Starting phenix.real_space_refine on Fri Jul 3 20:05:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2o_23135/07_2026/7l2o_23135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2o_23135/07_2026/7l2o_23135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7l2o_23135/07_2026/7l2o_23135.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2o_23135/07_2026/7l2o_23135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2o_23135/07_2026/7l2o_23135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2o_23135/07_2026/7l2o_23135.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2o_23135/07_2026/7l2o_23135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2o_23135/07_2026/7l2o_23135.cif" } resolution = 3.64 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= 0.004 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 96 5.16 5 C 10416 2.51 5 N 2492 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.77, per 1000 atoms: 0.24 Number of scatterers: 15800 At special positions: 0 Unit cell: (126.5, 125.35, 108.1, 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 96 16.00 O 2796 8.00 N 2492 7.00 C 10416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.02 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.02 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.02 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: 1.34 Conformation dependent library (CDL) restraints added in 671.5 milliseconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 4 sheets defined 66.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 250 through 259 removed outlier: 4.126A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 removed outlier: 4.220A pdb=" N VAL A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.582A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 4.357A pdb=" N LEU A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 removed outlier: 3.511A pdb=" N TYR A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.994A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.652A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 559 through 576 removed outlier: 4.597A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 removed outlier: 3.692A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 691 through 712 removed outlier: 3.794A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.916A pdb=" N LEU C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 removed outlier: 4.169A pdb=" N VAL C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 4.312A pdb=" N LEU C 421 " --> pdb=" O PRO C 417 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.515A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.787A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 550 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 559 through 576 removed outlier: 4.688A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 599 removed outlier: 3.914A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 691 through 712 removed outlier: 3.837A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 4.281A pdb=" N LEU D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 4.089A pdb=" N VAL D 264 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.647A pdb=" N VAL D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.963A pdb=" N LEU D 421 " --> pdb=" O PRO D 417 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.512A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 removed outlier: 3.514A pdb=" N TYR D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.661A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR D 550 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 559 through 576 removed outlier: 4.911A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 599 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 642 No H-bonds generated for 'chain 'D' and resid 640 through 642' Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 691 through 712 removed outlier: 3.862A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 4.247A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.559A pdb=" N LYS B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 4.136A pdb=" N LEU B 421 " --> pdb=" O PRO B 417 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 removed outlier: 3.523A pdb=" N TYR B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.754A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 559 through 576 removed outlier: 4.762A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 removed outlier: 3.516A pdb=" N PHE B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 691 through 712 removed outlier: 3.892A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.835A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.778A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.727A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.715A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3839 1.33 - 1.45: 3619 1.45 - 1.57: 8590 1.57 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 16204 Sorted by residual: bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C PHE D 649 " pdb=" N THR D 650 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.29e-02 6.01e+03 5.97e+00 ... (remaining 16199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 20937 1.87 - 3.74: 906 3.74 - 5.62: 111 5.62 - 7.49: 10 7.49 - 9.36: 20 Bond angle restraints: 21984 Sorted by residual: angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER C 711 " pdb=" N PHE C 712 " pdb=" CA PHE C 712 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C SER D 711 " pdb=" N PHE D 712 " pdb=" CA PHE D 712 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 110.53 115.72 -5.19 1.32e+00 5.74e-01 1.55e+01 ... (remaining 21979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 8658 17.44 - 34.89: 663 34.89 - 52.33: 119 52.33 - 69.77: 19 69.77 - 87.22: 9 Dihedral angle restraints: 9468 sinusoidal: 3796 harmonic: 5672 Sorted by residual: dihedral pdb=" CA PHE C 712 " pdb=" C PHE C 712 " pdb=" N LEU C 713 " pdb=" CA LEU C 713 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA PHE D 712 " pdb=" C PHE D 712 " pdb=" N LEU D 713 " pdb=" CA LEU D 713 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1947 0.057 - 0.115: 468 0.115 - 0.172: 53 0.172 - 0.230: 4 0.230 - 0.287: 4 Chirality restraints: 2476 Sorted by residual: chirality pdb=" CA ASN A 652 " pdb=" N ASN A 652 " pdb=" C ASN A 652 " pdb=" CB ASN A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN B 652 " pdb=" N ASN B 652 " pdb=" C ASN B 652 " pdb=" CB ASN B 652 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASN C 652 " pdb=" N ASN C 652 " pdb=" C ASN C 652 " pdb=" CB ASN C 652 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2473 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 548 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.48e+00 pdb=" C GLY D 548 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY D 548 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP D 549 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 548 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C GLY A 548 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY A 548 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP A 549 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 548 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C GLY B 548 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY B 548 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP B 549 " -0.015 2.00e-02 2.50e+03 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 142 2.57 - 3.15: 13758 3.15 - 3.74: 23618 3.74 - 4.32: 31807 4.32 - 4.90: 53600 Nonbonded interactions: 122925 Sorted by model distance: nonbonded pdb=" OH TYR D 495 " pdb=" OG SER D 510 " model vdw 1.989 3.040 nonbonded pdb=" OH TYR B 495 " pdb=" OG SER B 510 " model vdw 2.022 3.040 nonbonded pdb=" O LEU A 384 " pdb=" NH2 ARG A 721 " model vdw 2.130 3.120 nonbonded pdb=" OG SER A 379 " pdb=" OD1 ASP A 745 " model vdw 2.139 3.040 nonbonded pdb=" OH TYR A 495 " pdb=" OG SER A 510 " model vdw 2.140 3.040 ... (remaining 122920 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: 0.02 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.000 Find NCS groups from input model: 0.310 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.010 0.119 16208 Z= 0.441 Angle : 0.893 9.360 21992 Z= 0.483 Chirality : 0.050 0.287 2476 Planarity : 0.004 0.028 2692 Dihedral : 12.842 87.217 5808 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.87 % Allowed : 5.67 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.84 (0.18), residues: 1904 helix: 0.49 (0.14), residues: 1184 sheet: -4.24 (0.61), residues: 40 loop : -2.20 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 367 TYR 0.016 0.003 TYR C 511 PHE 0.034 0.003 PHE C 649 TRP 0.009 0.002 TRP B 697 HIS 0.005 0.002 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.44 (16204) covalent geometry : angle 0.89246 / 0.48 (21984) SS BOND : bond 0.00639 / 0.39 ( 4) SS BOND : angle 1.36180 / 0.75 ( 8) hydrogen bonds : bond 0.14358 / 9.79 ( 910) hydrogen bonds : angle 5.60232 / 4.00 ( 2655) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 620 time to evaluate : 0.539 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 267 LEU cc_start: 0.8350 (mt) cc_final: 0.7801 (tp) REVERT: A 305 VAL cc_start: 0.7629 (t) cc_final: 0.7113 (m) REVERT: A 311 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 345 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7836 (mmtm) REVERT: A 351 TYR cc_start: 0.7701 (t80) cc_final: 0.7386 (t80) REVERT: A 388 ASP cc_start: 0.7961 (p0) cc_final: 0.7739 (p0) REVERT: A 424 ASP cc_start: 0.8766 (t70) cc_final: 0.8467 (t0) REVERT: A 425 LYS cc_start: 0.8787 (mttm) cc_final: 0.8565 (mtpp) REVERT: A 428 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8387 (mtp180) REVERT: A 432 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7621 (mtt90) REVERT: A 439 PHE cc_start: 0.8502 (t80) cc_final: 0.8259 (t80) REVERT: A 496 PHE cc_start: 0.8338 (t80) cc_final: 0.7918 (m-80) REVERT: A 503 LEU cc_start: 0.8698 (mt) cc_final: 0.8494 (mm) REVERT: A 547 MET cc_start: 0.8756 (mtm) cc_final: 0.8411 (mtp) REVERT: A 551 ASN cc_start: 0.9109 (m-40) cc_final: 0.8630 (m110) REVERT: A 568 MET cc_start: 0.8510 (mmt) cc_final: 0.8194 (mmt) REVERT: A 650 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7666 (p) REVERT: A 669 LEU cc_start: 0.9332 (mt) cc_final: 0.9046 (mt) REVERT: A 677 MET cc_start: 0.8978 (mmm) cc_final: 0.8514 (tpp) REVERT: A 697 TRP cc_start: 0.9228 (t60) cc_final: 0.8918 (t60) REVERT: A 718 LYS cc_start: 0.8202 (mttt) cc_final: 0.7468 (pttt) REVERT: C 305 VAL cc_start: 0.7783 (t) cc_final: 0.7529 (m) REVERT: C 311 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 345 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8082 (mmtm) REVERT: C 378 HIS cc_start: 0.5994 (m90) cc_final: 0.5750 (m90) REVERT: C 424 ASP cc_start: 0.8670 (t70) cc_final: 0.8470 (t0) REVERT: C 425 LYS cc_start: 0.8814 (mttm) cc_final: 0.8540 (mtpp) REVERT: C 439 PHE cc_start: 0.8491 (t80) cc_final: 0.8262 (t80) REVERT: C 478 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8558 (mt-10) REVERT: C 496 PHE cc_start: 0.8315 (t80) cc_final: 0.8047 (m-80) REVERT: C 503 LEU cc_start: 0.8692 (mt) cc_final: 0.8487 (mm) REVERT: C 536 GLU cc_start: 0.7797 (pm20) cc_final: 0.7255 (pm20) REVERT: C 551 ASN cc_start: 0.9085 (m-40) cc_final: 0.8542 (m110) REVERT: C 572 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7795 (mtt) REVERT: C 644 MET cc_start: 0.8992 (mmm) cc_final: 0.8760 (mmp) REVERT: C 650 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7648 (p) REVERT: C 669 LEU cc_start: 0.9342 (mt) cc_final: 0.9033 (mt) REVERT: C 672 ILE cc_start: 0.9294 (mm) cc_final: 0.8955 (mt) REVERT: C 697 TRP cc_start: 0.9206 (t60) cc_final: 0.8928 (t60) REVERT: C 718 LYS cc_start: 0.8314 (mttt) cc_final: 0.7774 (pttt) REVERT: D 257 CYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5644 (m) REVERT: D 311 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8326 (mm-30) REVERT: D 318 LYS cc_start: 0.8217 (mttm) cc_final: 0.7903 (mmmt) REVERT: D 345 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8172 (mmtm) REVERT: D 423 GLN cc_start: 0.8956 (tp40) cc_final: 0.8674 (tp40) REVERT: D 424 ASP cc_start: 0.8789 (m-30) cc_final: 0.8437 (t70) REVERT: D 439 PHE cc_start: 0.8468 (t80) cc_final: 0.8264 (t80) REVERT: D 478 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8553 (mt-10) REVERT: D 496 PHE cc_start: 0.8210 (t80) cc_final: 0.7932 (m-80) REVERT: D 503 LEU cc_start: 0.8700 (mt) cc_final: 0.8476 (mm) REVERT: D 547 MET cc_start: 0.8729 (mtm) cc_final: 0.8416 (mtp) REVERT: D 551 ASN cc_start: 0.9138 (m-40) cc_final: 0.8606 (m110) REVERT: D 561 GLN cc_start: 0.6863 (pm20) cc_final: 0.6640 (mp10) REVERT: D 628 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6630 (t0) REVERT: D 650 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7541 (p) REVERT: D 707 ASP cc_start: 0.8583 (t70) cc_final: 0.8182 (t70) REVERT: D 718 LYS cc_start: 0.8376 (mttt) cc_final: 0.7918 (pttt) REVERT: B 309 TYR cc_start: 0.9052 (t80) cc_final: 0.8670 (t80) REVERT: B 345 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8140 (mmtm) REVERT: B 423 GLN cc_start: 0.8990 (tp40) cc_final: 0.8712 (mm-40) REVERT: B 424 ASP cc_start: 0.8750 (m-30) cc_final: 0.8307 (t0) REVERT: B 439 PHE cc_start: 0.8450 (t80) cc_final: 0.8245 (t80) REVERT: B 536 GLU cc_start: 0.7668 (pm20) cc_final: 0.7174 (pm20) REVERT: B 547 MET cc_start: 0.8758 (mtm) cc_final: 0.8433 (mtp) REVERT: B 551 ASN cc_start: 0.9097 (m-40) cc_final: 0.8512 (m110) REVERT: B 572 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7428 (mtt) REVERT: B 581 MET cc_start: 0.7784 (mmm) cc_final: 0.7378 (ptt) REVERT: B 669 LEU cc_start: 0.9301 (mt) cc_final: 0.8987 (mt) REVERT: B 677 MET cc_start: 0.8994 (mmm) cc_final: 0.8555 (mmm) outliers start: 32 outliers final: 10 residues processed: 634 average time/residue: 0.1446 time to fit residues: 130.8783 Evaluate side-chains 463 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 446 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.199443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124328 restraints weight = 22495.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.128699 restraints weight = 11496.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131223 restraints weight = 8169.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132490 restraints weight = 6871.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133322 restraints weight = 6303.240| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16208 Z= 0.165 Angle : 0.643 8.806 21992 Z= 0.336 Chirality : 0.041 0.172 2476 Planarity : 0.003 0.039 2692 Dihedral : 5.613 59.958 2169 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.28 % Allowed : 13.20 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1904 helix: 1.42 (0.15), residues: 1208 sheet: -2.88 (0.66), residues: 60 loop : -2.32 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 579 TYR 0.015 0.002 TYR D 565 PHE 0.022 0.001 PHE D 742 TRP 0.015 0.001 TRP B 697 HIS 0.002 0.000 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (16204) covalent geometry : angle 0.64290 / 0.34 (21984) SS BOND : bond 0.00295 / 0.17 ( 4) SS BOND : angle 0.62176 / 0.36 ( 8) hydrogen bonds : bond 0.04405 / 2.93 ( 910) hydrogen bonds : angle 4.19880 / 3.01 ( 2655) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 526 time to evaluate : 0.614 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: A 309 TYR cc_start: 0.9090 (t80) cc_final: 0.8741 (t80) REVERT: A 311 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8017 (mm-30) REVERT: A 404 SER cc_start: 0.8199 (m) cc_final: 0.7497 (t) REVERT: A 420 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8500 (mmm-85) REVERT: A 424 ASP cc_start: 0.8677 (t70) cc_final: 0.8472 (t0) REVERT: A 428 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8368 (mtp180) REVERT: A 439 PHE cc_start: 0.8395 (t80) cc_final: 0.8189 (t80) REVERT: A 496 PHE cc_start: 0.8224 (t80) cc_final: 0.7941 (m-80) REVERT: A 536 GLU cc_start: 0.7949 (mp0) cc_final: 0.7681 (mp0) REVERT: A 544 SER cc_start: 0.9457 (t) cc_final: 0.9099 (p) REVERT: A 568 MET cc_start: 0.8538 (mmt) cc_final: 0.8236 (mmt) REVERT: A 572 MET cc_start: 0.7770 (mtt) cc_final: 0.7297 (mtt) REVERT: A 589 PHE cc_start: 0.8423 (t80) cc_final: 0.8202 (t80) REVERT: A 650 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7873 (p) REVERT: A 689 ILE cc_start: 0.8884 (pt) cc_final: 0.8027 (mm) REVERT: C 311 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8220 (mm-30) REVERT: C 414 LEU cc_start: 0.8671 (mt) cc_final: 0.8450 (mm) REVERT: C 420 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8467 (mmm-85) REVERT: C 432 ARG cc_start: 0.7319 (mtp85) cc_final: 0.6666 (ptp90) REVERT: C 441 TYR cc_start: 0.8897 (t80) cc_final: 0.8502 (t80) REVERT: C 473 PHE cc_start: 0.8675 (m-80) cc_final: 0.8365 (m-10) REVERT: C 496 PHE cc_start: 0.8233 (t80) cc_final: 0.7990 (m-80) REVERT: C 504 LYS cc_start: 0.7966 (mttp) cc_final: 0.7159 (ptpp) REVERT: C 532 SER cc_start: 0.9308 (m) cc_final: 0.9088 (t) REVERT: C 540 SER cc_start: 0.9286 (OUTLIER) cc_final: 0.9051 (t) REVERT: C 541 MET cc_start: 0.8570 (ttm) cc_final: 0.8357 (ttm) REVERT: C 544 SER cc_start: 0.9469 (t) cc_final: 0.9095 (p) REVERT: C 568 MET cc_start: 0.7813 (mtm) cc_final: 0.7601 (mtm) REVERT: C 589 PHE cc_start: 0.8498 (t80) cc_final: 0.8280 (t80) REVERT: C 650 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7929 (p) REVERT: C 689 ILE cc_start: 0.8781 (pt) cc_final: 0.8376 (mm) REVERT: C 692 GLU cc_start: 0.7713 (mp0) cc_final: 0.7306 (mp0) REVERT: C 743 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8043 (mtp85) REVERT: D 311 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8240 (mm-30) REVERT: D 318 LYS cc_start: 0.8111 (mttm) cc_final: 0.7806 (mmmt) REVERT: D 372 TRP cc_start: 0.4687 (m100) cc_final: 0.4215 (m100) REVERT: D 424 ASP cc_start: 0.8622 (m-30) cc_final: 0.8344 (t0) REVERT: D 428 ARG cc_start: 0.8759 (ttm170) cc_final: 0.8210 (mtp180) REVERT: D 439 PHE cc_start: 0.8381 (t80) cc_final: 0.8176 (t80) REVERT: D 496 PHE cc_start: 0.8150 (t80) cc_final: 0.7892 (m-80) REVERT: D 503 LEU cc_start: 0.8613 (mt) cc_final: 0.8407 (mm) REVERT: D 536 GLU cc_start: 0.7954 (mp0) cc_final: 0.7674 (mp0) REVERT: D 544 SER cc_start: 0.9421 (t) cc_final: 0.9042 (p) REVERT: D 581 MET cc_start: 0.6908 (ptt) cc_final: 0.6647 (ttp) REVERT: D 584 TYR cc_start: 0.9072 (t80) cc_final: 0.8807 (t80) REVERT: D 589 PHE cc_start: 0.8528 (t80) cc_final: 0.8267 (t80) REVERT: D 650 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7860 (p) REVERT: D 689 ILE cc_start: 0.8778 (pt) cc_final: 0.8546 (mm) REVERT: D 692 GLU cc_start: 0.7923 (mp0) cc_final: 0.7697 (mp0) REVERT: B 404 SER cc_start: 0.8165 (m) cc_final: 0.7528 (t) REVERT: B 424 ASP cc_start: 0.8571 (m-30) cc_final: 0.8302 (t0) REVERT: B 432 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7546 (ptp-110) REVERT: B 581 MET cc_start: 0.7492 (mmm) cc_final: 0.7256 (ttp) REVERT: B 589 PHE cc_start: 0.8494 (t80) cc_final: 0.8237 (t80) REVERT: B 650 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7808 (p) outliers start: 39 outliers final: 14 residues processed: 543 average time/residue: 0.1298 time to fit residues: 103.8138 Evaluate side-chains 471 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 452 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 14 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 ASN D 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.195462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122057 restraints weight = 22710.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126236 restraints weight = 11352.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128677 restraints weight = 7932.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130057 restraints weight = 6603.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130716 restraints weight = 6004.616| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16208 Z= 0.156 Angle : 0.611 11.855 21992 Z= 0.314 Chirality : 0.041 0.175 2476 Planarity : 0.003 0.058 2692 Dihedral : 5.213 59.166 2148 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.28 % Allowed : 15.71 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.63 (0.20), residues: 1904 helix: 1.95 (0.15), residues: 1148 sheet: -2.92 (0.63), residues: 60 loop : -2.00 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 409 TYR 0.012 0.001 TYR C 309 PHE 0.024 0.001 PHE C 742 TRP 0.011 0.001 TRP A 697 HIS 0.003 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (16204) covalent geometry : angle 0.61109 / 0.31 (21984) SS BOND : bond 0.00311 / 0.19 ( 4) SS BOND : angle 0.57025 / 0.32 ( 8) hydrogen bonds : bond 0.03935 / 2.62 ( 910) hydrogen bonds : angle 4.09373 / 2.92 ( 2655) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 490 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9115 (t80) cc_final: 0.8857 (t80) REVERT: A 311 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7995 (mm-30) REVERT: A 392 LYS cc_start: 0.7154 (mttt) cc_final: 0.6331 (ptmm) REVERT: A 432 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7421 (mtt90) REVERT: A 487 TYR cc_start: 0.9009 (t80) cc_final: 0.8706 (t80) REVERT: A 496 PHE cc_start: 0.8182 (t80) cc_final: 0.7949 (m-80) REVERT: A 503 LEU cc_start: 0.8696 (mm) cc_final: 0.8488 (pp) REVERT: A 544 SER cc_start: 0.9450 (t) cc_final: 0.9101 (p) REVERT: A 581 MET cc_start: 0.7149 (ptt) cc_final: 0.6754 (ttp) REVERT: A 589 PHE cc_start: 0.8464 (t80) cc_final: 0.8262 (t80) REVERT: A 650 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 672 ILE cc_start: 0.9378 (mm) cc_final: 0.9015 (mt) REVERT: A 709 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 311 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8103 (mm-30) REVERT: C 414 LEU cc_start: 0.8579 (mt) cc_final: 0.8355 (mm) REVERT: C 432 ARG cc_start: 0.7334 (mtp85) cc_final: 0.6664 (ptp90) REVERT: C 473 PHE cc_start: 0.8593 (m-80) cc_final: 0.8362 (m-10) REVERT: C 496 PHE cc_start: 0.8189 (t80) cc_final: 0.7983 (m-80) REVERT: C 533 GLN cc_start: 0.8463 (tt0) cc_final: 0.7656 (tm-30) REVERT: C 535 LYS cc_start: 0.8766 (tppp) cc_final: 0.8362 (tppt) REVERT: C 540 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.9047 (t) REVERT: C 541 MET cc_start: 0.8562 (ttm) cc_final: 0.8358 (ttm) REVERT: C 544 SER cc_start: 0.9493 (t) cc_final: 0.9119 (p) REVERT: C 572 MET cc_start: 0.8089 (mmt) cc_final: 0.7607 (mmm) REVERT: C 709 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8071 (tm-30) REVERT: C 743 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8160 (mtp85) REVERT: D 311 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8346 (mm-30) REVERT: D 318 LYS cc_start: 0.8207 (mttm) cc_final: 0.7850 (mmmt) REVERT: D 372 TRP cc_start: 0.4434 (m100) cc_final: 0.4205 (m100) REVERT: D 397 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8023 (pt0) REVERT: D 424 ASP cc_start: 0.8635 (m-30) cc_final: 0.8306 (t0) REVERT: D 428 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8179 (mtp180) REVERT: D 473 PHE cc_start: 0.8571 (m-80) cc_final: 0.8319 (m-10) REVERT: D 496 PHE cc_start: 0.8130 (t80) cc_final: 0.7881 (m-80) REVERT: D 533 GLN cc_start: 0.8471 (tt0) cc_final: 0.7678 (tm-30) REVERT: D 536 GLU cc_start: 0.8045 (mp0) cc_final: 0.7589 (mp0) REVERT: D 544 SER cc_start: 0.9480 (t) cc_final: 0.9107 (p) REVERT: D 568 MET cc_start: 0.7901 (mtm) cc_final: 0.7694 (mtm) REVERT: D 581 MET cc_start: 0.6787 (ptt) cc_final: 0.6501 (ttp) REVERT: D 584 TYR cc_start: 0.9084 (t80) cc_final: 0.8791 (t80) REVERT: D 589 PHE cc_start: 0.8540 (t80) cc_final: 0.8323 (t80) REVERT: D 650 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7953 (p) REVERT: B 300 ASP cc_start: 0.7698 (m-30) cc_final: 0.7161 (p0) REVERT: B 420 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.8628 (tpp80) REVERT: B 424 ASP cc_start: 0.8624 (m-30) cc_final: 0.8298 (t0) REVERT: B 432 ARG cc_start: 0.7820 (ttm110) cc_final: 0.7404 (ptp-110) REVERT: B 445 MET cc_start: 0.9113 (mmp) cc_final: 0.8690 (mpp) REVERT: B 487 TYR cc_start: 0.9062 (t80) cc_final: 0.8570 (t80) REVERT: B 533 GLN cc_start: 0.8395 (tt0) cc_final: 0.7644 (tm-30) REVERT: B 547 MET cc_start: 0.8733 (mtp) cc_final: 0.8441 (tpp) REVERT: B 581 MET cc_start: 0.7480 (mmm) cc_final: 0.7233 (ttp) REVERT: B 650 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7942 (p) REVERT: B 672 ILE cc_start: 0.9365 (mm) cc_final: 0.9021 (mt) REVERT: B 674 LEU cc_start: 0.9342 (tp) cc_final: 0.9044 (tp) REVERT: B 707 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8639 (t70) outliers start: 39 outliers final: 14 residues processed: 508 average time/residue: 0.1281 time to fit residues: 96.4874 Evaluate side-chains 462 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 443 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 707 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 180 optimal weight: 0.0670 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 354 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.198825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125264 restraints weight = 22486.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129565 restraints weight = 11087.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132149 restraints weight = 7683.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133444 restraints weight = 6356.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134337 restraints weight = 5790.518| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16208 Z= 0.112 Angle : 0.568 11.378 21992 Z= 0.293 Chirality : 0.039 0.180 2476 Planarity : 0.003 0.049 2692 Dihedral : 4.964 59.220 2147 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.51 % Allowed : 17.35 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.20), residues: 1904 helix: 1.98 (0.15), residues: 1176 sheet: -2.78 (0.65), residues: 60 loop : -2.08 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.016 0.001 TYR D 565 PHE 0.024 0.001 PHE A 742 TRP 0.011 0.001 TRP D 697 HIS 0.002 0.000 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (16204) covalent geometry : angle 0.56822 / 0.29 (21984) SS BOND : bond 0.00290 / 0.16 ( 4) SS BOND : angle 0.53245 / 0.31 ( 8) hydrogen bonds : bond 0.03421 / 2.28 ( 910) hydrogen bonds : angle 3.93940 / 2.80 ( 2655) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 480 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9093 (t80) cc_final: 0.8832 (t80) REVERT: A 311 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 432 ARG cc_start: 0.7693 (mtt90) cc_final: 0.7326 (mtt90) REVERT: A 487 TYR cc_start: 0.8898 (t80) cc_final: 0.8688 (t80) REVERT: A 544 SER cc_start: 0.9438 (t) cc_final: 0.9099 (p) REVERT: A 568 MET cc_start: 0.8615 (mmt) cc_final: 0.8376 (mmt) REVERT: A 571 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8420 (tmtt) REVERT: A 576 ASP cc_start: 0.7629 (m-30) cc_final: 0.7297 (m-30) REVERT: A 709 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 311 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8099 (mm-30) REVERT: C 420 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8534 (mmm-85) REVERT: C 491 ARG cc_start: 0.8917 (mmm160) cc_final: 0.8166 (tpp80) REVERT: C 496 PHE cc_start: 0.8090 (t80) cc_final: 0.7871 (m-80) REVERT: C 533 GLN cc_start: 0.8389 (tt0) cc_final: 0.7533 (tm-30) REVERT: C 535 LYS cc_start: 0.8763 (tppp) cc_final: 0.8340 (tppt) REVERT: C 540 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8984 (t) REVERT: C 544 SER cc_start: 0.9423 (t) cc_final: 0.9105 (p) REVERT: C 674 LEU cc_start: 0.9125 (tp) cc_final: 0.8732 (mp) REVERT: C 743 ARG cc_start: 0.8435 (ttm110) cc_final: 0.8080 (mtp85) REVERT: D 311 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8347 (mm-30) REVERT: D 318 LYS cc_start: 0.8216 (mttm) cc_final: 0.7831 (mmmt) REVERT: D 420 ARG cc_start: 0.8999 (tpp80) cc_final: 0.8768 (tpp80) REVERT: D 478 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8594 (mt-10) REVERT: D 487 TYR cc_start: 0.9001 (t80) cc_final: 0.8705 (t80) REVERT: D 533 GLN cc_start: 0.8470 (tt0) cc_final: 0.7714 (tm-30) REVERT: D 536 GLU cc_start: 0.8043 (mp0) cc_final: 0.7599 (mp0) REVERT: D 544 SER cc_start: 0.9424 (t) cc_final: 0.9074 (p) REVERT: D 581 MET cc_start: 0.6866 (ptt) cc_final: 0.6584 (ttp) REVERT: D 584 TYR cc_start: 0.9050 (t80) cc_final: 0.8711 (t80) REVERT: D 697 TRP cc_start: 0.9079 (t60) cc_final: 0.8694 (t60) REVERT: B 300 ASP cc_start: 0.7680 (m-30) cc_final: 0.7187 (p0) REVERT: B 308 MET cc_start: 0.9079 (mpp) cc_final: 0.8863 (mpp) REVERT: B 424 ASP cc_start: 0.8615 (m-30) cc_final: 0.8299 (t0) REVERT: B 432 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7353 (ptp-110) REVERT: B 487 TYR cc_start: 0.8973 (t80) cc_final: 0.8319 (t80) REVERT: B 533 GLN cc_start: 0.8385 (tt0) cc_final: 0.7578 (tm-30) REVERT: B 547 MET cc_start: 0.8718 (mtp) cc_final: 0.8455 (tpp) REVERT: B 571 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8602 (tmtt) REVERT: B 581 MET cc_start: 0.7524 (mmm) cc_final: 0.7248 (ttp) REVERT: B 672 ILE cc_start: 0.9334 (mm) cc_final: 0.8947 (mt) REVERT: B 674 LEU cc_start: 0.9221 (tp) cc_final: 0.9007 (tp) REVERT: B 707 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8592 (t70) outliers start: 43 outliers final: 20 residues processed: 500 average time/residue: 0.1269 time to fit residues: 94.3021 Evaluate side-chains 452 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 429 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 707 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 17 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN D 354 GLN D 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.203993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131056 restraints weight = 23164.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135391 restraints weight = 11622.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137919 restraints weight = 8168.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139368 restraints weight = 6801.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140054 restraints weight = 6175.080| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16208 Z= 0.111 Angle : 0.581 11.366 21992 Z= 0.295 Chirality : 0.040 0.209 2476 Planarity : 0.003 0.046 2692 Dihedral : 4.833 59.471 2144 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.04 % Allowed : 18.52 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.87 (0.20), residues: 1904 helix: 2.17 (0.15), residues: 1148 sheet: -2.52 (0.65), residues: 60 loop : -2.01 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 579 TYR 0.014 0.001 TYR C 495 PHE 0.019 0.001 PHE A 742 TRP 0.017 0.001 TRP A 697 HIS 0.003 0.000 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16204) covalent geometry : angle 0.58086 / 0.29 (21984) SS BOND : bond 0.00198 / 0.11 ( 4) SS BOND : angle 0.40402 / 0.22 ( 8) hydrogen bonds : bond 0.03333 / 2.21 ( 910) hydrogen bonds : angle 3.91629 / 2.78 ( 2655) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 464 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9085 (t80) cc_final: 0.8863 (t80) REVERT: A 311 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 363 ARG cc_start: 0.5752 (ttt180) cc_final: 0.5463 (tpt-90) REVERT: A 432 ARG cc_start: 0.7673 (mtt90) cc_final: 0.7238 (mtt90) REVERT: A 491 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7845 (tpp80) REVERT: A 533 GLN cc_start: 0.8204 (tt0) cc_final: 0.7569 (tm-30) REVERT: A 544 SER cc_start: 0.9399 (t) cc_final: 0.9115 (p) REVERT: A 568 MET cc_start: 0.8610 (mmt) cc_final: 0.8327 (mmt) REVERT: A 571 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8511 (tmtt) REVERT: A 576 ASP cc_start: 0.7655 (m-30) cc_final: 0.7355 (m-30) REVERT: A 709 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 300 ASP cc_start: 0.7667 (m-30) cc_final: 0.7182 (p0) REVERT: C 311 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8293 (mm-30) REVERT: C 420 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8555 (mmm-85) REVERT: C 436 PHE cc_start: 0.9120 (t80) cc_final: 0.8841 (t80) REVERT: C 491 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8257 (tpp80) REVERT: C 533 GLN cc_start: 0.8217 (tt0) cc_final: 0.7491 (tm-30) REVERT: C 535 LYS cc_start: 0.8660 (tppp) cc_final: 0.8336 (tppt) REVERT: C 540 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.9000 (t) REVERT: C 544 SER cc_start: 0.9372 (t) cc_final: 0.9126 (p) REVERT: C 674 LEU cc_start: 0.9148 (tp) cc_final: 0.8766 (mp) REVERT: C 743 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7864 (mtp85) REVERT: D 311 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8371 (mm-30) REVERT: D 318 LYS cc_start: 0.8209 (mttm) cc_final: 0.7818 (mmmt) REVERT: D 533 GLN cc_start: 0.8200 (tt0) cc_final: 0.7551 (tm-30) REVERT: D 536 GLU cc_start: 0.7996 (mp0) cc_final: 0.7537 (mt-10) REVERT: D 544 SER cc_start: 0.9376 (t) cc_final: 0.9113 (p) REVERT: D 581 MET cc_start: 0.6825 (ptt) cc_final: 0.6555 (ttp) REVERT: D 584 TYR cc_start: 0.9031 (t80) cc_final: 0.8727 (t80) REVERT: D 689 ILE cc_start: 0.8935 (pt) cc_final: 0.8619 (mm) REVERT: B 300 ASP cc_start: 0.7743 (m-30) cc_final: 0.7301 (p0) REVERT: B 424 ASP cc_start: 0.8541 (m-30) cc_final: 0.8281 (t0) REVERT: B 432 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7457 (ptp-110) REVERT: B 487 TYR cc_start: 0.8995 (t80) cc_final: 0.8244 (t80) REVERT: B 533 GLN cc_start: 0.8223 (tt0) cc_final: 0.7479 (tm-30) REVERT: B 571 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8645 (tmtt) REVERT: B 672 ILE cc_start: 0.9352 (mm) cc_final: 0.8954 (mt) REVERT: B 674 LEU cc_start: 0.9273 (tp) cc_final: 0.9020 (tp) REVERT: B 707 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8534 (t70) outliers start: 35 outliers final: 22 residues processed: 480 average time/residue: 0.1255 time to fit residues: 89.7016 Evaluate side-chains 470 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 446 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 707 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 64 optimal weight: 0.0010 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 152 optimal weight: 0.4980 chunk 182 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 HIS C 560 GLN C 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.205003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132751 restraints weight = 23183.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136984 restraints weight = 11882.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139494 restraints weight = 8413.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140751 restraints weight = 7026.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141615 restraints weight = 6417.598| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16208 Z= 0.108 Angle : 0.592 11.949 21992 Z= 0.298 Chirality : 0.040 0.196 2476 Planarity : 0.003 0.047 2692 Dihedral : 4.775 59.558 2144 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.10 % Allowed : 19.63 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.20), residues: 1904 helix: 2.08 (0.15), residues: 1152 sheet: -2.27 (0.67), residues: 60 loop : -1.98 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 557 TYR 0.016 0.001 TYR A 487 PHE 0.024 0.001 PHE D 742 TRP 0.015 0.001 TRP C 697 HIS 0.006 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (16204) covalent geometry : angle 0.59179 / 0.30 (21984) SS BOND : bond 0.00172 / 0.09 ( 4) SS BOND : angle 0.43794 / 0.25 ( 8) hydrogen bonds : bond 0.03272 / 2.17 ( 910) hydrogen bonds : angle 3.95758 / 2.81 ( 2655) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 470 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9091 (t80) cc_final: 0.8881 (t80) REVERT: A 311 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 363 ARG cc_start: 0.5771 (ttt180) cc_final: 0.5497 (tpt-90) REVERT: A 432 ARG cc_start: 0.7450 (mtt90) cc_final: 0.6746 (ttm110) REVERT: A 491 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7832 (tpp80) REVERT: A 533 GLN cc_start: 0.8150 (tt0) cc_final: 0.7538 (tm-30) REVERT: A 544 SER cc_start: 0.9387 (t) cc_final: 0.9116 (p) REVERT: A 568 MET cc_start: 0.8590 (mmt) cc_final: 0.8270 (mmt) REVERT: A 571 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8478 (tmtt) REVERT: A 709 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7977 (tm-30) REVERT: C 300 ASP cc_start: 0.7774 (m-30) cc_final: 0.7290 (p0) REVERT: C 436 PHE cc_start: 0.9108 (t80) cc_final: 0.8851 (t80) REVERT: C 491 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8254 (tpp80) REVERT: C 535 LYS cc_start: 0.8670 (tppp) cc_final: 0.8413 (tppt) REVERT: C 536 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: C 540 SER cc_start: 0.9241 (OUTLIER) cc_final: 0.8949 (t) REVERT: C 544 SER cc_start: 0.9360 (t) cc_final: 0.9135 (p) REVERT: C 674 LEU cc_start: 0.9144 (tp) cc_final: 0.8761 (mp) REVERT: C 697 TRP cc_start: 0.9130 (t60) cc_final: 0.8706 (t60) REVERT: C 743 ARG cc_start: 0.8263 (ttm110) cc_final: 0.7830 (tpp80) REVERT: D 318 LYS cc_start: 0.8288 (mttm) cc_final: 0.7852 (mmmt) REVERT: D 533 GLN cc_start: 0.8174 (tt0) cc_final: 0.7544 (tm-30) REVERT: D 536 GLU cc_start: 0.7988 (mp0) cc_final: 0.7501 (mt-10) REVERT: D 544 SER cc_start: 0.9403 (t) cc_final: 0.9125 (p) REVERT: D 581 MET cc_start: 0.6761 (ptt) cc_final: 0.6482 (ttp) REVERT: D 584 TYR cc_start: 0.8998 (t80) cc_final: 0.8723 (t80) REVERT: D 598 LEU cc_start: 0.9326 (tt) cc_final: 0.9126 (tt) REVERT: D 689 ILE cc_start: 0.8984 (pt) cc_final: 0.8765 (mm) REVERT: B 300 ASP cc_start: 0.7738 (m-30) cc_final: 0.7313 (p0) REVERT: B 424 ASP cc_start: 0.8520 (m-30) cc_final: 0.8261 (t0) REVERT: B 432 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7419 (ptp-110) REVERT: B 487 TYR cc_start: 0.8962 (t80) cc_final: 0.7612 (t80) REVERT: B 533 GLN cc_start: 0.8210 (tt0) cc_final: 0.7484 (tm-30) REVERT: B 536 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: B 571 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8551 (tmtt) REVERT: B 672 ILE cc_start: 0.9390 (mm) cc_final: 0.8984 (mt) REVERT: B 674 LEU cc_start: 0.9212 (tp) cc_final: 0.9002 (tp) REVERT: B 707 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8537 (t70) outliers start: 36 outliers final: 21 residues processed: 490 average time/residue: 0.1210 time to fit residues: 88.5851 Evaluate side-chains 456 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 431 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 707 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 157 optimal weight: 0.0170 chunk 183 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 700 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 = 0.4338 r_free = 0.4338 target = 0.204565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131700 restraints weight = 23007.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135879 restraints weight = 11904.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138356 restraints weight = 8478.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139589 restraints weight = 7125.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140321 restraints weight = 6522.179| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16208 Z= 0.117 Angle : 0.625 12.518 21992 Z= 0.314 Chirality : 0.041 0.207 2476 Planarity : 0.003 0.048 2692 Dihedral : 4.755 59.792 2144 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.22 % Allowed : 20.62 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.76 (0.20), residues: 1904 helix: 2.01 (0.15), residues: 1152 sheet: -2.06 (0.69), residues: 60 loop : -1.98 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 557 TYR 0.023 0.001 TYR C 444 PHE 0.020 0.001 PHE A 742 TRP 0.009 0.001 TRP C 697 HIS 0.002 0.000 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (16204) covalent geometry : angle 0.62538 / 0.31 (21984) SS BOND : bond 0.00166 / 0.09 ( 4) SS BOND : angle 0.49546 / 0.29 ( 8) hydrogen bonds : bond 0.03377 / 2.24 ( 910) hydrogen bonds : angle 4.05387 / 2.86 ( 2655) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 452 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 363 ARG cc_start: 0.5772 (ttt180) cc_final: 0.5505 (tpt-90) REVERT: A 432 ARG cc_start: 0.7473 (mtt90) cc_final: 0.6974 (ptt180) REVERT: A 533 GLN cc_start: 0.8175 (tt0) cc_final: 0.7562 (tm-30) REVERT: A 544 SER cc_start: 0.9400 (t) cc_final: 0.9137 (p) REVERT: A 568 MET cc_start: 0.8548 (mmt) cc_final: 0.8209 (mmt) REVERT: A 571 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8493 (tmtt) REVERT: A 584 TYR cc_start: 0.9080 (t80) cc_final: 0.8865 (t80) REVERT: A 674 LEU cc_start: 0.9137 (tp) cc_final: 0.8765 (mp) REVERT: A 709 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7960 (tm-30) REVERT: C 300 ASP cc_start: 0.7762 (m-30) cc_final: 0.7284 (p0) REVERT: C 308 MET cc_start: 0.8259 (mpp) cc_final: 0.7882 (mtt) REVERT: C 491 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8323 (tpp80) REVERT: C 533 GLN cc_start: 0.8258 (tt0) cc_final: 0.7414 (tm-30) REVERT: C 535 LYS cc_start: 0.8707 (tppp) cc_final: 0.8429 (tppt) REVERT: C 540 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.8992 (t) REVERT: C 544 SER cc_start: 0.9382 (t) cc_final: 0.9141 (p) REVERT: C 674 LEU cc_start: 0.9188 (tp) cc_final: 0.8813 (mp) REVERT: C 697 TRP cc_start: 0.9144 (t60) cc_final: 0.8725 (t60) REVERT: C 743 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7724 (tpp80) REVERT: D 300 ASP cc_start: 0.7572 (m-30) cc_final: 0.7098 (p0) REVERT: D 311 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8067 (mm-30) REVERT: D 318 LYS cc_start: 0.8338 (mttm) cc_final: 0.7850 (mmmt) REVERT: D 491 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7621 (tpp80) REVERT: D 533 GLN cc_start: 0.8190 (tt0) cc_final: 0.7548 (tm-30) REVERT: D 536 GLU cc_start: 0.7948 (mp0) cc_final: 0.7447 (mt-10) REVERT: D 544 SER cc_start: 0.9406 (t) cc_final: 0.9140 (p) REVERT: D 581 MET cc_start: 0.6765 (ptt) cc_final: 0.6512 (ttp) REVERT: D 584 TYR cc_start: 0.8966 (t80) cc_final: 0.8726 (t80) REVERT: D 689 ILE cc_start: 0.8973 (pt) cc_final: 0.8714 (mm) REVERT: B 300 ASP cc_start: 0.7735 (m-30) cc_final: 0.7321 (p0) REVERT: B 424 ASP cc_start: 0.8521 (m-30) cc_final: 0.8255 (t0) REVERT: B 432 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7526 (ptp-110) REVERT: B 487 TYR cc_start: 0.8986 (t80) cc_final: 0.7502 (t80) REVERT: B 533 GLN cc_start: 0.8227 (tt0) cc_final: 0.7482 (tm-30) REVERT: B 672 ILE cc_start: 0.9416 (mm) cc_final: 0.9017 (mt) REVERT: B 707 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8584 (t70) outliers start: 38 outliers final: 28 residues processed: 469 average time/residue: 0.1148 time to fit residues: 80.5184 Evaluate side-chains 465 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 434 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 707 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 118 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 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 = 0.4323 r_free = 0.4323 target = 0.203026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129631 restraints weight = 23138.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133747 restraints weight = 12043.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136185 restraints weight = 8607.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137342 restraints weight = 7241.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138185 restraints weight = 6653.996| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.143 Angle : 0.658 11.708 21992 Z= 0.332 Chirality : 0.042 0.211 2476 Planarity : 0.003 0.048 2692 Dihedral : 4.766 59.122 2144 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.51 % Allowed : 20.68 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.65 (0.20), residues: 1904 helix: 1.91 (0.15), residues: 1152 sheet: -2.07 (0.69), residues: 60 loop : -2.01 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 420 TYR 0.020 0.001 TYR C 444 PHE 0.026 0.001 PHE D 742 TRP 0.007 0.001 TRP B 549 HIS 0.002 0.000 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16204) covalent geometry : angle 0.65804 / 0.33 (21984) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 0.50905 / 0.28 ( 8) hydrogen bonds : bond 0.03593 / 2.38 ( 910) hydrogen bonds : angle 4.19750 / 2.97 ( 2655) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 452 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 363 ARG cc_start: 0.5848 (ttt180) cc_final: 0.5574 (tpt-90) REVERT: A 432 ARG cc_start: 0.7520 (mtt90) cc_final: 0.6756 (ttm110) REVERT: A 533 GLN cc_start: 0.8248 (tt0) cc_final: 0.7621 (tm-30) REVERT: A 544 SER cc_start: 0.9397 (t) cc_final: 0.9111 (p) REVERT: A 568 MET cc_start: 0.8527 (mmt) cc_final: 0.8240 (mmt) REVERT: A 571 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8516 (tmtt) REVERT: A 581 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6707 (ttp) REVERT: A 674 LEU cc_start: 0.9219 (tp) cc_final: 0.8866 (mp) REVERT: A 709 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 300 ASP cc_start: 0.7785 (m-30) cc_final: 0.7321 (p0) REVERT: C 491 ARG cc_start: 0.8737 (mmm160) cc_final: 0.8341 (tpp80) REVERT: C 498 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 533 GLN cc_start: 0.8211 (tt0) cc_final: 0.7461 (tm-30) REVERT: C 535 LYS cc_start: 0.8760 (tppp) cc_final: 0.8498 (tppt) REVERT: C 540 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.9080 (t) REVERT: C 544 SER cc_start: 0.9377 (t) cc_final: 0.9143 (p) REVERT: C 674 LEU cc_start: 0.9277 (tp) cc_final: 0.8905 (mp) REVERT: C 743 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7831 (mtp85) REVERT: D 300 ASP cc_start: 0.7697 (m-30) cc_final: 0.7229 (p0) REVERT: D 311 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8156 (mm-30) REVERT: D 318 LYS cc_start: 0.8321 (mttm) cc_final: 0.7829 (mmmt) REVERT: D 420 ARG cc_start: 0.8963 (mmm160) cc_final: 0.8496 (tpp80) REVERT: D 491 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6586 (ttp80) REVERT: D 536 GLU cc_start: 0.7958 (mp0) cc_final: 0.7443 (mt-10) REVERT: D 544 SER cc_start: 0.9432 (t) cc_final: 0.9153 (p) REVERT: D 581 MET cc_start: 0.6881 (ptt) cc_final: 0.6627 (ttp) REVERT: D 669 LEU cc_start: 0.9530 (mt) cc_final: 0.9282 (mt) REVERT: D 674 LEU cc_start: 0.9254 (tp) cc_final: 0.8855 (mp) REVERT: D 688 LYS cc_start: 0.9137 (tmmt) cc_final: 0.8812 (tmmt) REVERT: D 689 ILE cc_start: 0.8884 (pt) cc_final: 0.8555 (mm) REVERT: B 300 ASP cc_start: 0.7733 (m-30) cc_final: 0.7296 (p0) REVERT: B 424 ASP cc_start: 0.8552 (m-30) cc_final: 0.8274 (t0) REVERT: B 473 PHE cc_start: 0.8370 (m-10) cc_final: 0.8163 (m-10) REVERT: B 487 TYR cc_start: 0.9065 (t80) cc_final: 0.7474 (t80) REVERT: B 533 GLN cc_start: 0.8229 (tt0) cc_final: 0.7501 (tm-30) REVERT: B 672 ILE cc_start: 0.9401 (mm) cc_final: 0.9006 (mt) REVERT: B 707 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8608 (t70) outliers start: 43 outliers final: 35 residues processed: 470 average time/residue: 0.1211 time to fit residues: 85.4355 Evaluate side-chains 469 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 430 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 707 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 0.0020 chunk 181 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 124 optimal weight: 0.3980 chunk 69 optimal weight: 0.0980 chunk 142 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 173 optimal weight: 0.8980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 498 GLN D 560 GLN ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.203639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136455 restraints weight = 22479.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140615 restraints weight = 11400.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143083 restraints weight = 7966.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144376 restraints weight = 6594.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145197 restraints weight = 5979.419| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16208 Z= 0.116 Angle : 0.645 11.302 21992 Z= 0.326 Chirality : 0.041 0.248 2476 Planarity : 0.003 0.048 2692 Dihedral : 4.714 59.537 2144 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.99 % Allowed : 21.73 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.64 (0.20), residues: 1904 helix: 1.91 (0.15), residues: 1156 sheet: -1.87 (0.71), residues: 60 loop : -2.08 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 420 TYR 0.018 0.001 TYR C 444 PHE 0.026 0.001 PHE D 742 TRP 0.016 0.001 TRP D 697 HIS 0.002 0.000 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (16204) covalent geometry : angle 0.64520 / 0.33 (21984) SS BOND : bond 0.00128 / 0.07 ( 4) SS BOND : angle 0.41931 / 0.24 ( 8) hydrogen bonds : bond 0.03346 / 2.22 ( 910) hydrogen bonds : angle 4.19178 / 2.95 ( 2655) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 457 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 363 ARG cc_start: 0.5923 (ttt180) cc_final: 0.5653 (tpt-90) REVERT: A 432 ARG cc_start: 0.7427 (mtt90) cc_final: 0.6950 (ptp-110) REVERT: A 460 LEU cc_start: 0.8372 (mt) cc_final: 0.7645 (tt) REVERT: A 491 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7921 (tpp80) REVERT: A 499 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: A 533 GLN cc_start: 0.8120 (tt0) cc_final: 0.7577 (tm-30) REVERT: A 544 SER cc_start: 0.9342 (t) cc_final: 0.9109 (p) REVERT: A 568 MET cc_start: 0.8492 (mmt) cc_final: 0.8144 (mmt) REVERT: A 584 TYR cc_start: 0.8977 (t80) cc_final: 0.8481 (t80) REVERT: A 637 LEU cc_start: 0.9323 (mt) cc_final: 0.9108 (mt) REVERT: A 674 LEU cc_start: 0.9065 (tp) cc_final: 0.8704 (mp) REVERT: A 709 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 300 ASP cc_start: 0.7708 (m-30) cc_final: 0.7254 (p0) REVERT: C 436 PHE cc_start: 0.9082 (t80) cc_final: 0.8819 (t80) REVERT: C 460 LEU cc_start: 0.8442 (mt) cc_final: 0.7494 (tt) REVERT: C 491 ARG cc_start: 0.8653 (mmm160) cc_final: 0.8363 (tpp80) REVERT: C 533 GLN cc_start: 0.8074 (tt0) cc_final: 0.7347 (tm-30) REVERT: C 535 LYS cc_start: 0.8709 (tppp) cc_final: 0.8468 (tppt) REVERT: C 540 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.8937 (t) REVERT: C 544 SER cc_start: 0.9325 (t) cc_final: 0.9116 (p) REVERT: C 674 LEU cc_start: 0.9188 (tp) cc_final: 0.8858 (mp) REVERT: C 707 ASP cc_start: 0.8518 (t70) cc_final: 0.8077 (t0) REVERT: C 743 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7734 (mtp180) REVERT: D 300 ASP cc_start: 0.7672 (m-30) cc_final: 0.7208 (p0) REVERT: D 311 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8227 (mm-30) REVERT: D 318 LYS cc_start: 0.8295 (mttm) cc_final: 0.7824 (mmmt) REVERT: D 420 ARG cc_start: 0.8935 (mmm160) cc_final: 0.8479 (tpp80) REVERT: D 436 PHE cc_start: 0.9089 (t80) cc_final: 0.8826 (t80) REVERT: D 460 LEU cc_start: 0.8528 (mt) cc_final: 0.7691 (tt) REVERT: D 491 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7633 (tpp80) REVERT: D 536 GLU cc_start: 0.7933 (mp0) cc_final: 0.7446 (mt-10) REVERT: D 581 MET cc_start: 0.6680 (ptt) cc_final: 0.6425 (ttp) REVERT: D 584 TYR cc_start: 0.8928 (t80) cc_final: 0.8619 (t80) REVERT: D 674 LEU cc_start: 0.9123 (tp) cc_final: 0.8695 (mp) REVERT: D 689 ILE cc_start: 0.8920 (pt) cc_final: 0.8514 (mm) REVERT: D 697 TRP cc_start: 0.9039 (t60) cc_final: 0.8818 (t60) REVERT: B 300 ASP cc_start: 0.7669 (m-30) cc_final: 0.7264 (p0) REVERT: B 424 ASP cc_start: 0.8529 (m-30) cc_final: 0.8251 (t0) REVERT: B 460 LEU cc_start: 0.8369 (mt) cc_final: 0.7521 (tt) REVERT: B 487 TYR cc_start: 0.8908 (t80) cc_final: 0.7662 (t80) REVERT: B 533 GLN cc_start: 0.8116 (tt0) cc_final: 0.7400 (tm-30) REVERT: B 701 ARG cc_start: 0.9069 (tpp80) cc_final: 0.8807 (tpp80) REVERT: B 709 GLU cc_start: 0.8265 (tm-30) cc_final: 0.8033 (tm-30) outliers start: 34 outliers final: 26 residues processed: 471 average time/residue: 0.1242 time to fit residues: 87.5219 Evaluate side-chains 458 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 430 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.201781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127702 restraints weight = 22996.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131670 restraints weight = 12147.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134028 restraints weight = 8762.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135312 restraints weight = 7413.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135942 restraints weight = 6789.382| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16208 Z= 0.170 Angle : 0.714 12.169 21992 Z= 0.360 Chirality : 0.044 0.226 2476 Planarity : 0.003 0.048 2692 Dihedral : 4.771 58.539 2144 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.69 % Allowed : 22.37 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.49 (0.19), residues: 1904 helix: 1.76 (0.15), residues: 1160 sheet: -2.02 (0.69), residues: 60 loop : -2.08 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 420 TYR 0.015 0.002 TYR C 309 PHE 0.027 0.001 PHE D 580 TRP 0.012 0.001 TRP D 697 HIS 0.002 0.000 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (16204) covalent geometry : angle 0.71427 / 0.36 (21984) SS BOND : bond 0.00177 / 0.09 ( 4) SS BOND : angle 0.59912 / 0.30 ( 8) hydrogen bonds : bond 0.03758 / 2.50 ( 910) hydrogen bonds : angle 4.34080 / 3.06 ( 2655) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 434 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 363 ARG cc_start: 0.5881 (ttt180) cc_final: 0.5622 (tpt-90) REVERT: A 432 ARG cc_start: 0.7420 (mtt90) cc_final: 0.6646 (ttm110) REVERT: A 533 GLN cc_start: 0.8265 (tt0) cc_final: 0.7667 (tm-30) REVERT: A 544 SER cc_start: 0.9391 (t) cc_final: 0.9112 (p) REVERT: A 571 LYS cc_start: 0.8484 (tmtt) cc_final: 0.8141 (ttmm) REVERT: A 576 ASP cc_start: 0.7661 (m-30) cc_final: 0.7344 (m-30) REVERT: A 581 MET cc_start: 0.7155 (ptt) cc_final: 0.6712 (ttp) REVERT: A 584 TYR cc_start: 0.9112 (t80) cc_final: 0.8772 (t80) REVERT: A 709 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7968 (tm-30) REVERT: C 300 ASP cc_start: 0.7764 (m-30) cc_final: 0.7296 (p0) REVERT: C 491 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8392 (tpp80) REVERT: C 504 LYS cc_start: 0.7731 (tttt) cc_final: 0.7110 (tptm) REVERT: C 533 GLN cc_start: 0.8203 (tt0) cc_final: 0.7483 (tm-30) REVERT: C 540 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.9078 (t) REVERT: C 544 SER cc_start: 0.9410 (t) cc_final: 0.9117 (p) REVERT: C 700 GLN cc_start: 0.7497 (mt0) cc_final: 0.7167 (mt0) REVERT: C 743 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7771 (mtp85) REVERT: D 300 ASP cc_start: 0.7682 (m-30) cc_final: 0.7227 (p0) REVERT: D 311 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8216 (mm-30) REVERT: D 318 LYS cc_start: 0.8325 (mttm) cc_final: 0.7817 (mmmt) REVERT: D 420 ARG cc_start: 0.8972 (mmm160) cc_final: 0.8547 (tpp80) REVERT: D 432 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7528 (ptp-110) REVERT: D 491 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6538 (ttp80) REVERT: D 536 GLU cc_start: 0.8022 (mp0) cc_final: 0.7469 (mt-10) REVERT: D 568 MET cc_start: 0.8130 (ptp) cc_final: 0.7904 (mtm) REVERT: D 581 MET cc_start: 0.6883 (ptt) cc_final: 0.6620 (ttp) REVERT: D 669 LEU cc_start: 0.9557 (mt) cc_final: 0.9308 (mt) REVERT: D 674 LEU cc_start: 0.9226 (tp) cc_final: 0.8824 (mp) REVERT: D 697 TRP cc_start: 0.9099 (t60) cc_final: 0.8835 (t60) REVERT: B 300 ASP cc_start: 0.7737 (m-30) cc_final: 0.7291 (p0) REVERT: B 487 TYR cc_start: 0.9106 (t80) cc_final: 0.7513 (t80) REVERT: B 533 GLN cc_start: 0.8319 (tt0) cc_final: 0.7588 (tm-30) REVERT: B 672 ILE cc_start: 0.9418 (mm) cc_final: 0.9001 (mt) REVERT: B 701 ARG cc_start: 0.9145 (tpp80) cc_final: 0.8896 (tpp80) REVERT: B 709 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8095 (tm-30) outliers start: 29 outliers final: 25 residues processed: 448 average time/residue: 0.1268 time to fit residues: 84.8242 Evaluate side-chains 445 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 418 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 498 GLN ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.204593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131475 restraints weight = 23027.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135563 restraints weight = 11907.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138037 restraints weight = 8525.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139230 restraints weight = 7155.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140104 restraints weight = 6567.689| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16208 Z= 0.131 Angle : 0.714 12.252 21992 Z= 0.357 Chirality : 0.043 0.219 2476 Planarity : 0.003 0.049 2692 Dihedral : 4.754 58.273 2144 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.69 % Allowed : 22.96 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.20), residues: 1904 helix: 1.80 (0.15), residues: 1156 sheet: -1.85 (0.70), residues: 60 loop : -2.10 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 420 TYR 0.022 0.001 TYR A 666 PHE 0.028 0.001 PHE D 742 TRP 0.013 0.001 TRP D 697 HIS 0.002 0.000 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16204) covalent geometry : angle 0.71280 / 0.36 (21984) SS BOND : bond 0.00294 / 0.20 ( 4) SS BOND : angle 1.80987 / 1.49 ( 8) hydrogen bonds : bond 0.03563 / 2.35 ( 910) hydrogen bonds : angle 4.35565 / 3.08 ( 2655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3478.38 seconds wall clock time: 60 minutes 40.35 seconds (3640.35 seconds total)