z= 0.255 Chirality : 0.034 0.121 2712 Planarity : 0.003 0.038 3012 Dihedral : 3.538 15.551 2388 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.84 % Allowed : 14.98 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.95 (0.18), residues: 2132 helix: 2.08 (0.14), residues: 1320 sheet: -4.01 (0.43), residues: 84 loop : -1.58 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 739 TYR 0.012 0.001 TYR A 537 PHE 0.011 0.001 PHE C 712 TRP 0.005 0.001 TRP C 697 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00340 (17924) covalent geometry : angle 0.46833 (24256) hydrogen bonds : bond 0.04212 ( 1028) hydrogen bonds : angle 4.25521 ( 3000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8500 (ttm170) cc_final: 0.8126 (ttm-80) REVERT: A 478 GLU cc_start: 0.5674 (tp30) cc_final: 0.5182 (tp30) REVERT: B 428 ARG cc_start: 0.8499 (ttm170) cc_final: 0.8126 (ttm-80) REVERT: B 478 GLU cc_start: 0.5670 (tp30) cc_final: 0.5189 (tp30) REVERT: C 428 ARG cc_start: 0.8493 (ttm170) cc_final: 0.8119 (ttm-80) REVERT: C 478 GLU cc_start: 0.5680 (tp30) cc_final: 0.5184 (tp30) REVERT: D 428 ARG cc_start: 0.8492 (ttm170) cc_final: 0.8118 (ttm-80) REVERT: D 478 GLU cc_start: 0.5681 (tp30) cc_final: 0.5181 (tp30) outliers start: 16 outliers final: 16 residues processed: 300 average time/residue: 0.2612 time to fit residues: 123.5826 Evaluate side-chains 288 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 173 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.193185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135007 restraints weight = 59713.472| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.27 r_work: 0.3430 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17924 Z= 0.188 Angle : 0.494 4.584 24256 Z= 0.271 Chirality : 0.036 0.198 2712 Planarity : 0.003 0.040 3012 Dihedral : 3.672 15.678 2388 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.05 % Allowed : 14.98 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.18), residues: 2132 helix: 1.95 (0.14), residues: 1320 sheet: -4.09 (0.44), residues: 84 loop : -1.58 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 739 TYR 0.014 0.001 TYR D 309 PHE 0.008 0.001 PHE C 659 TRP 0.004 0.001 TRP C 697 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00432 (17924) covalent geometry : angle 0.49388 (24256) hydrogen bonds : bond 0.04482 ( 1028) hydrogen bonds : angle 4.30332 ( 3000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8571 (ttm170) cc_final: 0.8172 (ttm-80) REVERT: A 676 ASN cc_start: 0.8740 (m-40) cc_final: 0.8506 (m110) REVERT: B 428 ARG cc_start: 0.8569 (ttm170) cc_final: 0.8169 (ttm-80) REVERT: B 676 ASN cc_start: 0.8737 (m-40) cc_final: 0.8496 (m110) REVERT: C 428 ARG cc_start: 0.8556 (ttm170) cc_final: 0.8156 (ttm-80) REVERT: C 676 ASN cc_start: 0.8742 (m-40) cc_final: 0.8497 (m110) REVERT: D 428 ARG cc_start: 0.8554 (ttm170) cc_final: 0.8154 (ttm-80) REVERT: D 676 ASN cc_start: 0.8743 (m-40) cc_final: 0.8495 (m110) outliers start: 20 outliers final: 16 residues processed: 300 average time/residue: 0.2619 time to fit residues: 123.7131 Evaluate side-chains 272 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 256 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 48 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 79 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.197253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144572 restraints weight = 60017.100| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.49 r_work: 0.3415 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17924 Z= 0.117 Angle : 0.455 4.809 24256 Z= 0.248 Chirality : 0.034 0.125 2712 Planarity : 0.003 0.041 3012 Dihedral : 3.484 14.943 2388 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.84 % Allowed : 15.40 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2132 helix: 2.20 (0.14), residues: 1312 sheet: -4.07 (0.45), residues: 84 loop : -1.52 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 212 TYR 0.009 0.001 TYR D 537 PHE 0.008 0.001 PHE A 742 TRP 0.009 0.001 TRP C 697 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00259 (17924) covalent geometry : angle 0.45525 (24256) hydrogen bonds : bond 0.04023 ( 1028) hydrogen bonds : angle 4.16109 ( 3000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8573 (ttm170) cc_final: 0.8225 (ttm-80) REVERT: B 428 ARG cc_start: 0.8574 (ttm170) cc_final: 0.8227 (ttm-80) REVERT: C 428 ARG cc_start: 0.8574 (ttm170) cc_final: 0.8227 (ttm-80) REVERT: D 428 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8210 (ttm-80) outliers start: 16 outliers final: 12 residues processed: 276 average time/residue: 0.2810 time to fit residues: 120.8923 Evaluate side-chains 264 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 21 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 748 ASN D 748 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.194821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141882 restraints weight = 60371.559| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.56 r_work: 0.3355 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17924 Z= 0.193 Angle : 0.491 4.546 24256 Z= 0.270 Chirality : 0.035 0.127 2712 Planarity : 0.003 0.040 3012 Dihedral : 3.622 15.173 2388 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.84 % Allowed : 14.87 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.86 (0.18), residues: 2132 helix: 1.97 (0.14), residues: 1320 sheet: -4.14 (0.46), residues: 84 loop : -1.52 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 739 TYR 0.013 0.001 TYR A 453 PHE 0.009 0.001 PHE A 659 TRP 0.005 0.001 TRP B 697 HIS 0.002 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00444 (17924) covalent geometry : angle 0.49140 (24256) hydrogen bonds : bond 0.04394 ( 1028) hydrogen bonds : angle 4.27382 ( 3000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8601 (ttm170) cc_final: 0.8235 (ttm-80) REVERT: A 676 ASN cc_start: 0.8711 (m-40) cc_final: 0.8464 (m110) REVERT: B 428 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8230 (ttm-80) REVERT: B 676 ASN cc_start: 0.8719 (m-40) cc_final: 0.8450 (m110) REVERT: C 428 ARG cc_start: 0.8583 (ttm170) cc_final: 0.8217 (ttm-80) REVERT: C 676 ASN cc_start: 0.8726 (m-40) cc_final: 0.8457 (m110) REVERT: D 428 ARG cc_start: 0.8585 (ttm170) cc_final: 0.8219 (ttm-80) REVERT: D 676 ASN cc_start: 0.8718 (m-40) cc_final: 0.8449 (m110) outliers start: 16 outliers final: 16 residues processed: 272 average time/residue: 0.2724 time to fit residues: 115.7373 Evaluate side-chains 272 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 256 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 210 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 163 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.195907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137335 restraints weight = 59715.728| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.33 r_work: 0.3442 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17924 Z= 0.111 Angle : 0.454 4.669 24256 Z= 0.247 Chirality : 0.033 0.134 2712 Planarity : 0.003 0.041 3012 Dihedral : 3.464 15.722 2388 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.63 % Allowed : 15.56 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 2132 helix: 2.28 (0.14), residues: 1312 sheet: -3.96 (0.48), residues: 84 loop : -1.46 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 212 TYR 0.015 0.001 TYR D 309 PHE 0.008 0.001 PHE D 742 TRP 0.011 0.001 TRP D 697 HIS 0.002 0.000 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00243 (17924) covalent geometry : angle 0.45391 (24256) hydrogen bonds : bond 0.04003 ( 1028) hydrogen bonds : angle 4.13843 ( 3000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 260 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8519 (ttm170) cc_final: 0.8135 (ttm-80) REVERT: B 428 ARG cc_start: 0.8518 (ttm170) cc_final: 0.8135 (ttm-80) REVERT: C 428 ARG cc_start: 0.8517 (ttm170) cc_final: 0.8133 (ttm-80) REVERT: D 428 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8119 (ttm-80) outliers start: 12 outliers final: 12 residues processed: 272 average time/residue: 0.2594 time to fit residues: 109.9748 Evaluate side-chains 264 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 92 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.193660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134880 restraints weight = 59583.454| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.27 r_work: 0.3433 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17924 Z= 0.140 Angle : 0.466 4.499 24256 Z= 0.255 Chirality : 0.034 0.133 2712 Planarity : 0.003 0.041 3012 Dihedral : 3.478 15.279 2388 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.63 % Allowed : 15.98 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.17 (0.18), residues: 2132 helix: 2.21 (0.14), residues: 1320 sheet: -3.96 (0.49), residues: 84 loop : -1.40 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 212 TYR 0.013 0.001 TYR D 309 PHE 0.007 0.001 PHE B 649 TRP 0.008 0.001 TRP D 697 HIS 0.002 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00317 (17924) covalent geometry : angle 0.46561 (24256) hydrogen bonds : bond 0.04061 ( 1028) hydrogen bonds : angle 4.16928 ( 3000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 266 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8537 (ttm170) cc_final: 0.8154 (ttm-80) REVERT: A 478 GLU cc_start: 0.5955 (tp30) cc_final: 0.5559 (tp30) REVERT: A 676 ASN cc_start: 0.8795 (m-40) cc_final: 0.8554 (m110) REVERT: B 428 ARG cc_start: 0.8538 (ttm170) cc_final: 0.8158 (ttm-80) REVERT: B 676 ASN cc_start: 0.8800 (m-40) cc_final: 0.8549 (m110) REVERT: C 428 ARG cc_start: 0.8526 (ttm170) cc_final: 0.8144 (ttm-80) REVERT: C 478 GLU cc_start: 0.5950 (tp30) cc_final: 0.5562 (tp30) REVERT: C 676 ASN cc_start: 0.8799 (m-40) cc_final: 0.8545 (m110) REVERT: D 428 ARG cc_start: 0.8519 (ttm170) cc_final: 0.8134 (ttm-80) REVERT: D 676 ASN cc_start: 0.8801 (m-40) cc_final: 0.8542 (m110) outliers start: 12 outliers final: 12 residues processed: 278 average time/residue: 0.2797 time to fit residues: 120.3448 Evaluate side-chains 272 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 260 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 60 optimal weight: 0.0000 chunk 115 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 0.0370 chunk 58 optimal weight: 6.9990 overall best weight: 1.4068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.194038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142713 restraints weight = 59481.625| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.41 r_work: 0.3440 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17924 Z= 0.124 Angle : 0.460 4.531 24256 Z= 0.250 Chirality : 0.033 0.129 2712 Planarity : 0.003 0.041 3012 Dihedral : 3.429 15.229 2388 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.42 % Allowed : 16.03 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.27 (0.19), residues: 2132 helix: 2.28 (0.14), residues: 1320 sheet: -3.89 (0.50), residues: 84 loop : -1.35 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 212 TYR 0.014 0.001 TYR D 309 PHE 0.007 0.001 PHE D 742 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.000 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00279 (17924) covalent geometry : angle 0.46001 (24256) hydrogen bonds : bond 0.03919 ( 1028) hydrogen bonds : angle 4.11683 ( 3000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9536.53 seconds wall clock time: 162 minutes 4.01 seconds (9724.01 seconds total)