Starting phenix.real_space_refine on Thu Mar 5 01:38:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mz7_24085/03_2026/7mz7_24085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mz7_24085/03_2026/7mz7_24085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mz7_24085/03_2026/7mz7_24085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mz7_24085/03_2026/7mz7_24085.map" model { file = "/net/cci-nas-00/data/ceres_data/7mz7_24085/03_2026/7mz7_24085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mz7_24085/03_2026/7mz7_24085.cif" } resolution = 3.35 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= 0.002 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: 5 Type Number sf(0) Gaussians S 100 5.16 5 Na 1 4.78 5 C 11744 2.51 5 N 2864 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 17889 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4426 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 530} Chain: "D" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4426 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 530} Chain: "B" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4426 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 530} Chain: "C" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4426 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 530} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "C" 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: 4.28, per 1000 atoms: 0.24 Number of scatterers: 17889 At special positions: 0 Unit cell: (129.27, 126.768, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 Na 1 11.00 O 3180 8.00 N 2864 7.00 C 11744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 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: 1.78 Conformation dependent library (CDL) restraints added in 771.6 milliseconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 4 sheets defined 67.1% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.620A pdb=" N ASN A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.533A pdb=" N LYS A 237 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.687A pdb=" N PHE A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 4.007A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) 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 454 removed outlier: 5.028A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.592A pdb=" N ASP A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.535A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.557A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.777A pdb=" N ILE A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.920A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 712 Processing helix chain 'A' and resid 716 through 720 removed outlier: 3.985A pdb=" N ALA A 719 " --> pdb=" O MET A 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.686A pdb=" N LYS D 237 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.712A pdb=" N PHE D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.856A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) 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 454 removed outlier: 5.074A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 504 through 509 removed outlier: 3.687A pdb=" N ASP D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.604A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.544A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 575 removed outlier: 3.605A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.987A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 689 through 712 Processing helix chain 'D' and resid 716 through 720 removed outlier: 4.008A pdb=" N ALA D 719 " --> pdb=" O MET D 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.582A pdb=" N ASN B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.575A pdb=" N LYS B 237 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.778A pdb=" N PHE B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.971A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) 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 454 removed outlier: 5.067A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.711A pdb=" N ASP B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.616A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.521A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 3.533A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 599 Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.882A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 689 through 712 Processing helix chain 'B' and resid 716 through 720 removed outlier: 4.110A pdb=" N ALA B 719 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.686A pdb=" N LYS C 237 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.770A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.851A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) 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 454 removed outlier: 5.079A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.300A 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 504 through 509 removed outlier: 3.688A pdb=" N ASP C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.599A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 559 through 575 removed outlier: 3.638A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 Processing helix chain 'C' and resid 629 through 642 removed outlier: 4.001A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 689 through 712 Processing helix chain 'C' and resid 716 through 720 removed outlier: 4.025A pdb=" N ALA C 719 " --> pdb=" O MET C 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 5.492A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 373 removed outlier: 5.549A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 5.519A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.902A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2994 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: 2.72 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2779 1.31 - 1.44: 5279 1.44 - 1.57: 10103 1.57 - 1.71: 15 1.71 - 1.84: 164 Bond restraints: 18340 Sorted by residual: bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.195 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.196 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.198 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.201 0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" CAV 6EU C 901 " pdb=" CBB 6EU C 901 " ideal model delta sigma weight residual 1.330 1.541 -0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 18335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 24625 3.42 - 6.84: 207 6.84 - 10.27: 36 10.27 - 13.69: 9 13.69 - 17.11: 7 Bond angle restraints: 24884 Sorted by residual: angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAO 6EU D 901 " ideal model delta sigma weight residual 115.38 132.49 -17.11 3.00e+00 1.11e-01 3.25e+01 angle pdb=" CAN 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAO 6EU A 901 " ideal model delta sigma weight residual 115.38 132.35 -16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C SER C 711 " pdb=" N PHE C 712 " pdb=" CA PHE C 712 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.88e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 131.38 -16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 ... (remaining 24879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 10214 16.45 - 32.90: 654 32.90 - 49.35: 130 49.35 - 65.80: 32 65.80 - 82.25: 17 Dihedral angle restraints: 11047 sinusoidal: 4619 harmonic: 6428 Sorted by residual: dihedral pdb=" CA PHE A 429 " pdb=" C PHE A 429 " pdb=" N VAL A 430 " pdb=" CA VAL A 430 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TYR B 653 " pdb=" C TYR B 653 " pdb=" N ASP B 654 " pdb=" CA ASP B 654 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA TYR C 653 " pdb=" C TYR C 653 " pdb=" N ASP C 654 " pdb=" CA ASP C 654 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 11044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2760 0.131 - 0.261: 16 0.261 - 0.392: 4 0.392 - 0.522: 8 0.522 - 0.653: 4 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CAJ 6EU A 901 " pdb=" CAK 6EU A 901 " pdb=" CAN 6EU A 901 " pdb=" CAO 6EU A 901 " both_signs ideal model delta sigma weight residual False 2.66 2.00 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CAJ 6EU D 901 " pdb=" CAK 6EU D 901 " pdb=" CAN 6EU D 901 " pdb=" CAO 6EU D 901 " both_signs ideal model delta sigma weight residual False 2.66 2.00 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CAJ 6EU B 901 " pdb=" CAK 6EU B 901 " pdb=" CAN 6EU B 901 " pdb=" CAO 6EU B 901 " both_signs ideal model delta sigma weight residual False 2.66 2.02 0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2789 not shown) Planarity restraints: 3064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " -0.095 2.00e-02 2.50e+03 1.67e-01 2.78e+02 pdb=" CAV 6EU B 901 " 0.289 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " -0.094 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU C 901 " 0.094 2.00e-02 2.50e+03 1.63e-01 2.66e+02 pdb=" CAV 6EU C 901 " -0.283 2.00e-02 2.50e+03 pdb=" CBB 6EU C 901 " 0.092 2.00e-02 2.50e+03 pdb=" CBD 6EU C 901 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU A 901 " -0.092 2.00e-02 2.50e+03 1.61e-01 2.60e+02 pdb=" CAV 6EU A 901 " 0.279 2.00e-02 2.50e+03 pdb=" CBB 6EU A 901 " -0.091 2.00e-02 2.50e+03 pdb=" CBD 6EU A 901 " -0.096 2.00e-02 2.50e+03 ... (remaining 3061 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 206 2.62 - 3.19: 17113 3.19 - 3.76: 27477 3.76 - 4.33: 38310 4.33 - 4.90: 63850 Nonbonded interactions: 146956 Sorted by model distance: nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.046 3.040 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.077 3.040 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.110 3.040 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.126 3.040 nonbonded pdb=" O ILE C 672 " pdb=" ND2 ASN C 676 " model vdw 2.204 3.120 ... (remaining 146951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 185 through 901) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.830 Find NCS groups from input model: 0.490 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.013 0.227 18341 Z= 0.610 Angle : 0.958 17.110 24886 Z= 0.482 Chirality : 0.058 0.653 2792 Planarity : 0.008 0.167 3064 Dihedral : 12.078 82.246 6916 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.71 % Favored : 94.11 % Rotamer: Outliers : 0.41 % Allowed : 3.37 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2172 helix: 1.16 (0.14), residues: 1348 sheet: -1.26 (0.49), residues: 76 loop : -1.61 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 355 TYR 0.019 0.002 TYR D 511 PHE 0.019 0.002 PHE C 649 TRP 0.008 0.001 TRP A 749 HIS 0.005 0.002 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.01286 (18340) covalent geometry : angle 0.95778 (24884) SS BOND : bond 0.00563 ( 1) SS BOND : angle 2.88641 ( 2) hydrogen bonds : bond 0.13766 ( 1032) hydrogen bonds : angle 5.68605 ( 2994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 717 time to evaluate : 0.683 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: A 310 ASN cc_start: 0.9013 (t0) cc_final: 0.8737 (t0) REVERT: A 378 HIS cc_start: 0.7733 (p-80) cc_final: 0.7478 (p-80) REVERT: A 394 SER cc_start: 0.8830 (m) cc_final: 0.8522 (p) REVERT: A 420 ARG cc_start: 0.8382 (mtt-85) cc_final: 0.8128 (mtp85) REVERT: A 465 LEU cc_start: 0.8934 (tp) cc_final: 0.8389 (tp) REVERT: A 483 SER cc_start: 0.9512 (m) cc_final: 0.9217 (p) REVERT: A 562 MET cc_start: 0.8673 (mmm) cc_final: 0.8419 (mmm) REVERT: A 687 ASN cc_start: 0.9067 (t0) cc_final: 0.8645 (t0) REVERT: A 688 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8498 (mptt) REVERT: D 236 PHE cc_start: 0.8701 (m-80) cc_final: 0.8500 (m-10) REVERT: D 310 ASN cc_start: 0.8833 (t0) cc_final: 0.8561 (t0) REVERT: D 394 SER cc_start: 0.8931 (m) cc_final: 0.8694 (p) REVERT: D 404 SER cc_start: 0.7732 (m) cc_final: 0.7366 (p) REVERT: D 428 ARG cc_start: 0.8456 (mmt180) cc_final: 0.8036 (mmt180) REVERT: D 536 GLU cc_start: 0.8280 (mp0) cc_final: 0.7735 (mp0) REVERT: D 561 GLN cc_start: 0.8339 (tp40) cc_final: 0.8106 (mp10) REVERT: D 687 ASN cc_start: 0.9092 (t0) cc_final: 0.8680 (t0) REVERT: D 688 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8091 (mmtp) REVERT: D 698 LYS cc_start: 0.9030 (mttp) cc_final: 0.8819 (mttm) REVERT: D 725 LEU cc_start: 0.8750 (mt) cc_final: 0.8540 (mp) REVERT: B 226 ASP cc_start: 0.8483 (t0) cc_final: 0.7861 (t0) REVERT: B 360 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.7758 (Cg_endo) REVERT: B 363 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7514 (tpp80) REVERT: B 372 TRP cc_start: 0.8846 (p-90) cc_final: 0.8626 (p-90) REVERT: B 483 SER cc_start: 0.9443 (m) cc_final: 0.9129 (p) REVERT: B 509 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: B 562 MET cc_start: 0.8739 (mmm) cc_final: 0.8511 (mmm) REVERT: B 682 MET cc_start: 0.8599 (mtp) cc_final: 0.8224 (mtm) REVERT: B 687 ASN cc_start: 0.9119 (t0) cc_final: 0.8566 (t0) REVERT: C 358 HIS cc_start: 0.7347 (m-70) cc_final: 0.6303 (m-70) REVERT: C 363 ARG cc_start: 0.7902 (tpp-160) cc_final: 0.7238 (mmm-85) REVERT: C 420 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8082 (mtp85) REVERT: C 652 ASN cc_start: 0.7803 (m-40) cc_final: 0.7467 (t0) REVERT: C 687 ASN cc_start: 0.9141 (t0) cc_final: 0.8759 (t0) REVERT: C 688 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8297 (mptt) outliers start: 8 outliers final: 4 residues processed: 722 average time/residue: 0.1542 time to fit residues: 162.6477 Evaluate side-chains 486 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 481 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain C residue 512 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 228 GLN D 393 ASN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 393 ASN C 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116163 restraints weight = 30337.623| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.81 r_work: 0.3199 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18341 Z= 0.155 Angle : 0.654 12.413 24886 Z= 0.339 Chirality : 0.041 0.196 2792 Planarity : 0.004 0.052 3064 Dihedral : 7.494 59.997 2782 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.76 % Favored : 94.06 % Rotamer: Outliers : 2.02 % Allowed : 12.60 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2172 helix: 1.70 (0.14), residues: 1352 sheet: -1.04 (0.51), residues: 76 loop : -1.37 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 420 TYR 0.021 0.001 TYR D 309 PHE 0.022 0.001 PHE D 266 TRP 0.022 0.001 TRP A 697 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00336 (18340) covalent geometry : angle 0.65261 (24884) SS BOND : bond 0.01294 ( 1) SS BOND : angle 4.77521 ( 2) hydrogen bonds : bond 0.05269 ( 1032) hydrogen bonds : angle 4.31798 ( 2994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 548 time to evaluate : 0.740 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: A 214 MET cc_start: 0.8760 (pmm) cc_final: 0.8397 (ttp) REVERT: A 309 TYR cc_start: 0.9187 (t80) cc_final: 0.8955 (t80) REVERT: A 310 ASN cc_start: 0.8903 (t0) cc_final: 0.8701 (t0) REVERT: A 343 SER cc_start: 0.9314 (m) cc_final: 0.9073 (m) REVERT: A 394 SER cc_start: 0.9072 (m) cc_final: 0.8864 (p) REVERT: A 420 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.8437 (mtp85) REVERT: A 499 ARG cc_start: 0.8097 (tpp-160) cc_final: 0.7535 (mmt-90) REVERT: A 509 ASP cc_start: 0.8089 (m-30) cc_final: 0.7817 (m-30) REVERT: A 562 MET cc_start: 0.8790 (mmm) cc_final: 0.8551 (mmm) REVERT: A 687 ASN cc_start: 0.9318 (t0) cc_final: 0.9115 (t0) REVERT: D 246 TYR cc_start: 0.7661 (t80) cc_final: 0.7385 (t80) REVERT: D 428 ARG cc_start: 0.9089 (mmt180) cc_final: 0.8853 (mmt180) REVERT: D 561 GLN cc_start: 0.8506 (tp40) cc_final: 0.8036 (mp10) REVERT: D 687 ASN cc_start: 0.9316 (t0) cc_final: 0.9114 (t0) REVERT: B 214 MET cc_start: 0.8752 (pmm) cc_final: 0.8290 (tpp) REVERT: B 226 ASP cc_start: 0.8445 (t0) cc_final: 0.7820 (t0) REVERT: B 359 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: B 372 TRP cc_start: 0.8861 (p-90) cc_final: 0.8615 (p-90) REVERT: B 509 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: B 560 GLN cc_start: 0.8803 (tp40) cc_final: 0.8514 (tp40) REVERT: C 198 TYR cc_start: 0.7632 (t80) cc_final: 0.7303 (t80) REVERT: C 372 TRP cc_start: 0.8828 (p-90) cc_final: 0.8428 (p-90) REVERT: C 420 ARG cc_start: 0.8658 (mtt-85) cc_final: 0.8373 (mtp85) REVERT: C 509 ASP cc_start: 0.8075 (m-30) cc_final: 0.7734 (m-30) REVERT: C 572 MET cc_start: 0.8584 (mmt) cc_final: 0.7988 (mmt) REVERT: C 600 GLU cc_start: 0.8148 (pm20) cc_final: 0.7813 (pm20) REVERT: C 652 ASN cc_start: 0.7990 (m-40) cc_final: 0.7380 (t0) REVERT: C 682 MET cc_start: 0.8732 (mtp) cc_final: 0.8458 (mtt) REVERT: C 687 ASN cc_start: 0.9329 (t0) cc_final: 0.9071 (t0) outliers start: 39 outliers final: 25 residues processed: 564 average time/residue: 0.1338 time to fit residues: 115.7565 Evaluate side-chains 512 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 485 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 106 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 HIS ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN C 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108779 restraints weight = 30682.033| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.87 r_work: 0.3138 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18341 Z= 0.127 Angle : 0.593 13.420 24886 Z= 0.304 Chirality : 0.040 0.163 2792 Planarity : 0.004 0.050 3064 Dihedral : 7.148 59.590 2779 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.28 % Allowed : 13.59 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2172 helix: 1.83 (0.14), residues: 1348 sheet: -0.93 (0.52), residues: 76 loop : -1.30 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 721 TYR 0.020 0.001 TYR B 374 PHE 0.016 0.001 PHE D 266 TRP 0.022 0.001 TRP A 372 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00266 (18340) covalent geometry : angle 0.59282 (24884) SS BOND : bond 0.00610 ( 1) SS BOND : angle 0.88509 ( 2) hydrogen bonds : bond 0.04461 ( 1032) hydrogen bonds : angle 4.10167 ( 2994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 518 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.8222 (t0) cc_final: 0.7482 (t0) REVERT: A 214 MET cc_start: 0.8771 (pmm) cc_final: 0.8277 (ttp) REVERT: A 246 TYR cc_start: 0.7734 (t80) cc_final: 0.7529 (t80) REVERT: A 293 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8792 (mt-10) REVERT: A 343 SER cc_start: 0.9227 (m) cc_final: 0.8978 (m) REVERT: A 391 GLU cc_start: 0.8543 (mp0) cc_final: 0.8336 (pt0) REVERT: A 394 SER cc_start: 0.9055 (m) cc_final: 0.8769 (p) REVERT: A 420 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8370 (mtp85) REVERT: A 509 ASP cc_start: 0.8040 (m-30) cc_final: 0.7616 (m-30) REVERT: A 562 MET cc_start: 0.8886 (mmm) cc_final: 0.8524 (mmt) REVERT: A 684 GLU cc_start: 0.8286 (tp30) cc_final: 0.8023 (tp30) REVERT: D 276 ASP cc_start: 0.8334 (t0) cc_final: 0.7837 (t0) REVERT: D 428 ARG cc_start: 0.9066 (mmt180) cc_final: 0.8832 (mmt180) REVERT: D 464 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7995 (mmmt) REVERT: D 491 ARG cc_start: 0.9221 (mmm160) cc_final: 0.8820 (mtp85) REVERT: D 561 GLN cc_start: 0.8494 (tp40) cc_final: 0.7994 (mp10) REVERT: D 684 GLU cc_start: 0.8169 (tp30) cc_final: 0.7918 (tp30) REVERT: D 687 ASN cc_start: 0.9294 (t0) cc_final: 0.9073 (t0) REVERT: B 213 ASN cc_start: 0.8098 (t0) cc_final: 0.7498 (t0) REVERT: B 214 MET cc_start: 0.8780 (pmm) cc_final: 0.8415 (tpp) REVERT: B 226 ASP cc_start: 0.8414 (t0) cc_final: 0.7763 (t0) REVERT: B 360 PRO cc_start: 0.8639 (Cg_exo) cc_final: 0.8281 (Cg_endo) REVERT: B 372 TRP cc_start: 0.8648 (p-90) cc_final: 0.8284 (p-90) REVERT: B 491 ARG cc_start: 0.9221 (mmm160) cc_final: 0.8286 (ttp-170) REVERT: B 746 GLU cc_start: 0.8485 (tp30) cc_final: 0.8276 (tm-30) REVERT: C 198 TYR cc_start: 0.7653 (t80) cc_final: 0.7327 (t80) REVERT: C 372 TRP cc_start: 0.8749 (p-90) cc_final: 0.8300 (p-90) REVERT: C 378 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6956 (p90) REVERT: C 420 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8271 (mtp85) REVERT: C 491 ARG cc_start: 0.9166 (mmm160) cc_final: 0.8815 (mtp85) REVERT: C 509 ASP cc_start: 0.7965 (m-30) cc_final: 0.7603 (m-30) REVERT: C 524 LEU cc_start: 0.9174 (mt) cc_final: 0.8971 (mt) REVERT: C 562 MET cc_start: 0.8708 (mmt) cc_final: 0.8265 (mmt) REVERT: C 572 MET cc_start: 0.8490 (mmt) cc_final: 0.7888 (mmt) REVERT: C 584 TYR cc_start: 0.9299 (t80) cc_final: 0.9076 (t80) REVERT: C 600 GLU cc_start: 0.8239 (pm20) cc_final: 0.7820 (pm20) REVERT: C 652 ASN cc_start: 0.7785 (m-40) cc_final: 0.7163 (t0) REVERT: C 682 MET cc_start: 0.8884 (mtp) cc_final: 0.8555 (mtt) REVERT: C 684 GLU cc_start: 0.8439 (tp30) cc_final: 0.8070 (tp30) outliers start: 44 outliers final: 25 residues processed: 535 average time/residue: 0.1268 time to fit residues: 106.1342 Evaluate side-chains 497 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 471 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 122 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 204 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS A 260 GLN A 727 GLN D 206 HIS D 652 ASN B 727 GLN C 687 ASN C 727 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104394 restraints weight = 30693.103| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.88 r_work: 0.3074 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18341 Z= 0.189 Angle : 0.608 14.234 24886 Z= 0.314 Chirality : 0.040 0.196 2792 Planarity : 0.004 0.052 3064 Dihedral : 6.949 59.854 2776 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.22 % Allowed : 14.42 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2172 helix: 1.82 (0.14), residues: 1356 sheet: -0.81 (0.53), residues: 76 loop : -1.34 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 721 TYR 0.011 0.001 TYR D 309 PHE 0.014 0.001 PHE B 720 TRP 0.015 0.001 TRP A 372 HIS 0.024 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00430 (18340) covalent geometry : angle 0.60753 (24884) SS BOND : bond 0.00382 ( 1) SS BOND : angle 1.73232 ( 2) hydrogen bonds : bond 0.04560 ( 1032) hydrogen bonds : angle 4.14553 ( 2994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 472 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.8217 (t0) cc_final: 0.7485 (t0) REVERT: A 214 MET cc_start: 0.8864 (pmm) cc_final: 0.8277 (ttp) REVERT: A 293 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8818 (mt-10) REVERT: A 343 SER cc_start: 0.9208 (m) cc_final: 0.8979 (m) REVERT: A 372 TRP cc_start: 0.8040 (p-90) cc_final: 0.7604 (p-90) REVERT: A 394 SER cc_start: 0.9132 (m) cc_final: 0.8829 (p) REVERT: A 420 ARG cc_start: 0.8715 (mtt-85) cc_final: 0.8365 (mtp85) REVERT: A 445 MET cc_start: 0.9473 (mmm) cc_final: 0.9220 (mmm) REVERT: A 509 ASP cc_start: 0.8186 (m-30) cc_final: 0.7756 (m-30) REVERT: A 562 MET cc_start: 0.8997 (mmm) cc_final: 0.8680 (mmt) REVERT: A 684 GLU cc_start: 0.8443 (tp30) cc_final: 0.8196 (tp30) REVERT: D 211 ARG cc_start: 0.8837 (mmp80) cc_final: 0.8617 (mmt180) REVERT: D 323 LEU cc_start: 0.8438 (tp) cc_final: 0.8197 (tp) REVERT: D 363 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7640 (mmm-85) REVERT: D 464 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8053 (mmmt) REVERT: D 491 ARG cc_start: 0.9203 (mmm160) cc_final: 0.8788 (mtp85) REVERT: D 561 GLN cc_start: 0.8573 (tp40) cc_final: 0.8034 (mp10) REVERT: D 684 GLU cc_start: 0.8273 (tp30) cc_final: 0.8025 (tp30) REVERT: D 687 ASN cc_start: 0.9353 (t0) cc_final: 0.9123 (t0) REVERT: B 213 ASN cc_start: 0.8196 (t0) cc_final: 0.7387 (t0) REVERT: B 214 MET cc_start: 0.8802 (pmm) cc_final: 0.8427 (tpp) REVERT: B 216 LEU cc_start: 0.9442 (mt) cc_final: 0.9065 (mt) REVERT: B 226 ASP cc_start: 0.8432 (t0) cc_final: 0.7792 (t0) REVERT: B 359 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7627 (tm-30) REVERT: B 372 TRP cc_start: 0.8653 (p-90) cc_final: 0.8274 (p-90) REVERT: B 491 ARG cc_start: 0.9207 (mmm160) cc_final: 0.8359 (ttp-170) REVERT: B 631 TYR cc_start: 0.8649 (t80) cc_final: 0.8327 (t80) REVERT: C 198 TYR cc_start: 0.7702 (t80) cc_final: 0.7380 (t80) REVERT: C 293 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8754 (mt-10) REVERT: C 372 TRP cc_start: 0.8713 (p-90) cc_final: 0.8269 (p-90) REVERT: C 378 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.6702 (p90) REVERT: C 420 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8286 (mtp85) REVERT: C 491 ARG cc_start: 0.9201 (mmm160) cc_final: 0.8833 (mtp85) REVERT: C 509 ASP cc_start: 0.8056 (m-30) cc_final: 0.7678 (m-30) REVERT: C 600 GLU cc_start: 0.8348 (pm20) cc_final: 0.7893 (pm20) REVERT: C 652 ASN cc_start: 0.7712 (m-40) cc_final: 0.7178 (t0) outliers start: 62 outliers final: 42 residues processed: 506 average time/residue: 0.1276 time to fit residues: 101.3785 Evaluate side-chains 510 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 467 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 704 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 108 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 HIS ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107237 restraints weight = 30307.991| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.89 r_work: 0.3117 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18341 Z= 0.119 Angle : 0.585 15.585 24886 Z= 0.296 Chirality : 0.039 0.164 2792 Planarity : 0.004 0.051 3064 Dihedral : 6.558 59.462 2776 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.65 % Allowed : 15.61 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 2172 helix: 1.88 (0.14), residues: 1352 sheet: -0.78 (0.55), residues: 76 loop : -1.31 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 420 TYR 0.013 0.001 TYR A 309 PHE 0.014 0.001 PHE A 304 TRP 0.015 0.001 TRP A 372 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00248 (18340) covalent geometry : angle 0.58482 (24884) SS BOND : bond 0.00424 ( 1) SS BOND : angle 1.57405 ( 2) hydrogen bonds : bond 0.04116 ( 1032) hydrogen bonds : angle 4.00648 ( 2994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 489 time to evaluate : 0.694 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: A 214 MET cc_start: 0.8810 (pmm) cc_final: 0.8236 (ttp) REVERT: A 293 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8825 (mt-10) REVERT: A 310 ASN cc_start: 0.8793 (t0) cc_final: 0.8592 (t0) REVERT: A 343 SER cc_start: 0.9177 (m) cc_final: 0.8948 (m) REVERT: A 372 TRP cc_start: 0.8040 (p-90) cc_final: 0.7440 (p-90) REVERT: A 394 SER cc_start: 0.9112 (m) cc_final: 0.8810 (p) REVERT: A 420 ARG cc_start: 0.8677 (mtt-85) cc_final: 0.8330 (mtp85) REVERT: A 509 ASP cc_start: 0.8098 (m-30) cc_final: 0.7721 (m-30) REVERT: A 562 MET cc_start: 0.8918 (mmm) cc_final: 0.8669 (mmm) REVERT: A 652 ASN cc_start: 0.8129 (t0) cc_final: 0.7792 (t0) REVERT: A 684 GLU cc_start: 0.8431 (tp30) cc_final: 0.8172 (tp30) REVERT: D 228 GLN cc_start: 0.9156 (mm110) cc_final: 0.8934 (mm-40) REVERT: D 323 LEU cc_start: 0.8467 (tp) cc_final: 0.8204 (tp) REVERT: D 372 TRP cc_start: 0.8539 (p-90) cc_final: 0.8233 (p-90) REVERT: D 464 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8058 (mmmt) REVERT: D 491 ARG cc_start: 0.9192 (mmm160) cc_final: 0.8781 (mtp85) REVERT: D 561 GLN cc_start: 0.8509 (tp40) cc_final: 0.7948 (mp10) REVERT: D 684 GLU cc_start: 0.8282 (tp30) cc_final: 0.7995 (tp30) REVERT: D 687 ASN cc_start: 0.9337 (t0) cc_final: 0.9111 (t0) REVERT: B 213 ASN cc_start: 0.8247 (t0) cc_final: 0.7382 (t0) REVERT: B 214 MET cc_start: 0.8749 (pmm) cc_final: 0.8419 (tpp) REVERT: B 216 LEU cc_start: 0.9443 (mt) cc_final: 0.9055 (mt) REVERT: B 226 ASP cc_start: 0.8440 (t0) cc_final: 0.7812 (t0) REVERT: B 359 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 372 TRP cc_start: 0.8589 (p-90) cc_final: 0.8243 (p-90) REVERT: B 491 ARG cc_start: 0.9193 (mmm160) cc_final: 0.8362 (ttp-170) REVERT: B 631 TYR cc_start: 0.8578 (t80) cc_final: 0.8223 (t80) REVERT: C 198 TYR cc_start: 0.7649 (t80) cc_final: 0.7336 (t80) REVERT: C 293 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8764 (mt-10) REVERT: C 372 TRP cc_start: 0.8723 (p-90) cc_final: 0.8309 (p-90) REVERT: C 378 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6998 (p-80) REVERT: C 420 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8247 (mtp85) REVERT: C 491 ARG cc_start: 0.9168 (mmm160) cc_final: 0.8829 (mtp85) REVERT: C 509 ASP cc_start: 0.7918 (m-30) cc_final: 0.7589 (m-30) REVERT: C 584 TYR cc_start: 0.9249 (t80) cc_final: 0.8998 (t80) REVERT: C 600 GLU cc_start: 0.8323 (pm20) cc_final: 0.7952 (pm20) REVERT: C 652 ASN cc_start: 0.7609 (m-40) cc_final: 0.7250 (t0) outliers start: 51 outliers final: 30 residues processed: 511 average time/residue: 0.1225 time to fit residues: 98.9869 Evaluate side-chains 494 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 463 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 167 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN D 206 HIS D 560 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106545 restraints weight = 30300.210| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.87 r_work: 0.3107 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18341 Z= 0.143 Angle : 0.596 15.061 24886 Z= 0.301 Chirality : 0.040 0.159 2792 Planarity : 0.004 0.052 3064 Dihedral : 6.337 59.072 2776 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.90 % Allowed : 15.77 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2172 helix: 1.85 (0.14), residues: 1356 sheet: -0.68 (0.56), residues: 76 loop : -1.31 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 420 TYR 0.015 0.001 TYR A 309 PHE 0.015 0.001 PHE A 304 TRP 0.023 0.001 TRP D 749 HIS 0.006 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00321 (18340) covalent geometry : angle 0.59551 (24884) SS BOND : bond 0.00388 ( 1) SS BOND : angle 1.50641 ( 2) hydrogen bonds : bond 0.04161 ( 1032) hydrogen bonds : angle 4.03075 ( 2994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 473 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8758 (pmm) cc_final: 0.8169 (ttp) REVERT: A 343 SER cc_start: 0.9182 (m) cc_final: 0.8960 (m) REVERT: A 372 TRP cc_start: 0.8122 (p-90) cc_final: 0.7570 (p-90) REVERT: A 394 SER cc_start: 0.9117 (m) cc_final: 0.8814 (p) REVERT: A 420 ARG cc_start: 0.8704 (mtt-85) cc_final: 0.8345 (mtp85) REVERT: A 460 LEU cc_start: 0.8497 (mt) cc_final: 0.8190 (pp) REVERT: A 509 ASP cc_start: 0.8144 (m-30) cc_final: 0.7729 (m-30) REVERT: A 562 MET cc_start: 0.8956 (mmm) cc_final: 0.8734 (mmm) REVERT: A 652 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7835 (t0) REVERT: A 684 GLU cc_start: 0.8433 (tp30) cc_final: 0.8180 (tp30) REVERT: D 228 GLN cc_start: 0.9170 (mm110) cc_final: 0.8943 (mm-40) REVERT: D 323 LEU cc_start: 0.8460 (tp) cc_final: 0.8201 (tp) REVERT: D 363 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7626 (mmm-85) REVERT: D 372 TRP cc_start: 0.8563 (p-90) cc_final: 0.8248 (p-90) REVERT: D 445 MET cc_start: 0.9575 (mmm) cc_final: 0.9360 (mmm) REVERT: D 464 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8046 (mmmt) REVERT: D 491 ARG cc_start: 0.9189 (mmm160) cc_final: 0.8775 (mtp85) REVERT: D 684 GLU cc_start: 0.8271 (tp30) cc_final: 0.7933 (tp30) REVERT: D 687 ASN cc_start: 0.9314 (t0) cc_final: 0.9101 (t0) REVERT: B 213 ASN cc_start: 0.8288 (t0) cc_final: 0.7394 (t0) REVERT: B 214 MET cc_start: 0.8723 (pmm) cc_final: 0.8401 (tpp) REVERT: B 216 LEU cc_start: 0.9456 (mt) cc_final: 0.9040 (mt) REVERT: B 226 ASP cc_start: 0.8450 (t0) cc_final: 0.7831 (t0) REVERT: B 359 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7531 (tm-30) REVERT: B 372 TRP cc_start: 0.8594 (p-90) cc_final: 0.8248 (p-90) REVERT: B 491 ARG cc_start: 0.9184 (mmm160) cc_final: 0.8345 (ttp-170) REVERT: B 631 TYR cc_start: 0.8583 (t80) cc_final: 0.8226 (t80) REVERT: C 198 TYR cc_start: 0.7727 (t80) cc_final: 0.7385 (t80) REVERT: C 372 TRP cc_start: 0.8736 (p-90) cc_final: 0.8319 (p-90) REVERT: C 420 ARG cc_start: 0.8647 (mtt-85) cc_final: 0.8252 (mtp85) REVERT: C 491 ARG cc_start: 0.9173 (mmm160) cc_final: 0.8754 (mtp-110) REVERT: C 509 ASP cc_start: 0.7959 (m-30) cc_final: 0.7605 (m-30) REVERT: C 600 GLU cc_start: 0.8369 (pm20) cc_final: 0.7975 (pm20) REVERT: C 652 ASN cc_start: 0.7510 (m-40) cc_final: 0.7218 (t0) outliers start: 56 outliers final: 42 residues processed: 497 average time/residue: 0.1219 time to fit residues: 95.6578 Evaluate side-chains 501 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 458 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 28 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106972 restraints weight = 30484.477| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.86 r_work: 0.3107 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18341 Z= 0.149 Angle : 0.604 14.827 24886 Z= 0.305 Chirality : 0.040 0.246 2792 Planarity : 0.004 0.053 3064 Dihedral : 6.090 57.936 2776 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.27 % Allowed : 15.98 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2172 helix: 1.84 (0.14), residues: 1356 sheet: -0.66 (0.59), residues: 76 loop : -1.31 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 420 TYR 0.017 0.001 TYR A 309 PHE 0.016 0.001 PHE B 496 TRP 0.017 0.001 TRP C 749 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00333 (18340) covalent geometry : angle 0.60408 (24884) SS BOND : bond 0.00407 ( 1) SS BOND : angle 1.61914 ( 2) hydrogen bonds : bond 0.04163 ( 1032) hydrogen bonds : angle 4.01775 ( 2994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 464 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8644 (pmm) cc_final: 0.8249 (ttp) REVERT: A 293 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8633 (mt-10) REVERT: A 343 SER cc_start: 0.9241 (m) cc_final: 0.9039 (m) REVERT: A 372 TRP cc_start: 0.8186 (p-90) cc_final: 0.7645 (p-90) REVERT: A 394 SER cc_start: 0.9120 (m) cc_final: 0.8825 (p) REVERT: A 420 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8374 (mtp85) REVERT: A 460 LEU cc_start: 0.8467 (mt) cc_final: 0.8247 (pp) REVERT: A 509 ASP cc_start: 0.8158 (m-30) cc_final: 0.7770 (m-30) REVERT: A 562 MET cc_start: 0.8929 (mmm) cc_final: 0.8714 (mmm) REVERT: A 652 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7865 (t0) REVERT: A 684 GLU cc_start: 0.8436 (tp30) cc_final: 0.8198 (tp30) REVERT: D 228 GLN cc_start: 0.9153 (mm110) cc_final: 0.8924 (mm-40) REVERT: D 323 LEU cc_start: 0.8476 (tp) cc_final: 0.8206 (tp) REVERT: D 372 TRP cc_start: 0.8630 (p-90) cc_final: 0.8340 (p-90) REVERT: D 464 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8011 (mmmt) REVERT: D 491 ARG cc_start: 0.9214 (mmm160) cc_final: 0.8804 (mtp85) REVERT: D 684 GLU cc_start: 0.8318 (tp30) cc_final: 0.8036 (tp30) REVERT: B 213 ASN cc_start: 0.8318 (t0) cc_final: 0.7735 (t0) REVERT: B 226 ASP cc_start: 0.8378 (t0) cc_final: 0.7918 (t70) REVERT: B 359 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7578 (tm-30) REVERT: B 372 TRP cc_start: 0.8672 (p-90) cc_final: 0.8338 (p-90) REVERT: B 491 ARG cc_start: 0.9223 (mmm160) cc_final: 0.8386 (ttp-170) REVERT: B 631 TYR cc_start: 0.8575 (t80) cc_final: 0.8213 (t80) REVERT: C 198 TYR cc_start: 0.7746 (t80) cc_final: 0.7398 (t80) REVERT: C 372 TRP cc_start: 0.8755 (p-90) cc_final: 0.8333 (p-90) REVERT: C 420 ARG cc_start: 0.8614 (mtt-85) cc_final: 0.8273 (mtp85) REVERT: C 491 ARG cc_start: 0.9162 (mmm160) cc_final: 0.8724 (mtp-110) REVERT: C 509 ASP cc_start: 0.7967 (m-30) cc_final: 0.7626 (m-30) REVERT: C 600 GLU cc_start: 0.8388 (pm20) cc_final: 0.8069 (pm20) REVERT: C 652 ASN cc_start: 0.7484 (m-40) cc_final: 0.7250 (t0) outliers start: 63 outliers final: 49 residues processed: 499 average time/residue: 0.1243 time to fit residues: 98.2874 Evaluate side-chains 508 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 458 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 127 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 152 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN D 652 ASN B 748 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104386 restraints weight = 30547.381| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.85 r_work: 0.3084 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18341 Z= 0.199 Angle : 0.636 14.892 24886 Z= 0.323 Chirality : 0.041 0.258 2792 Planarity : 0.004 0.054 3064 Dihedral : 6.066 56.184 2776 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.63 % Allowed : 16.39 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2172 helix: 1.75 (0.14), residues: 1356 sheet: -0.80 (0.58), residues: 76 loop : -1.39 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 420 TYR 0.017 0.001 TYR A 309 PHE 0.015 0.001 PHE A 304 TRP 0.018 0.001 TRP C 749 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00454 (18340) covalent geometry : angle 0.63601 (24884) SS BOND : bond 0.00435 ( 1) SS BOND : angle 1.63432 ( 2) hydrogen bonds : bond 0.04497 ( 1032) hydrogen bonds : angle 4.14417 ( 2994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 455 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8738 (pmm) cc_final: 0.8161 (ttp) REVERT: A 293 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8701 (mt-10) REVERT: A 343 SER cc_start: 0.9232 (m) cc_final: 0.9028 (m) REVERT: A 372 TRP cc_start: 0.8167 (p-90) cc_final: 0.7723 (p-90) REVERT: A 394 SER cc_start: 0.9117 (m) cc_final: 0.8762 (p) REVERT: A 420 ARG cc_start: 0.8714 (mtt-85) cc_final: 0.8342 (mtp85) REVERT: A 445 MET cc_start: 0.9453 (mmm) cc_final: 0.9228 (mmm) REVERT: A 509 ASP cc_start: 0.8228 (m-30) cc_final: 0.7816 (m-30) REVERT: A 652 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7904 (t0) REVERT: A 684 GLU cc_start: 0.8466 (tp30) cc_final: 0.8226 (tp30) REVERT: D 228 GLN cc_start: 0.9200 (mm110) cc_final: 0.8962 (mm-40) REVERT: D 304 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8457 (p90) REVERT: D 323 LEU cc_start: 0.8543 (tp) cc_final: 0.8260 (tp) REVERT: D 372 TRP cc_start: 0.8643 (p-90) cc_final: 0.8322 (p-90) REVERT: D 464 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8049 (mmmt) REVERT: D 491 ARG cc_start: 0.9213 (mmm160) cc_final: 0.8795 (mtp85) REVERT: D 560 GLN cc_start: 0.9108 (tp40) cc_final: 0.8675 (tp40) REVERT: D 592 SER cc_start: 0.9586 (m) cc_final: 0.9206 (t) REVERT: D 684 GLU cc_start: 0.8425 (tp30) cc_final: 0.8187 (tp30) REVERT: D 720 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7787 (t80) REVERT: B 213 ASN cc_start: 0.8272 (t0) cc_final: 0.7715 (t0) REVERT: B 226 ASP cc_start: 0.8345 (t0) cc_final: 0.7877 (t70) REVERT: B 359 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7626 (tm-30) REVERT: B 372 TRP cc_start: 0.8685 (p-90) cc_final: 0.8335 (p-90) REVERT: B 491 ARG cc_start: 0.9199 (mmm160) cc_final: 0.8347 (ttp-170) REVERT: B 631 TYR cc_start: 0.8644 (t80) cc_final: 0.8302 (t80) REVERT: C 198 TYR cc_start: 0.7764 (t80) cc_final: 0.7352 (t80) REVERT: C 372 TRP cc_start: 0.8733 (p-90) cc_final: 0.8259 (p-90) REVERT: C 420 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.8377 (mtp85) REVERT: C 491 ARG cc_start: 0.9159 (mmm160) cc_final: 0.8716 (mtp-110) REVERT: C 509 ASP cc_start: 0.8078 (m-30) cc_final: 0.7742 (m-30) REVERT: C 584 TYR cc_start: 0.9292 (t80) cc_final: 0.9027 (t80) REVERT: C 600 GLU cc_start: 0.8453 (pm20) cc_final: 0.8090 (pm20) REVERT: C 652 ASN cc_start: 0.7518 (m-40) cc_final: 0.7239 (t0) REVERT: C 688 LYS cc_start: 0.8656 (mptt) cc_final: 0.8403 (mptt) outliers start: 70 outliers final: 60 residues processed: 492 average time/residue: 0.1248 time to fit residues: 96.8131 Evaluate side-chains 505 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 442 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 130 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 197 optimal weight: 0.2980 chunk 203 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN D 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104950 restraints weight = 30599.480| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.93 r_work: 0.3091 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18341 Z= 0.156 Angle : 0.626 15.472 24886 Z= 0.315 Chirality : 0.041 0.323 2792 Planarity : 0.004 0.053 3064 Dihedral : 5.880 53.198 2776 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.22 % Allowed : 17.22 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 2172 helix: 1.75 (0.14), residues: 1356 sheet: -0.86 (0.58), residues: 76 loop : -1.36 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 420 TYR 0.020 0.001 TYR A 309 PHE 0.021 0.001 PHE C 304 TRP 0.012 0.001 TRP C 749 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00352 (18340) covalent geometry : angle 0.62552 (24884) SS BOND : bond 0.00431 ( 1) SS BOND : angle 1.54597 ( 2) hydrogen bonds : bond 0.04307 ( 1032) hydrogen bonds : angle 4.09208 ( 2994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 460 time to evaluate : 0.675 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: A 214 MET cc_start: 0.8671 (pmm) cc_final: 0.8181 (ttp) REVERT: A 293 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8694 (mt-10) REVERT: A 372 TRP cc_start: 0.8196 (p-90) cc_final: 0.7635 (p-90) REVERT: A 394 SER cc_start: 0.9120 (m) cc_final: 0.8789 (p) REVERT: A 420 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8352 (mtp85) REVERT: A 445 MET cc_start: 0.9467 (mmm) cc_final: 0.9251 (mmm) REVERT: A 460 LEU cc_start: 0.8577 (mt) cc_final: 0.8308 (pp) REVERT: A 509 ASP cc_start: 0.8269 (m-30) cc_final: 0.7891 (m-30) REVERT: A 652 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7918 (t0) REVERT: A 684 GLU cc_start: 0.8472 (tp30) cc_final: 0.8260 (tp30) REVERT: D 304 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8387 (p90) REVERT: D 323 LEU cc_start: 0.8562 (tp) cc_final: 0.8280 (tp) REVERT: D 372 TRP cc_start: 0.8654 (p-90) cc_final: 0.8349 (p-90) REVERT: D 464 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8050 (mmmt) REVERT: D 491 ARG cc_start: 0.9205 (mmm160) cc_final: 0.8807 (mtp85) REVERT: D 560 GLN cc_start: 0.9131 (tp40) cc_final: 0.8668 (tp40) REVERT: D 592 SER cc_start: 0.9564 (m) cc_final: 0.9184 (t) REVERT: D 684 GLU cc_start: 0.8413 (tp30) cc_final: 0.8211 (tp30) REVERT: B 213 ASN cc_start: 0.8297 (t0) cc_final: 0.7714 (t0) REVERT: B 226 ASP cc_start: 0.8313 (t0) cc_final: 0.7851 (t70) REVERT: B 359 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7574 (tm-30) REVERT: B 372 TRP cc_start: 0.8681 (p-90) cc_final: 0.8337 (p-90) REVERT: B 491 ARG cc_start: 0.9210 (mmm160) cc_final: 0.8362 (ttp-170) REVERT: B 631 TYR cc_start: 0.8599 (t80) cc_final: 0.8218 (t80) REVERT: C 198 TYR cc_start: 0.7784 (t80) cc_final: 0.7381 (t80) REVERT: C 293 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8506 (mt-10) REVERT: C 372 TRP cc_start: 0.8748 (p-90) cc_final: 0.8312 (p-90) REVERT: C 420 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.8399 (mtp85) REVERT: C 491 ARG cc_start: 0.9171 (mmm160) cc_final: 0.8728 (mtp-110) REVERT: C 509 ASP cc_start: 0.7998 (m-30) cc_final: 0.7678 (m-30) REVERT: C 600 GLU cc_start: 0.8438 (pm20) cc_final: 0.8153 (pm20) REVERT: C 652 ASN cc_start: 0.7463 (m-40) cc_final: 0.7234 (t0) REVERT: C 688 LYS cc_start: 0.8626 (mptt) cc_final: 0.8373 (mptt) outliers start: 62 outliers final: 54 residues processed: 492 average time/residue: 0.1209 time to fit residues: 94.0963 Evaluate side-chains 505 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 449 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 18 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 199 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.141974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106847 restraints weight = 30244.875| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.84 r_work: 0.3107 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18341 Z= 0.139 Angle : 0.624 16.014 24886 Z= 0.313 Chirality : 0.041 0.323 2792 Planarity : 0.004 0.053 3064 Dihedral : 5.649 48.704 2776 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.01 % Allowed : 17.79 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.19), residues: 2172 helix: 1.73 (0.14), residues: 1356 sheet: -0.92 (0.57), residues: 76 loop : -1.33 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 212 TYR 0.028 0.001 TYR A 309 PHE 0.017 0.001 PHE C 304 TRP 0.010 0.001 TRP A 372 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00310 (18340) covalent geometry : angle 0.62423 (24884) SS BOND : bond 0.00417 ( 1) SS BOND : angle 1.51002 ( 2) hydrogen bonds : bond 0.04232 ( 1032) hydrogen bonds : angle 4.06105 ( 2994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 461 time to evaluate : 0.617 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: A 214 MET cc_start: 0.8679 (pmm) cc_final: 0.8161 (ttp) REVERT: A 293 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8684 (mt-10) REVERT: A 372 TRP cc_start: 0.8185 (p-90) cc_final: 0.7639 (p-90) REVERT: A 394 SER cc_start: 0.9128 (m) cc_final: 0.8802 (p) REVERT: A 420 ARG cc_start: 0.8688 (mtt-85) cc_final: 0.8349 (mtp85) REVERT: A 460 LEU cc_start: 0.8544 (mt) cc_final: 0.8287 (pp) REVERT: A 509 ASP cc_start: 0.8241 (m-30) cc_final: 0.7871 (m-30) REVERT: A 652 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7950 (t0) REVERT: A 684 GLU cc_start: 0.8455 (tp30) cc_final: 0.8241 (tp30) REVERT: D 304 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8276 (p90) REVERT: D 323 LEU cc_start: 0.8572 (tp) cc_final: 0.8283 (tp) REVERT: D 372 TRP cc_start: 0.8659 (p-90) cc_final: 0.8352 (p-90) REVERT: D 464 LYS cc_start: 0.8334 (mmtt) cc_final: 0.8051 (mmmt) REVERT: D 491 ARG cc_start: 0.9205 (mmm160) cc_final: 0.8806 (mtp85) REVERT: D 560 GLN cc_start: 0.9133 (tp40) cc_final: 0.8662 (tp40) REVERT: D 592 SER cc_start: 0.9565 (m) cc_final: 0.9192 (t) REVERT: D 720 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7676 (t80) REVERT: B 213 ASN cc_start: 0.8293 (t0) cc_final: 0.7711 (t0) REVERT: B 226 ASP cc_start: 0.8312 (t0) cc_final: 0.7860 (t70) REVERT: B 359 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7666 (tm-30) REVERT: B 372 TRP cc_start: 0.8675 (p-90) cc_final: 0.8335 (p-90) REVERT: B 491 ARG cc_start: 0.9196 (mmm160) cc_final: 0.8346 (ttp-170) REVERT: B 631 TYR cc_start: 0.8566 (t80) cc_final: 0.8192 (t80) REVERT: C 198 TYR cc_start: 0.7811 (t80) cc_final: 0.7366 (t80) REVERT: C 293 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8485 (mt-10) REVERT: C 372 TRP cc_start: 0.8710 (p-90) cc_final: 0.8261 (p-90) REVERT: C 420 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.8381 (mtp85) REVERT: C 491 ARG cc_start: 0.9169 (mmm160) cc_final: 0.8729 (mtp-110) REVERT: C 509 ASP cc_start: 0.7982 (m-30) cc_final: 0.7679 (m-30) REVERT: C 584 TYR cc_start: 0.9270 (t80) cc_final: 0.8920 (t80) REVERT: C 600 GLU cc_start: 0.8416 (pm20) cc_final: 0.8166 (pm20) REVERT: C 652 ASN cc_start: 0.7438 (m-40) cc_final: 0.7201 (t0) REVERT: C 688 LYS cc_start: 0.8637 (mptt) cc_final: 0.8286 (mptt) outliers start: 58 outliers final: 53 residues processed: 489 average time/residue: 0.1219 time to fit residues: 94.2732 Evaluate side-chains 504 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 448 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 213 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 81 optimal weight: 0.0570 chunk 146 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106484 restraints weight = 30422.497| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.85 r_work: 0.3106 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18341 Z= 0.148 Angle : 0.635 16.024 24886 Z= 0.319 Chirality : 0.042 0.322 2792 Planarity : 0.004 0.053 3064 Dihedral : 5.466 42.793 2776 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.37 % Allowed : 17.53 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2172 helix: 1.69 (0.14), residues: 1356 sheet: -0.90 (0.58), residues: 76 loop : -1.34 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 211 TYR 0.025 0.001 TYR A 309 PHE 0.021 0.001 PHE C 304 TRP 0.020 0.001 TRP C 749 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00335 (18340) covalent geometry : angle 0.63469 (24884) SS BOND : bond 0.00425 ( 1) SS BOND : angle 1.53033 ( 2) hydrogen bonds : bond 0.04236 ( 1032) hydrogen bonds : angle 4.08575 ( 2994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4518.09 seconds wall clock time: 78 minutes 10.12 seconds (4690.12 seconds total)