Starting phenix.real_space_refine on Wed Mar 4 19:49:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2o_23135/03_2026/7l2o_23135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2o_23135/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2o_23135/03_2026/7l2o_23135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2o_23135/03_2026/7l2o_23135.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2o_23135/03_2026/7l2o_23135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2o_23135/03_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-5986/lib/python3.9/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: 3.90, per 1000 atoms: 0.25 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: 1.44 Conformation dependent library (CDL) restraints added in 663.5 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: 0.45 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: 2.25 Time building geometry restraints manager: 1.88 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: 8950 17.44 - 34.89: 675 34.89 - 52.33: 143 52.33 - 69.77: 35 69.77 - 87.22: 9 Dihedral angle restraints: 9812 sinusoidal: 4140 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 9809 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: 0.01 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: 0.940 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.630 Find NCS groups from input model: 0.280 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 13.303 87.217 6152 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 covalent geometry : bond 0.00974 (16204) covalent geometry : angle 0.89246 (21984) SS BOND : bond 0.00639 ( 4) SS BOND : angle 1.36180 ( 8) hydrogen bonds : bond 0.14358 ( 910) hydrogen bonds : angle 5.60232 ( 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 : 0.419 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: 0.1354 time to fit residues: 122.0494 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 : 0.575 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.199490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124335 restraints weight = 22484.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128669 restraints weight = 11544.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131247 restraints weight = 8202.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132518 restraints weight = 6885.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133398 restraints weight = 6315.256| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2775 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 8.434 21992 Z= 0.336 Chirality : 0.041 0.163 2476 Planarity : 0.003 0.039 2692 Dihedral : 6.752 51.531 2513 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.34 % Allowed : 13.20 % Favored : 84.46 % 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: 0.12 (0.20), residues: 1904 helix: 1.42 (0.15), residues: 1208 sheet: -2.89 (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 A 378 Details of bonding type rmsd covalent geometry : bond 0.00374 (16204) covalent geometry : angle 0.64335 (21984) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.70115 ( 8) hydrogen bonds : bond 0.04383 ( 910) hydrogen bonds : angle 4.19817 ( 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 567 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 527 time to evaluate : 0.533 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: 0.9085 (t80) cc_final: 0.8738 (t80) REVERT: A 311 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8017 (mm-30) REVERT: A 345 LYS cc_start: 0.7821 (mmtt) cc_final: 0.7575 (mmtm) REVERT: A 404 SER cc_start: 0.8200 (m) cc_final: 0.7500 (t) REVERT: A 420 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8500 (mmm-85) REVERT: A 424 ASP cc_start: 0.8676 (t70) cc_final: 0.8472 (t0) REVERT: A 428 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8368 (mtp180) REVERT: A 439 PHE cc_start: 0.8396 (t80) cc_final: 0.8191 (t80) REVERT: A 496 PHE cc_start: 0.8221 (t80) cc_final: 0.7947 (m-80) REVERT: A 536 GLU cc_start: 0.7952 (mp0) cc_final: 0.7683 (mp0) REVERT: A 544 SER cc_start: 0.9454 (t) cc_final: 0.9099 (p) REVERT: A 568 MET cc_start: 0.8556 (mmt) cc_final: 0.8264 (mmt) REVERT: A 589 PHE cc_start: 0.8422 (t80) cc_final: 0.8200 (t80) REVERT: A 650 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7875 (p) REVERT: A 689 ILE cc_start: 0.8884 (pt) cc_final: 0.8057 (mm) REVERT: A 700 GLN cc_start: 0.7852 (mt0) cc_final: 0.7585 (mt0) REVERT: C 311 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8221 (mm-30) REVERT: C 414 LEU cc_start: 0.8673 (mt) cc_final: 0.8450 (mm) REVERT: C 420 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8470 (mmm-85) REVERT: C 432 ARG cc_start: 0.7316 (mtp85) cc_final: 0.6666 (ptp90) REVERT: C 441 TYR cc_start: 0.8895 (t80) cc_final: 0.8499 (t80) REVERT: C 473 PHE cc_start: 0.8676 (m-80) cc_final: 0.8366 (m-10) REVERT: C 496 PHE cc_start: 0.8225 (t80) cc_final: 0.7991 (m-80) REVERT: C 504 LYS cc_start: 0.7967 (mttp) cc_final: 0.7162 (ptpp) REVERT: C 532 SER cc_start: 0.9310 (m) cc_final: 0.9094 (t) REVERT: C 540 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.9047 (t) REVERT: C 541 MET cc_start: 0.8572 (ttm) cc_final: 0.8365 (ttm) REVERT: C 544 SER cc_start: 0.9466 (t) cc_final: 0.9093 (p) REVERT: C 568 MET cc_start: 0.7812 (mtm) cc_final: 0.7603 (mtm) REVERT: C 589 PHE cc_start: 0.8494 (t80) cc_final: 0.8279 (t80) REVERT: C 650 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7925 (p) REVERT: C 689 ILE cc_start: 0.8778 (pt) cc_final: 0.8381 (mm) REVERT: C 692 GLU cc_start: 0.7711 (mp0) cc_final: 0.7306 (mp0) REVERT: C 743 ARG cc_start: 0.8389 (ttm110) cc_final: 0.8042 (mtp85) REVERT: D 311 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8243 (mm-30) REVERT: D 318 LYS cc_start: 0.8110 (mttm) cc_final: 0.7805 (mmmt) REVERT: D 372 TRP cc_start: 0.4692 (m100) cc_final: 0.4222 (m100) REVERT: D 424 ASP cc_start: 0.8626 (m-30) cc_final: 0.8348 (t0) REVERT: D 428 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8210 (mtp180) REVERT: D 439 PHE cc_start: 0.8383 (t80) cc_final: 0.8181 (t80) REVERT: D 496 PHE cc_start: 0.8144 (t80) cc_final: 0.7893 (m-80) REVERT: D 536 GLU cc_start: 0.7955 (mp0) cc_final: 0.7678 (mp0) REVERT: D 544 SER cc_start: 0.9409 (t) cc_final: 0.9029 (p) REVERT: D 581 MET cc_start: 0.6904 (ptt) cc_final: 0.6638 (ttp) REVERT: D 584 TYR cc_start: 0.9072 (t80) cc_final: 0.8806 (t80) REVERT: D 589 PHE cc_start: 0.8524 (t80) cc_final: 0.8266 (t80) REVERT: D 650 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7865 (p) REVERT: D 689 ILE cc_start: 0.8774 (pt) cc_final: 0.8548 (mm) REVERT: D 692 GLU cc_start: 0.7922 (mp0) cc_final: 0.7699 (mp0) REVERT: B 404 SER cc_start: 0.8168 (m) cc_final: 0.7530 (t) REVERT: B 420 ARG cc_start: 0.8938 (tpp80) cc_final: 0.8579 (mmm-85) REVERT: B 432 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7548 (ptp-110) REVERT: B 581 MET cc_start: 0.7486 (mmm) cc_final: 0.7251 (ttp) REVERT: B 589 PHE cc_start: 0.8489 (t80) cc_final: 0.8236 (t80) REVERT: B 650 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7810 (p) outliers start: 40 outliers final: 14 residues processed: 544 average time/residue: 0.1246 time to fit residues: 99.4605 Evaluate side-chains 470 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 451 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4228 r_free = 0.4228 target = 0.196363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122501 restraints weight = 22705.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126436 restraints weight = 11977.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128770 restraints weight = 8595.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129942 restraints weight = 7238.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130760 restraints weight = 6640.943| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16208 Z= 0.169 Angle : 0.621 11.675 21992 Z= 0.319 Chirality : 0.041 0.175 2476 Planarity : 0.004 0.059 2692 Dihedral : 5.939 46.810 2492 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.69 % Allowed : 15.71 % Favored : 81.60 % 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: 0.58 (0.20), residues: 1904 helix: 1.91 (0.15), residues: 1148 sheet: -2.97 (0.63), residues: 60 loop : -2.03 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 409 TYR 0.012 0.002 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 covalent geometry : bond 0.00386 (16204) covalent geometry : angle 0.62057 (21984) SS BOND : bond 0.00505 ( 4) SS BOND : angle 0.60964 ( 8) hydrogen bonds : bond 0.04037 ( 910) hydrogen bonds : angle 4.12478 ( 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 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 495 time to evaluate : 0.568 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: 0.9112 (t80) cc_final: 0.8851 (t80) REVERT: A 311 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 392 LYS cc_start: 0.7163 (mttt) cc_final: 0.6340 (ptmm) REVERT: A 432 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7452 (mtt90) REVERT: A 487 TYR cc_start: 0.9016 (t80) cc_final: 0.8716 (t80) REVERT: A 496 PHE cc_start: 0.8198 (t80) cc_final: 0.7953 (m-80) REVERT: A 544 SER cc_start: 0.9447 (t) cc_final: 0.9091 (p) REVERT: A 568 MET cc_start: 0.8521 (mmt) cc_final: 0.8304 (mmt) REVERT: A 581 MET cc_start: 0.7039 (ptt) cc_final: 0.6638 (ttp) REVERT: A 650 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7996 (p) REVERT: A 672 ILE cc_start: 0.9383 (mm) cc_final: 0.9030 (mt) REVERT: A 689 ILE cc_start: 0.8920 (pt) cc_final: 0.8361 (mm) REVERT: A 709 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 311 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 414 LEU cc_start: 0.8578 (mt) cc_final: 0.8350 (mm) REVERT: C 432 ARG cc_start: 0.7359 (mtp85) cc_final: 0.6721 (ptp90) REVERT: C 473 PHE cc_start: 0.8600 (m-80) cc_final: 0.8364 (m-10) REVERT: C 496 PHE cc_start: 0.8212 (t80) cc_final: 0.7992 (m-80) REVERT: C 532 SER cc_start: 0.9372 (m) cc_final: 0.9106 (t) REVERT: C 541 MET cc_start: 0.8590 (ttm) cc_final: 0.8387 (ttm) REVERT: C 544 SER cc_start: 0.9500 (t) cc_final: 0.9118 (p) REVERT: C 572 MET cc_start: 0.8008 (mmt) cc_final: 0.7585 (mmm) REVERT: C 709 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 311 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8350 (mm-30) REVERT: D 318 LYS cc_start: 0.8207 (mttm) cc_final: 0.7845 (mmmt) REVERT: D 372 TRP cc_start: 0.4446 (m100) cc_final: 0.4217 (m100) REVERT: D 397 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8032 (pt0) REVERT: D 424 ASP cc_start: 0.8635 (m-30) cc_final: 0.8300 (t0) REVERT: D 428 ARG cc_start: 0.8782 (ttm170) cc_final: 0.8196 (mtp180) REVERT: D 473 PHE cc_start: 0.8583 (m-80) cc_final: 0.8322 (m-10) REVERT: D 496 PHE cc_start: 0.8150 (t80) cc_final: 0.7885 (m-80) REVERT: D 533 GLN cc_start: 0.8490 (tt0) cc_final: 0.7710 (tm-30) REVERT: D 536 GLU cc_start: 0.8038 (mp0) cc_final: 0.7587 (mp0) REVERT: D 544 SER cc_start: 0.9484 (t) cc_final: 0.9107 (p) REVERT: D 581 MET cc_start: 0.6840 (ptt) cc_final: 0.6543 (ttp) REVERT: D 584 TYR cc_start: 0.9090 (t80) cc_final: 0.8790 (t80) REVERT: D 589 PHE cc_start: 0.8545 (t80) cc_final: 0.8322 (t80) REVERT: D 650 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7866 (p) REVERT: B 300 ASP cc_start: 0.7694 (m-30) cc_final: 0.7151 (p0) REVERT: B 432 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7416 (ptp-110) REVERT: B 445 MET cc_start: 0.9112 (mmp) cc_final: 0.8711 (mpp) REVERT: B 487 TYR cc_start: 0.9080 (t80) cc_final: 0.8584 (t80) REVERT: B 533 GLN cc_start: 0.8397 (tt0) cc_final: 0.7650 (tm-30) REVERT: B 547 MET cc_start: 0.8734 (mtp) cc_final: 0.8448 (tpp) REVERT: B 581 MET cc_start: 0.7495 (mmm) cc_final: 0.7254 (ttp) REVERT: B 650 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 672 ILE cc_start: 0.9378 (mm) cc_final: 0.9037 (mt) REVERT: B 674 LEU cc_start: 0.9361 (tp) cc_final: 0.9043 (tp) REVERT: B 707 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8649 (t0) outliers start: 46 outliers final: 18 residues processed: 514 average time/residue: 0.1182 time to fit residues: 90.1516 Evaluate side-chains 461 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 439 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 541 MET Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain B residue 443 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: 1.9990 chunk 108 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.197525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124858 restraints weight = 22483.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129063 restraints weight = 11210.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131553 restraints weight = 7802.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132949 restraints weight = 6473.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133653 restraints weight = 5879.589| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16208 Z= 0.122 Angle : 0.582 11.053 21992 Z= 0.299 Chirality : 0.040 0.180 2476 Planarity : 0.003 0.050 2692 Dihedral : 5.456 43.064 2491 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.28 % Allowed : 18.11 % Favored : 79.61 % 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: 0.66 (0.20), residues: 1904 helix: 1.94 (0.15), residues: 1176 sheet: -2.82 (0.64), residues: 60 loop : -2.11 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 409 TYR 0.015 0.001 TYR C 309 PHE 0.024 0.001 PHE A 742 TRP 0.011 0.001 TRP D 697 HIS 0.002 0.000 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00267 (16204) covalent geometry : angle 0.58196 (21984) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.58466 ( 8) hydrogen bonds : bond 0.03554 ( 910) hydrogen bonds : angle 3.96067 ( 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 515 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 476 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9087 (t80) cc_final: 0.8814 (t80) REVERT: A 311 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 432 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7328 (mtt90) REVERT: A 473 PHE cc_start: 0.8322 (m-10) cc_final: 0.8082 (m-10) REVERT: A 533 GLN cc_start: 0.8349 (tt0) cc_final: 0.7613 (tm-30) REVERT: A 544 SER cc_start: 0.9450 (t) cc_final: 0.9103 (p) REVERT: A 568 MET cc_start: 0.8481 (mmt) cc_final: 0.8244 (mmt) REVERT: A 576 ASP cc_start: 0.7726 (m-30) cc_final: 0.7462 (m-30) REVERT: A 581 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6719 (ttp) REVERT: A 689 ILE cc_start: 0.8870 (pt) cc_final: 0.8386 (mm) REVERT: A 709 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8189 (tm-30) REVERT: C 270 ASN cc_start: 0.8035 (m-40) cc_final: 0.7796 (m110) REVERT: C 311 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8162 (mm-30) REVERT: C 414 LEU cc_start: 0.8588 (mt) cc_final: 0.8374 (mm) REVERT: C 420 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8472 (mmm-85) REVERT: C 491 ARG cc_start: 0.8936 (mmm160) cc_final: 0.8172 (tpp80) REVERT: C 496 PHE cc_start: 0.8088 (t80) cc_final: 0.7871 (m-80) REVERT: C 532 SER cc_start: 0.9345 (m) cc_final: 0.9042 (t) REVERT: C 535 LYS cc_start: 0.8771 (tppp) cc_final: 0.8358 (tppt) REVERT: C 544 SER cc_start: 0.9449 (t) cc_final: 0.9109 (p) REVERT: C 572 MET cc_start: 0.8029 (mmt) cc_final: 0.7578 (mmm) REVERT: C 674 LEU cc_start: 0.9171 (tp) cc_final: 0.8790 (mp) REVERT: C 700 GLN cc_start: 0.7806 (mt0) cc_final: 0.7489 (mt0) REVERT: D 311 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8350 (mm-30) REVERT: D 318 LYS cc_start: 0.8213 (mttm) cc_final: 0.7818 (mmmt) REVERT: D 420 ARG cc_start: 0.9002 (tpp80) cc_final: 0.8774 (tpp80) REVERT: D 473 PHE cc_start: 0.8568 (m-80) cc_final: 0.8311 (m-10) REVERT: D 487 TYR cc_start: 0.9010 (t80) cc_final: 0.8015 (t80) REVERT: D 533 GLN cc_start: 0.8428 (tt0) cc_final: 0.7688 (tm-30) REVERT: D 536 GLU cc_start: 0.8043 (mp0) cc_final: 0.7600 (mp0) REVERT: D 544 SER cc_start: 0.9439 (t) cc_final: 0.9092 (p) REVERT: D 581 MET cc_start: 0.6943 (ptt) cc_final: 0.6682 (ttp) REVERT: D 697 TRP cc_start: 0.9109 (t60) cc_final: 0.8748 (t60) REVERT: B 300 ASP cc_start: 0.7655 (m-30) cc_final: 0.7144 (p0) REVERT: B 432 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7383 (ptp-110) REVERT: B 487 TYR cc_start: 0.9019 (t80) cc_final: 0.8347 (t80) REVERT: B 533 GLN cc_start: 0.8344 (tt0) cc_final: 0.7533 (tm-30) REVERT: B 547 MET cc_start: 0.8753 (mtp) cc_final: 0.8428 (tpp) REVERT: B 571 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8617 (tmtt) REVERT: B 581 MET cc_start: 0.7510 (mmm) cc_final: 0.7245 (ttp) REVERT: B 672 ILE cc_start: 0.9349 (mm) cc_final: 0.8978 (mt) REVERT: B 674 LEU cc_start: 0.9273 (tp) cc_final: 0.8980 (tp) outliers start: 39 outliers final: 25 residues processed: 496 average time/residue: 0.1176 time to fit residues: 86.3240 Evaluate side-chains 466 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 440 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 445 MET Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 581 MET 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 468 THR 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 D residue 335 THR 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 678 LEU 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 504 LYS Chi-restraints excluded: chain B residue 512 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 17 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN D 354 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 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 = 0.4315 r_free = 0.4315 target = 0.202327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129622 restraints weight = 23144.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134128 restraints weight = 13328.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135172 restraints weight = 8425.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135504 restraints weight = 8137.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135900 restraints weight = 7779.328| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16208 Z= 0.128 Angle : 0.600 11.322 21992 Z= 0.303 Chirality : 0.041 0.215 2476 Planarity : 0.003 0.047 2692 Dihedral : 5.277 42.537 2488 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.39 % Allowed : 18.28 % Favored : 79.32 % 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: 0.67 (0.20), residues: 1904 helix: 1.96 (0.15), residues: 1176 sheet: -2.66 (0.64), residues: 60 loop : -2.14 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 579 TYR 0.014 0.001 TYR A 441 PHE 0.020 0.001 PHE A 742 TRP 0.018 0.001 TRP A 697 HIS 0.002 0.000 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00284 (16204) covalent geometry : angle 0.59970 (21984) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.41835 ( 8) hydrogen bonds : bond 0.03500 ( 910) hydrogen bonds : angle 3.95107 ( 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 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 470 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.9088 (t80) cc_final: 0.8872 (t80) REVERT: A 311 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8113 (mm-30) REVERT: A 363 ARG cc_start: 0.5614 (ttt180) cc_final: 0.5326 (tpt-90) REVERT: A 432 ARG cc_start: 0.7515 (mtt90) cc_final: 0.6996 (mtt90) REVERT: A 473 PHE cc_start: 0.8332 (m-10) cc_final: 0.8095 (m-10) REVERT: A 491 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7876 (tpp80) REVERT: A 533 GLN cc_start: 0.8281 (tt0) cc_final: 0.7609 (tm-30) REVERT: A 544 SER cc_start: 0.9390 (t) cc_final: 0.9107 (p) REVERT: A 568 MET cc_start: 0.8524 (mmt) cc_final: 0.8203 (mmt) REVERT: A 576 ASP cc_start: 0.7758 (m-30) cc_final: 0.7493 (m-30) REVERT: A 581 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6648 (ttp) REVERT: A 689 ILE cc_start: 0.8873 (pt) cc_final: 0.8332 (mm) REVERT: A 709 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 270 ASN cc_start: 0.8031 (m-40) cc_final: 0.7746 (m110) REVERT: C 311 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8292 (mm-30) REVERT: C 436 PHE cc_start: 0.9161 (t80) cc_final: 0.8888 (t80) REVERT: C 491 ARG cc_start: 0.8703 (mmm160) cc_final: 0.8234 (tpp80) REVERT: C 532 SER cc_start: 0.9316 (m) cc_final: 0.9024 (t) REVERT: C 535 LYS cc_start: 0.8747 (tppp) cc_final: 0.8409 (tppt) REVERT: C 544 SER cc_start: 0.9392 (t) cc_final: 0.9126 (p) REVERT: C 572 MET cc_start: 0.8095 (mmt) cc_final: 0.7721 (mmm) REVERT: C 674 LEU cc_start: 0.9229 (tp) cc_final: 0.8853 (mp) REVERT: C 700 GLN cc_start: 0.7821 (mt0) cc_final: 0.7530 (mt0) REVERT: D 311 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8349 (mm-30) REVERT: D 318 LYS cc_start: 0.8209 (mttm) cc_final: 0.7803 (mmmt) REVERT: D 473 PHE cc_start: 0.8626 (m-80) cc_final: 0.8381 (m-10) REVERT: D 487 TYR cc_start: 0.8782 (t80) cc_final: 0.8426 (t80) REVERT: D 533 GLN cc_start: 0.8361 (tt0) cc_final: 0.7679 (tm-30) REVERT: D 536 GLU cc_start: 0.8043 (mp0) cc_final: 0.7582 (mt-10) REVERT: D 544 SER cc_start: 0.9401 (t) cc_final: 0.9121 (p) REVERT: D 581 MET cc_start: 0.6778 (ptt) cc_final: 0.6518 (ttp) REVERT: D 584 TYR cc_start: 0.9042 (t80) cc_final: 0.8749 (t80) REVERT: B 300 ASP cc_start: 0.7657 (m-30) cc_final: 0.7148 (p0) REVERT: B 487 TYR cc_start: 0.9063 (t80) cc_final: 0.7592 (t80) REVERT: B 533 GLN cc_start: 0.8304 (tt0) cc_final: 0.7538 (tm-30) REVERT: B 571 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8659 (tmtt) REVERT: B 672 ILE cc_start: 0.9385 (mm) cc_final: 0.9015 (mt) REVERT: B 674 LEU cc_start: 0.9312 (tp) cc_final: 0.9056 (tp) REVERT: B 707 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8633 (t0) outliers start: 41 outliers final: 27 residues processed: 491 average time/residue: 0.1184 time to fit residues: 86.1489 Evaluate side-chains 478 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 449 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 412 MET Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 503 LEU 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 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 512 SER Chi-restraints excluded: chain C residue 533 GLN 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 678 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 437 ASN 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 678 LEU 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: 2.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS D 354 GLN ** B 676 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 = 0.4327 r_free = 0.4327 target = 0.203693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130700 restraints weight = 23110.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134820 restraints weight = 12005.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137242 restraints weight = 8537.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138642 restraints weight = 7140.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139166 restraints weight = 6491.460| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16208 Z= 0.119 Angle : 0.605 11.946 21992 Z= 0.305 Chirality : 0.041 0.217 2476 Planarity : 0.003 0.049 2692 Dihedral : 5.174 45.600 2488 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.51 % Allowed : 19.28 % Favored : 78.21 % 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: 0.79 (0.20), residues: 1904 helix: 2.11 (0.15), residues: 1148 sheet: -2.41 (0.65), residues: 60 loop : -2.07 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 491 TYR 0.016 0.001 TYR D 666 PHE 0.024 0.001 PHE D 742 TRP 0.013 0.001 TRP A 697 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00261 (16204) covalent geometry : angle 0.60543 (21984) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.46742 ( 8) hydrogen bonds : bond 0.03401 ( 910) hydrogen bonds : angle 3.93248 ( 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 494 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 451 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 363 ARG cc_start: 0.5771 (ttt180) cc_final: 0.5483 (tpt-90) REVERT: A 432 ARG cc_start: 0.7498 (mtt90) cc_final: 0.6967 (ptt180) REVERT: A 533 GLN cc_start: 0.8183 (tt0) cc_final: 0.7557 (tm-30) REVERT: A 544 SER cc_start: 0.9399 (t) cc_final: 0.9117 (p) REVERT: A 572 MET cc_start: 0.7240 (mtt) cc_final: 0.6871 (mtt) REVERT: A 576 ASP cc_start: 0.7466 (m-30) cc_final: 0.7241 (m-30) REVERT: A 581 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6716 (ttp) REVERT: A 637 LEU cc_start: 0.9334 (mt) cc_final: 0.9106 (mt) REVERT: A 689 ILE cc_start: 0.8963 (pt) cc_final: 0.8494 (mm) REVERT: A 709 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8099 (tm-30) REVERT: C 300 ASP cc_start: 0.7652 (m-30) cc_final: 0.7173 (p0) REVERT: C 491 ARG cc_start: 0.8734 (mmm160) cc_final: 0.8251 (tpp80) REVERT: C 532 SER cc_start: 0.9260 (m) cc_final: 0.8996 (t) REVERT: C 544 SER cc_start: 0.9395 (t) cc_final: 0.9126 (p) REVERT: C 572 MET cc_start: 0.8070 (mmt) cc_final: 0.7726 (mmm) REVERT: C 674 LEU cc_start: 0.9204 (tp) cc_final: 0.8798 (mp) REVERT: C 700 GLN cc_start: 0.7797 (mt0) cc_final: 0.7550 (mt0) REVERT: C 743 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7990 (mtp85) REVERT: D 311 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8367 (mm-30) REVERT: D 318 LYS cc_start: 0.8278 (mttm) cc_final: 0.7826 (mmmt) REVERT: D 473 PHE cc_start: 0.8596 (m-80) cc_final: 0.8378 (m-10) REVERT: D 533 GLN cc_start: 0.8230 (tt0) cc_final: 0.7616 (tm-30) REVERT: D 536 GLU cc_start: 0.8011 (mp0) cc_final: 0.7505 (mt-10) REVERT: D 544 SER cc_start: 0.9400 (t) cc_final: 0.9139 (p) REVERT: D 581 MET cc_start: 0.6898 (ptt) cc_final: 0.6651 (ttp) REVERT: D 584 TYR cc_start: 0.9022 (t80) cc_final: 0.8720 (t80) REVERT: D 689 ILE cc_start: 0.8931 (pt) cc_final: 0.8560 (mm) REVERT: B 300 ASP cc_start: 0.7626 (m-30) cc_final: 0.7129 (p0) REVERT: B 487 TYR cc_start: 0.9038 (t80) cc_final: 0.7594 (t80) REVERT: B 533 GLN cc_start: 0.8220 (tt0) cc_final: 0.7504 (tm-30) REVERT: B 536 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: B 571 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8599 (tmtt) REVERT: B 674 LEU cc_start: 0.9284 (tp) cc_final: 0.9014 (tp) outliers start: 43 outliers final: 35 residues processed: 469 average time/residue: 0.1238 time to fit residues: 85.8242 Evaluate side-chains 473 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 436 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 398 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 503 LEU Chi-restraints excluded: chain A residue 581 MET 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 512 SER Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 571 LYS 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 678 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 443 LEU 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 536 GLU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 183 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 560 GLN ** B 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 = 0.4292 r_free = 0.4292 target = 0.199437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129163 restraints weight = 22969.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131901 restraints weight = 12867.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131674 restraints weight = 8606.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132790 restraints weight = 8354.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132930 restraints weight = 7926.935| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16208 Z= 0.162 Angle : 0.659 12.037 21992 Z= 0.329 Chirality : 0.043 0.235 2476 Planarity : 0.003 0.047 2692 Dihedral : 5.257 44.367 2488 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.63 % Allowed : 20.44 % Favored : 76.93 % 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: 0.59 (0.20), residues: 1904 helix: 1.89 (0.15), residues: 1156 sheet: -2.47 (0.65), residues: 60 loop : -2.07 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.014 0.002 TYR C 487 PHE 0.019 0.001 PHE B 742 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00374 (16204) covalent geometry : angle 0.65882 (21984) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.56425 ( 8) hydrogen bonds : bond 0.03752 ( 910) hydrogen bonds : angle 4.12607 ( 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 507 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 462 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8100 (mm-30) REVERT: A 363 ARG cc_start: 0.5581 (ttt180) cc_final: 0.5309 (tpt-90) REVERT: A 432 ARG cc_start: 0.7553 (mtt90) cc_final: 0.6918 (mtt90) REVERT: A 473 PHE cc_start: 0.8369 (m-10) cc_final: 0.8153 (m-10) REVERT: A 533 GLN cc_start: 0.8250 (tt0) cc_final: 0.7593 (tm-30) REVERT: A 544 SER cc_start: 0.9446 (t) cc_final: 0.9122 (p) REVERT: A 581 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6600 (ttp) REVERT: A 637 LEU cc_start: 0.9369 (mt) cc_final: 0.9163 (mt) REVERT: A 669 LEU cc_start: 0.9432 (mt) cc_final: 0.9113 (mt) REVERT: A 674 LEU cc_start: 0.9229 (tp) cc_final: 0.8870 (mp) REVERT: A 709 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 300 ASP cc_start: 0.7754 (m-30) cc_final: 0.7278 (p0) REVERT: C 308 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8081 (mtt) REVERT: C 532 SER cc_start: 0.9316 (m) cc_final: 0.9043 (t) REVERT: C 544 SER cc_start: 0.9406 (t) cc_final: 0.9115 (p) REVERT: C 572 MET cc_start: 0.8073 (mmt) cc_final: 0.7621 (mmm) REVERT: C 674 LEU cc_start: 0.9320 (tp) cc_final: 0.8960 (mp) REVERT: D 300 ASP cc_start: 0.7541 (m-30) cc_final: 0.7091 (p0) REVERT: D 311 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8382 (mm-30) REVERT: D 318 LYS cc_start: 0.8315 (mttm) cc_final: 0.7831 (mmmt) REVERT: D 432 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7555 (ptp-110) REVERT: D 473 PHE cc_start: 0.8677 (m-80) cc_final: 0.8438 (m-10) REVERT: D 491 ARG cc_start: 0.6010 (ttp-170) cc_final: 0.5594 (tpp80) REVERT: D 536 GLU cc_start: 0.7969 (mp0) cc_final: 0.7463 (mt-10) REVERT: D 544 SER cc_start: 0.9443 (t) cc_final: 0.9162 (p) REVERT: D 581 MET cc_start: 0.6935 (ptt) cc_final: 0.6685 (ttp) REVERT: D 674 LEU cc_start: 0.9251 (tp) cc_final: 0.8785 (mp) REVERT: B 300 ASP cc_start: 0.7632 (m-30) cc_final: 0.7138 (p0) REVERT: B 487 TYR cc_start: 0.9139 (t80) cc_final: 0.7564 (t80) REVERT: B 533 GLN cc_start: 0.8308 (tt0) cc_final: 0.7568 (tm-30) REVERT: B 571 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8562 (tmtt) REVERT: B 674 LEU cc_start: 0.9263 (tp) cc_final: 0.9003 (tp) REVERT: B 701 ARG cc_start: 0.9113 (tpp80) cc_final: 0.8891 (tpp80) REVERT: B 707 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8698 (t0) outliers start: 45 outliers final: 36 residues processed: 482 average time/residue: 0.1206 time to fit residues: 86.3448 Evaluate side-chains 477 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 438 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain A residue 581 MET 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 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 520 SER Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 412 MET 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 520 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 437 ASN 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 707 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 118 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 167 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 0.3980 chunk 7 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS ** B 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 = 0.4321 r_free = 0.4321 target = 0.202804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129539 restraints weight = 23052.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133561 restraints weight = 12028.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135938 restraints weight = 8593.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137343 restraints weight = 7220.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137756 restraints weight = 6568.044| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16208 Z= 0.134 Angle : 0.650 12.289 21992 Z= 0.325 Chirality : 0.042 0.224 2476 Planarity : 0.003 0.048 2692 Dihedral : 5.151 48.769 2488 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.39 % Allowed : 21.03 % Favored : 76.58 % 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: 0.57 (0.20), residues: 1904 helix: 1.89 (0.15), residues: 1156 sheet: -2.36 (0.66), residues: 60 loop : -2.13 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 499 TYR 0.017 0.001 TYR C 309 PHE 0.025 0.001 PHE D 742 TRP 0.012 0.001 TRP C 697 HIS 0.005 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00305 (16204) covalent geometry : angle 0.65050 (21984) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.50837 ( 8) hydrogen bonds : bond 0.03525 ( 910) hydrogen bonds : angle 4.17297 ( 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 493 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 452 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8136 (mm-30) REVERT: A 363 ARG cc_start: 0.5888 (ttt180) cc_final: 0.5607 (tpt-90) REVERT: A 432 ARG cc_start: 0.7498 (mtt90) cc_final: 0.6713 (ttm110) REVERT: A 491 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7952 (tpp80) REVERT: A 533 GLN cc_start: 0.8239 (tt0) cc_final: 0.7616 (tm-30) REVERT: A 544 SER cc_start: 0.9393 (t) cc_final: 0.9110 (p) REVERT: A 581 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6652 (ttp) REVERT: A 584 TYR cc_start: 0.9168 (t80) cc_final: 0.8858 (t80) REVERT: A 637 LEU cc_start: 0.9337 (mt) cc_final: 0.9118 (mt) REVERT: A 669 LEU cc_start: 0.9439 (mt) cc_final: 0.9166 (mt) REVERT: A 709 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7962 (tm-30) REVERT: C 300 ASP cc_start: 0.7703 (m-30) cc_final: 0.7234 (p0) REVERT: C 308 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7937 (mtt) REVERT: C 345 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7731 (mmtp) REVERT: C 436 PHE cc_start: 0.9177 (t80) cc_final: 0.8916 (t80) REVERT: C 491 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7524 (tpp80) REVERT: C 532 SER cc_start: 0.9265 (m) cc_final: 0.9006 (t) REVERT: C 536 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: C 544 SER cc_start: 0.9365 (t) cc_final: 0.9120 (p) REVERT: C 572 MET cc_start: 0.8048 (mmt) cc_final: 0.7673 (mmm) REVERT: C 674 LEU cc_start: 0.9250 (tp) cc_final: 0.8881 (mp) REVERT: C 743 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7915 (mtp85) REVERT: D 300 ASP cc_start: 0.7604 (m-30) cc_final: 0.7139 (p0) REVERT: D 311 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8559 (mm-30) REVERT: D 318 LYS cc_start: 0.8296 (mttm) cc_final: 0.7801 (mmmt) REVERT: D 491 ARG cc_start: 0.5929 (ttp-170) cc_final: 0.5665 (tpp80) REVERT: D 536 GLU cc_start: 0.7951 (mp0) cc_final: 0.7438 (mt-10) REVERT: D 544 SER cc_start: 0.9397 (t) cc_final: 0.9142 (p) REVERT: D 551 ASN cc_start: 0.8921 (m-40) cc_final: 0.8706 (m110) REVERT: D 581 MET cc_start: 0.6766 (ptt) cc_final: 0.6486 (ttp) REVERT: D 584 TYR cc_start: 0.9047 (t80) cc_final: 0.8786 (t80) REVERT: D 637 LEU cc_start: 0.9426 (mt) cc_final: 0.8982 (mt) REVERT: D 674 LEU cc_start: 0.9222 (tp) cc_final: 0.8782 (mp) REVERT: D 697 TRP cc_start: 0.9197 (t60) cc_final: 0.8693 (t60) REVERT: D 709 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 300 ASP cc_start: 0.7581 (m-30) cc_final: 0.7076 (p0) REVERT: B 323 LEU cc_start: 0.4421 (OUTLIER) cc_final: 0.4128 (pp) REVERT: B 487 TYR cc_start: 0.9074 (t80) cc_final: 0.7588 (t80) REVERT: B 533 GLN cc_start: 0.8291 (tt0) cc_final: 0.7587 (tm-30) REVERT: B 552 MET cc_start: 0.9000 (ttp) cc_final: 0.8772 (ttp) REVERT: B 571 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8647 (tmtt) REVERT: B 581 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6641 (ttp) REVERT: B 674 LEU cc_start: 0.9200 (tp) cc_final: 0.8931 (tp) outliers start: 41 outliers final: 33 residues processed: 469 average time/residue: 0.1183 time to fit residues: 82.1574 Evaluate side-chains 473 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 435 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain A residue 581 MET 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 394 SER Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 412 MET 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 533 GLN Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 406 THR 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 741 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 437 ASN 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 581 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 0.2980 chunk 181 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 142 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** 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 = 0.4314 r_free = 0.4314 target = 0.201302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133341 restraints weight = 22471.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137435 restraints weight = 11422.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139905 restraints weight = 8014.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141262 restraints weight = 6633.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142009 restraints weight = 6002.218| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16208 Z= 0.119 Angle : 0.655 12.277 21992 Z= 0.327 Chirality : 0.042 0.216 2476 Planarity : 0.003 0.048 2692 Dihedral : 5.043 57.374 2488 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.39 % Allowed : 21.96 % Favored : 75.64 % 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: 0.58 (0.20), residues: 1904 helix: 1.89 (0.15), residues: 1156 sheet: -2.22 (0.68), residues: 60 loop : -2.13 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 557 TYR 0.024 0.001 TYR C 444 PHE 0.026 0.001 PHE C 742 TRP 0.009 0.001 TRP C 697 HIS 0.002 0.000 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00261 (16204) covalent geometry : angle 0.65488 (21984) SS BOND : bond 0.00179 ( 4) SS BOND : angle 1.24863 ( 8) hydrogen bonds : bond 0.03379 ( 910) hydrogen bonds : angle 4.13843 ( 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 490 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 449 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 363 ARG cc_start: 0.6063 (ttt180) cc_final: 0.5781 (tpt-90) REVERT: A 432 ARG cc_start: 0.7428 (mtt90) cc_final: 0.6684 (ttm110) REVERT: A 460 LEU cc_start: 0.8428 (mt) cc_final: 0.7586 (tt) REVERT: A 491 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7926 (tpp80) REVERT: A 533 GLN cc_start: 0.8145 (tt0) cc_final: 0.7594 (tm-30) REVERT: A 571 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8409 (tmtt) REVERT: A 581 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6716 (ttp) REVERT: A 584 TYR cc_start: 0.9124 (t80) cc_final: 0.8790 (t80) REVERT: A 598 LEU cc_start: 0.9406 (tt) cc_final: 0.9180 (tt) REVERT: A 637 LEU cc_start: 0.9322 (mt) cc_final: 0.9089 (mt) REVERT: A 709 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 300 ASP cc_start: 0.7669 (m-30) cc_final: 0.7232 (p0) REVERT: C 345 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7667 (mmtm) REVERT: C 436 PHE cc_start: 0.9123 (t80) cc_final: 0.8870 (t80) REVERT: C 491 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7668 (tpp80) REVERT: C 532 SER cc_start: 0.9283 (m) cc_final: 0.9023 (t) REVERT: C 536 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: C 544 SER cc_start: 0.9387 (t) cc_final: 0.9137 (p) REVERT: C 572 MET cc_start: 0.7940 (mmt) cc_final: 0.7646 (mmm) REVERT: C 674 LEU cc_start: 0.9184 (tp) cc_final: 0.8814 (mp) REVERT: C 677 MET cc_start: 0.7155 (ttt) cc_final: 0.6741 (mtt) REVERT: C 743 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7850 (mtp180) REVERT: D 300 ASP cc_start: 0.7632 (m-30) cc_final: 0.7176 (p0) REVERT: D 318 LYS cc_start: 0.8255 (mttm) cc_final: 0.7776 (mmmt) REVERT: D 460 LEU cc_start: 0.8389 (mt) cc_final: 0.7516 (tt) REVERT: D 491 ARG cc_start: 0.5834 (ttp-170) cc_final: 0.5614 (tpp80) REVERT: D 536 GLU cc_start: 0.7951 (mp0) cc_final: 0.7413 (mt-10) REVERT: D 581 MET cc_start: 0.6820 (ptt) cc_final: 0.6543 (ttp) REVERT: D 584 TYR cc_start: 0.8957 (t80) cc_final: 0.8709 (t80) REVERT: D 674 LEU cc_start: 0.9143 (tp) cc_final: 0.8786 (mp) REVERT: B 300 ASP cc_start: 0.7492 (m-30) cc_final: 0.7068 (p0) REVERT: B 323 LEU cc_start: 0.4524 (OUTLIER) cc_final: 0.4224 (pp) REVERT: B 487 TYR cc_start: 0.8964 (t80) cc_final: 0.7644 (t80) REVERT: B 533 GLN cc_start: 0.8179 (tt0) cc_final: 0.7525 (tm-30) REVERT: B 571 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8629 (tmtt) REVERT: B 581 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6661 (ttp) REVERT: B 674 LEU cc_start: 0.9239 (tp) cc_final: 0.8989 (tp) REVERT: B 709 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8036 (tm-30) outliers start: 41 outliers final: 31 residues processed: 465 average time/residue: 0.1211 time to fit residues: 84.1495 Evaluate side-chains 463 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 428 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain A residue 581 MET 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 533 GLN Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 406 THR 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 741 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 581 MET 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: 0.9980 chunk 39 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 676 ASN D 700 GLN ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 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 = 0.4327 r_free = 0.4327 target = 0.202235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133854 restraints weight = 22388.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137920 restraints weight = 11504.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140347 restraints weight = 8088.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141681 restraints weight = 6721.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142322 restraints weight = 6097.783| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16208 Z= 0.124 Angle : 0.668 12.832 21992 Z= 0.334 Chirality : 0.043 0.231 2476 Planarity : 0.003 0.049 2692 Dihedral : 5.009 58.236 2488 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.28 % Allowed : 23.07 % Favored : 74.65 % 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: 0.57 (0.20), residues: 1904 helix: 1.85 (0.15), residues: 1160 sheet: -2.04 (0.69), residues: 60 loop : -2.10 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 499 TYR 0.017 0.001 TYR C 309 PHE 0.026 0.001 PHE D 742 TRP 0.009 0.001 TRP B 549 HIS 0.002 0.000 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00275 (16204) covalent geometry : angle 0.66756 (21984) SS BOND : bond 0.00233 ( 4) SS BOND : angle 1.28943 ( 8) hydrogen bonds : bond 0.03452 ( 910) hydrogen bonds : angle 4.18703 ( 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 481 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 442 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 363 ARG cc_start: 0.5950 (ttt180) cc_final: 0.5673 (tpt-90) REVERT: A 432 ARG cc_start: 0.7423 (mtt90) cc_final: 0.6929 (ptp-110) REVERT: A 460 LEU cc_start: 0.8483 (mt) cc_final: 0.7648 (tt) REVERT: A 533 GLN cc_start: 0.8136 (tt0) cc_final: 0.7574 (tm-30) REVERT: A 571 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8385 (tmtt) REVERT: A 581 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6700 (ttp) REVERT: A 584 TYR cc_start: 0.9130 (t80) cc_final: 0.8807 (t80) REVERT: A 637 LEU cc_start: 0.9332 (mt) cc_final: 0.9104 (mt) REVERT: A 709 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 300 ASP cc_start: 0.7517 (m-30) cc_final: 0.7068 (p0) REVERT: C 436 PHE cc_start: 0.9095 (t80) cc_final: 0.8841 (t80) REVERT: C 491 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7993 (tpp80) REVERT: C 532 SER cc_start: 0.9268 (m) cc_final: 0.8990 (t) REVERT: C 536 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: C 544 SER cc_start: 0.9372 (t) cc_final: 0.9103 (p) REVERT: C 572 MET cc_start: 0.7950 (mmt) cc_final: 0.7654 (mmm) REVERT: C 674 LEU cc_start: 0.9200 (tp) cc_final: 0.8808 (mp) REVERT: C 677 MET cc_start: 0.7115 (ttt) cc_final: 0.6906 (mtt) REVERT: C 743 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7952 (mtp85) REVERT: D 300 ASP cc_start: 0.7636 (m-30) cc_final: 0.7188 (p0) REVERT: D 311 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8337 (mm-30) REVERT: D 318 LYS cc_start: 0.8267 (mttm) cc_final: 0.7776 (mmmt) REVERT: D 460 LEU cc_start: 0.8442 (mt) cc_final: 0.7565 (tt) REVERT: D 536 GLU cc_start: 0.7959 (mp0) cc_final: 0.7425 (mt-10) REVERT: D 584 TYR cc_start: 0.8968 (t80) cc_final: 0.8647 (t80) REVERT: D 674 LEU cc_start: 0.9202 (tp) cc_final: 0.8745 (mp) REVERT: B 300 ASP cc_start: 0.7585 (m-30) cc_final: 0.7179 (p0) REVERT: B 323 LEU cc_start: 0.4509 (OUTLIER) cc_final: 0.4207 (pp) REVERT: B 487 TYR cc_start: 0.8985 (t80) cc_final: 0.7644 (t80) REVERT: B 533 GLN cc_start: 0.8186 (tt0) cc_final: 0.7533 (tm-30) REVERT: B 581 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6658 (ttp) REVERT: B 674 LEU cc_start: 0.9150 (tp) cc_final: 0.8914 (tp) REVERT: B 709 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8113 (tm-30) outliers start: 39 outliers final: 33 residues processed: 458 average time/residue: 0.1182 time to fit residues: 80.3417 Evaluate side-chains 466 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 429 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 406 THR 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 533 GLN Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain D residue 406 THR 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 700 GLN Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 581 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 0.0980 chunk 107 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 700 GLN ** B 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 = 0.4361 r_free = 0.4361 target = 0.206967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134385 restraints weight = 22967.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138647 restraints weight = 11779.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141193 restraints weight = 8311.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142454 restraints weight = 6935.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143369 restraints weight = 6328.800| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 16208 Z= 0.121 Angle : 0.687 12.301 21992 Z= 0.342 Chirality : 0.042 0.214 2476 Planarity : 0.003 0.048 2692 Dihedral : 4.816 55.164 2488 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.04 % Allowed : 23.19 % Favored : 74.77 % 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: 0.59 (0.20), residues: 1904 helix: 1.86 (0.15), residues: 1160 sheet: -1.90 (0.70), residues: 60 loop : -2.09 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 499 TYR 0.020 0.001 TYR C 487 PHE 0.026 0.001 PHE D 742 TRP 0.005 0.001 TRP B 549 HIS 0.002 0.000 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00264 (16204) covalent geometry : angle 0.68711 (21984) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.98503 ( 8) hydrogen bonds : bond 0.03345 ( 910) hydrogen bonds : angle 4.18709 ( 2655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.65 seconds wall clock time: 55 minutes 57.18 seconds (3357.18 seconds total)