Starting phenix.real_space_refine on Thu Mar 5 00:41:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mzd_24090/03_2026/7mzd_24090.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mzd_24090/03_2026/7mzd_24090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mzd_24090/03_2026/7mzd_24090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mzd_24090/03_2026/7mzd_24090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mzd_24090/03_2026/7mzd_24090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mzd_24090/03_2026/7mzd_24090.map" } resolution = 2.9 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 2 4.78 5 C 11488 2.51 5 N 2800 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 17486 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "D" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "B" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "C" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' NA': 2, '6EU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.24 Number of scatterers: 17486 At special positions: 0 Unit cell: (125.934, 125.934, 112.59, 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 2 11.00 O 3096 8.00 N 2800 7.00 C 11488 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=2.03 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: 1.59 Conformation dependent library (CDL) restraints added in 786.2 milliseconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 4 sheets defined 66.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... 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 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 294 Processing helix chain 'A' and resid 298 through 320 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: 3.625A 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 408 through 413 removed outlier: 4.445A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 removed outlier: 4.152A 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: 4.136A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.779A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.633A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 576 through 599 removed outlier: 3.515A pdb=" N PHE A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 655 through 683 Processing helix chain 'A' and resid 687 through 712 removed outlier: 3.968A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) 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 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 294 Processing helix chain 'D' and resid 298 through 320 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: 3.584A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 removed outlier: 4.179A 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: 3.872A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.776A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.634A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 576 through 599 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 655 through 683 Processing helix chain 'D' and resid 687 through 712 removed outlier: 3.688A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (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 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 294 Processing helix chain 'B' and resid 298 through 320 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: 3.652A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.471A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 454 removed outlier: 5.360A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.206A 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: 3.860A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.775A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.636A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 576 through 599 removed outlier: 3.510A pdb=" N PHE B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.883A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 683 Processing helix chain 'B' and resid 687 through 712 removed outlier: 3.727A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) 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 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 294 Processing helix chain 'C' and resid 298 through 320 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: 3.587A 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 408 through 413 removed outlier: 4.431A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 removed outlier: 4.133A 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: 4.115A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.780A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.612A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.714A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 4.025A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 683 Processing helix chain 'C' and resid 687 through 712 removed outlier: 3.734A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.737A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.847A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.720A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.835A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2991 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: 2.86 Time building geometry restraints manager: 2.03 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: 2701 1.31 - 1.44: 5136 1.44 - 1.57: 9903 1.57 - 1.70: 20 1.70 - 1.83: 164 Bond restraints: 17924 Sorted by residual: bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.199 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.199 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.199 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.199 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAV 6EU D 901 " pdb=" CBB 6EU D 901 " ideal model delta sigma weight residual 1.330 1.521 -0.191 2.00e-02 2.50e+03 9.09e+01 ... (remaining 17919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 24047 2.93 - 5.86: 218 5.86 - 8.79: 30 8.79 - 11.72: 17 11.72 - 14.65: 8 Bond angle restraints: 24320 Sorted by residual: angle pdb=" CAN 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAO 6EU A 901 " ideal model delta sigma weight residual 115.38 130.03 -14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 129.98 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAO 6EU D 901 " ideal model delta sigma weight residual 115.38 129.91 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAO 6EU C 901 " ideal model delta sigma weight residual 115.38 129.88 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 ... (remaining 24315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10267 17.95 - 35.90: 416 35.90 - 53.85: 96 53.85 - 71.80: 9 71.80 - 89.75: 11 Dihedral angle restraints: 10799 sinusoidal: 4531 harmonic: 6268 Sorted by residual: dihedral pdb=" CA PHE D 712 " pdb=" C PHE D 712 " pdb=" N LEU D 713 " pdb=" CA LEU D 713 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE B 712 " pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta harmonic sigma weight residual 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 10796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2697 0.127 - 0.254: 15 0.254 - 0.382: 4 0.382 - 0.509: 8 0.509 - 0.636: 4 Chirality restraints: 2728 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 2.02 0.64 2.00e-01 2.50e+01 1.01e+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 0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CAJ 6EU C 901 " pdb=" CAK 6EU C 901 " pdb=" CAN 6EU C 901 " pdb=" CAO 6EU C 901 " both_signs ideal model delta sigma weight residual False 2.66 2.02 0.63 2.00e-01 2.50e+01 9.99e+00 ... (remaining 2725 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " -0.098 2.00e-02 2.50e+03 1.72e-01 2.96e+02 pdb=" CAV 6EU B 901 " 0.298 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " -0.100 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 D 901 " 0.098 2.00e-02 2.50e+03 1.72e-01 2.95e+02 pdb=" CAV 6EU D 901 " -0.298 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " 0.100 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU A 901 " -0.098 2.00e-02 2.50e+03 1.71e-01 2.93e+02 pdb=" CAV 6EU A 901 " 0.297 2.00e-02 2.50e+03 pdb=" CBB 6EU A 901 " -0.100 2.00e-02 2.50e+03 pdb=" CBD 6EU A 901 " -0.099 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3756 2.78 - 3.31: 17407 3.31 - 3.84: 29128 3.84 - 4.37: 34460 4.37 - 4.90: 59138 Nonbonded interactions: 143889 Sorted by model distance: nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.299 3.040 nonbonded pdb=" O GLY A 643 " pdb="NA NA A 902 " model vdw 2.334 2.470 nonbonded pdb=" O GLY B 643 " pdb="NA NA A 902 " model vdw 2.336 2.470 nonbonded pdb=" O GLY C 643 " pdb="NA NA A 902 " model vdw 2.341 2.470 ... (remaining 143884 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 198 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.630 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.223 17925 Z= 0.494 Angle : 0.791 14.649 24322 Z= 0.380 Chirality : 0.053 0.636 2728 Planarity : 0.007 0.172 2992 Dihedral : 10.897 89.753 6772 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.59 % Allowed : 0.48 % Favored : 98.94 % 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: 1.32 (0.18), residues: 2120 helix: 2.09 (0.14), residues: 1288 sheet: -0.44 (0.50), residues: 84 loop : -1.19 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.012 0.001 TYR A 511 PHE 0.022 0.002 PHE C 304 TRP 0.008 0.001 TRP A 749 HIS 0.002 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01003 (17924) covalent geometry : angle 0.79052 (24320) SS BOND : bond 0.00190 ( 1) SS BOND : angle 2.14984 ( 2) hydrogen bonds : bond 0.11640 ( 1034) hydrogen bonds : angle 5.05645 ( 2991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 646 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8511 (mt0) cc_final: 0.8123 (mt0) REVERT: A 272 TRP cc_start: 0.8323 (m-90) cc_final: 0.7971 (m-90) REVERT: A 273 GLN cc_start: 0.8249 (tp40) cc_final: 0.7927 (tp-100) REVERT: A 378 HIS cc_start: 0.8189 (p-80) cc_final: 0.7858 (p90) REVERT: A 383 ASP cc_start: 0.7822 (t0) cc_final: 0.7534 (t0) REVERT: A 385 SER cc_start: 0.8469 (t) cc_final: 0.8167 (m) REVERT: A 406 THR cc_start: 0.8613 (m) cc_final: 0.8398 (m) REVERT: A 408 ASN cc_start: 0.8321 (m-40) cc_final: 0.8050 (m-40) REVERT: A 506 LEU cc_start: 0.9157 (tp) cc_final: 0.8866 (tp) REVERT: A 536 GLU cc_start: 0.8833 (mp0) cc_final: 0.8617 (mp0) REVERT: A 741 CYS cc_start: 0.8321 (m) cc_final: 0.8074 (m) REVERT: A 748 ASN cc_start: 0.9077 (t0) cc_final: 0.8718 (t0) REVERT: D 273 GLN cc_start: 0.8142 (tp40) cc_final: 0.7887 (tp-100) REVERT: D 378 HIS cc_start: 0.8374 (p-80) cc_final: 0.8065 (p90) REVERT: D 385 SER cc_start: 0.8941 (t) cc_final: 0.8615 (m) REVERT: D 506 LEU cc_start: 0.9194 (tp) cc_final: 0.8886 (tp) REVERT: D 509 ASP cc_start: 0.7833 (t0) cc_final: 0.7511 (t0) REVERT: D 536 GLU cc_start: 0.8834 (mp0) cc_final: 0.8612 (mp0) REVERT: D 748 ASN cc_start: 0.9053 (t0) cc_final: 0.8736 (t0) REVERT: B 260 GLN cc_start: 0.8485 (mt0) cc_final: 0.8153 (mt0) REVERT: B 266 PHE cc_start: 0.8500 (t80) cc_final: 0.8138 (t80) REVERT: B 378 HIS cc_start: 0.8150 (p-80) cc_final: 0.7851 (p90) REVERT: B 385 SER cc_start: 0.8607 (t) cc_final: 0.8304 (m) REVERT: B 506 LEU cc_start: 0.9180 (tp) cc_final: 0.8882 (tp) REVERT: B 509 ASP cc_start: 0.7866 (t0) cc_final: 0.7477 (t0) REVERT: B 536 GLU cc_start: 0.8838 (mp0) cc_final: 0.8630 (mp0) REVERT: B 748 ASN cc_start: 0.9068 (t0) cc_final: 0.8719 (t0) REVERT: C 260 GLN cc_start: 0.8506 (mt0) cc_final: 0.8124 (mt0) REVERT: C 266 PHE cc_start: 0.8476 (t80) cc_final: 0.8224 (t80) REVERT: C 378 HIS cc_start: 0.8404 (p-80) cc_final: 0.8065 (p90) REVERT: C 383 ASP cc_start: 0.7912 (t0) cc_final: 0.7556 (t0) REVERT: C 385 SER cc_start: 0.8883 (t) cc_final: 0.8581 (m) REVERT: C 406 THR cc_start: 0.8623 (m) cc_final: 0.8402 (m) REVERT: C 506 LEU cc_start: 0.9176 (tp) cc_final: 0.8863 (tp) REVERT: C 536 GLU cc_start: 0.8826 (mp0) cc_final: 0.8624 (mp0) REVERT: C 741 CYS cc_start: 0.8420 (m) cc_final: 0.8150 (m) REVERT: C 748 ASN cc_start: 0.8974 (t0) cc_final: 0.8717 (t0) outliers start: 11 outliers final: 0 residues processed: 649 average time/residue: 0.6315 time to fit residues: 453.9931 Evaluate side-chains 412 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 232 ASN A 393 ASN A 408 ASN A 560 GLN ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN D 260 GLN D 393 ASN B 206 HIS B 228 GLN B 269 GLN B 310 ASN B 560 GLN B 561 GLN C 206 HIS C 310 ASN C 560 GLN C 561 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.086970 restraints weight = 25810.665| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.32 r_work: 0.2752 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17925 Z= 0.168 Angle : 0.615 9.881 24322 Z= 0.316 Chirality : 0.040 0.157 2728 Planarity : 0.004 0.042 2992 Dihedral : 7.431 59.877 2720 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.45 % Allowed : 13.09 % Favored : 84.47 % 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: 1.87 (0.19), residues: 2120 helix: 2.54 (0.14), residues: 1280 sheet: -0.16 (0.55), residues: 76 loop : -0.96 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 491 TYR 0.011 0.001 TYR D 627 PHE 0.015 0.001 PHE D 489 TRP 0.010 0.001 TRP A 272 HIS 0.005 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00389 (17924) covalent geometry : angle 0.61437 (24320) SS BOND : bond 0.00538 ( 1) SS BOND : angle 1.60666 ( 2) hydrogen bonds : bond 0.04440 ( 1034) hydrogen bonds : angle 3.97292 ( 2991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 444 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7262 (mp-120) REVERT: A 246 TYR cc_start: 0.8998 (t80) cc_final: 0.8587 (t80) REVERT: A 260 GLN cc_start: 0.8075 (mt0) cc_final: 0.7677 (mt0) REVERT: A 272 TRP cc_start: 0.8032 (m-90) cc_final: 0.7605 (m-90) REVERT: A 273 GLN cc_start: 0.8353 (tp40) cc_final: 0.7892 (tp40) REVERT: A 378 HIS cc_start: 0.8102 (p-80) cc_final: 0.7819 (p90) REVERT: A 383 ASP cc_start: 0.8328 (t0) cc_final: 0.7984 (t0) REVERT: A 385 SER cc_start: 0.8721 (t) cc_final: 0.8512 (m) REVERT: A 406 THR cc_start: 0.8751 (m) cc_final: 0.8508 (m) REVERT: A 408 ASN cc_start: 0.8723 (m110) cc_final: 0.8505 (m-40) REVERT: A 420 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8555 (mtt90) REVERT: A 428 ARG cc_start: 0.8924 (ttm110) cc_final: 0.8673 (ttm110) REVERT: A 572 MET cc_start: 0.9105 (tpp) cc_final: 0.8743 (tpp) REVERT: A 741 CYS cc_start: 0.8896 (m) cc_final: 0.8561 (m) REVERT: A 748 ASN cc_start: 0.9074 (t0) cc_final: 0.8678 (t0) REVERT: D 228 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7188 (mp-120) REVERT: D 246 TYR cc_start: 0.9001 (t80) cc_final: 0.8649 (t80) REVERT: D 273 GLN cc_start: 0.8192 (tp40) cc_final: 0.7695 (tp40) REVERT: D 293 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8727 (mm-30) REVERT: D 308 MET cc_start: 0.9434 (tpp) cc_final: 0.9182 (tpp) REVERT: D 471 ASP cc_start: 0.8673 (m-30) cc_final: 0.8218 (t0) REVERT: D 748 ASN cc_start: 0.9108 (t0) cc_final: 0.8709 (t0) REVERT: B 228 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7278 (mp-120) REVERT: B 246 TYR cc_start: 0.8942 (t80) cc_final: 0.8590 (t80) REVERT: B 260 GLN cc_start: 0.8172 (mt0) cc_final: 0.7734 (mt0) REVERT: B 315 LEU cc_start: 0.9220 (mm) cc_final: 0.8930 (mt) REVERT: B 408 ASN cc_start: 0.8724 (m-40) cc_final: 0.8444 (m-40) REVERT: B 676 ASN cc_start: 0.9544 (m-40) cc_final: 0.8985 (m-40) REVERT: B 748 ASN cc_start: 0.9123 (t0) cc_final: 0.8742 (t0) REVERT: C 246 TYR cc_start: 0.8979 (t80) cc_final: 0.8573 (t80) REVERT: C 260 GLN cc_start: 0.8095 (mt0) cc_final: 0.7790 (mt0) REVERT: C 267 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8805 (mp) REVERT: C 315 LEU cc_start: 0.9185 (mm) cc_final: 0.8827 (mt) REVERT: C 385 SER cc_start: 0.8991 (t) cc_final: 0.8790 (m) REVERT: C 406 THR cc_start: 0.8747 (m) cc_final: 0.8519 (m) REVERT: C 428 ARG cc_start: 0.8875 (ttm110) cc_final: 0.8046 (ttm110) REVERT: C 467 ASN cc_start: 0.8428 (t0) cc_final: 0.7851 (p0) REVERT: C 572 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8977 (ttp) REVERT: C 741 CYS cc_start: 0.8930 (m) cc_final: 0.8625 (m) outliers start: 46 outliers final: 17 residues processed: 462 average time/residue: 0.5402 time to fit residues: 280.8288 Evaluate side-chains 410 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 388 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 725 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 228 GLN B 206 HIS B 228 GLN B 378 HIS C 206 HIS C 378 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.085177 restraints weight = 25991.346| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.34 r_work: 0.2720 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17925 Z= 0.201 Angle : 0.617 13.721 24322 Z= 0.316 Chirality : 0.041 0.151 2728 Planarity : 0.004 0.039 2992 Dihedral : 7.363 59.680 2720 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.98 % Allowed : 15.16 % Favored : 81.86 % 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: 1.75 (0.19), residues: 2120 helix: 2.47 (0.14), residues: 1284 sheet: 0.64 (0.55), residues: 56 loop : -1.13 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 491 TYR 0.011 0.002 TYR C 627 PHE 0.015 0.001 PHE B 304 TRP 0.011 0.001 TRP D 272 HIS 0.006 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00468 (17924) covalent geometry : angle 0.61673 (24320) SS BOND : bond 0.00461 ( 1) SS BOND : angle 1.25678 ( 2) hydrogen bonds : bond 0.04445 ( 1034) hydrogen bonds : angle 3.90193 ( 2991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 418 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 TYR cc_start: 0.9026 (t80) cc_final: 0.8651 (t80) REVERT: A 260 GLN cc_start: 0.8138 (mt0) cc_final: 0.7786 (mt0) REVERT: A 272 TRP cc_start: 0.8141 (m-90) cc_final: 0.7690 (m-90) REVERT: A 273 GLN cc_start: 0.8349 (tp40) cc_final: 0.7844 (tp40) REVERT: A 327 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8751 (mt-10) REVERT: A 383 ASP cc_start: 0.8388 (t0) cc_final: 0.7944 (t0) REVERT: A 385 SER cc_start: 0.8833 (t) cc_final: 0.8615 (m) REVERT: A 428 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8010 (ttm110) REVERT: A 471 ASP cc_start: 0.8805 (m-30) cc_final: 0.8381 (t0) REVERT: A 738 TYR cc_start: 0.8726 (m-80) cc_final: 0.8412 (m-80) REVERT: A 741 CYS cc_start: 0.9002 (m) cc_final: 0.8680 (m) REVERT: A 748 ASN cc_start: 0.9094 (t0) cc_final: 0.8719 (t0) REVERT: D 246 TYR cc_start: 0.9048 (t80) cc_final: 0.8764 (t80) REVERT: D 271 SER cc_start: 0.8623 (m) cc_final: 0.8163 (p) REVERT: D 272 TRP cc_start: 0.7918 (m-90) cc_final: 0.7481 (m-90) REVERT: D 273 GLN cc_start: 0.8145 (tp40) cc_final: 0.7736 (tp40) REVERT: D 293 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8738 (mm-30) REVERT: D 716 MET cc_start: 0.4546 (mpp) cc_final: 0.3945 (tpp) REVERT: D 738 TYR cc_start: 0.8649 (m-10) cc_final: 0.8249 (m-10) REVERT: D 748 ASN cc_start: 0.9136 (t0) cc_final: 0.8747 (t0) REVERT: B 246 TYR cc_start: 0.9002 (t80) cc_final: 0.8572 (t80) REVERT: B 260 GLN cc_start: 0.8190 (mt0) cc_final: 0.7693 (mt0) REVERT: B 273 GLN cc_start: 0.8093 (tp40) cc_final: 0.7716 (tp-100) REVERT: B 315 LEU cc_start: 0.9212 (mm) cc_final: 0.8899 (mt) REVERT: B 327 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8644 (mt-10) REVERT: B 360 PRO cc_start: 0.9118 (Cg_exo) cc_final: 0.8914 (Cg_endo) REVERT: B 405 GLU cc_start: 0.7866 (pm20) cc_final: 0.7618 (pm20) REVERT: B 748 ASN cc_start: 0.9114 (t0) cc_final: 0.8773 (t0) REVERT: C 246 TYR cc_start: 0.9021 (t80) cc_final: 0.8717 (t80) REVERT: C 260 GLN cc_start: 0.8245 (mt0) cc_final: 0.7777 (mt0) REVERT: C 293 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8759 (mm-30) REVERT: C 315 LEU cc_start: 0.9202 (mm) cc_final: 0.8846 (mt) REVERT: C 324 LYS cc_start: 0.8602 (mttp) cc_final: 0.8366 (mtmm) REVERT: C 327 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8730 (mt-10) REVERT: C 385 SER cc_start: 0.9023 (t) cc_final: 0.8786 (m) REVERT: C 428 ARG cc_start: 0.8902 (ttm110) cc_final: 0.8006 (ttp-110) REVERT: C 741 CYS cc_start: 0.9045 (m) cc_final: 0.8736 (m) outliers start: 56 outliers final: 25 residues processed: 443 average time/residue: 0.5803 time to fit residues: 287.8771 Evaluate side-chains 406 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 381 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 725 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 75 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 49 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 206 HIS B 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.090228 restraints weight = 25642.587| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.31 r_work: 0.2807 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17925 Z= 0.112 Angle : 0.571 13.943 24322 Z= 0.286 Chirality : 0.038 0.152 2728 Planarity : 0.003 0.041 2992 Dihedral : 7.036 59.925 2720 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.39 % Allowed : 17.93 % Favored : 79.68 % 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: 2.01 (0.19), residues: 2120 helix: 2.75 (0.14), residues: 1288 sheet: 0.82 (0.57), residues: 56 loop : -1.22 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 491 TYR 0.010 0.001 TYR C 374 PHE 0.014 0.001 PHE B 304 TRP 0.012 0.001 TRP C 272 HIS 0.007 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00239 (17924) covalent geometry : angle 0.57083 (24320) SS BOND : bond 0.00679 ( 1) SS BOND : angle 2.68035 ( 2) hydrogen bonds : bond 0.03575 ( 1034) hydrogen bonds : angle 3.67676 ( 2991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 420 time to evaluate : 0.714 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 246 TYR cc_start: 0.8996 (t80) cc_final: 0.8622 (t80) REVERT: A 260 GLN cc_start: 0.8258 (mt0) cc_final: 0.7638 (mt0) REVERT: A 272 TRP cc_start: 0.8142 (m-90) cc_final: 0.7543 (m-90) REVERT: A 273 GLN cc_start: 0.8306 (tp40) cc_final: 0.7831 (tp40) REVERT: A 293 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8764 (mm-30) REVERT: A 383 ASP cc_start: 0.8417 (t0) cc_final: 0.7888 (t0) REVERT: A 385 SER cc_start: 0.8709 (t) cc_final: 0.8489 (m) REVERT: A 428 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8051 (ttp-110) REVERT: A 471 ASP cc_start: 0.8789 (m-30) cc_final: 0.8339 (t0) REVERT: A 572 MET cc_start: 0.9430 (tpp) cc_final: 0.9183 (ttp) REVERT: A 741 CYS cc_start: 0.8892 (m) cc_final: 0.8646 (m) REVERT: D 214 MET cc_start: 0.8311 (tpt) cc_final: 0.7779 (tpt) REVERT: D 216 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8810 (tp) REVERT: D 246 TYR cc_start: 0.9051 (t80) cc_final: 0.8723 (t80) REVERT: D 271 SER cc_start: 0.8801 (m) cc_final: 0.8504 (p) REVERT: D 273 GLN cc_start: 0.8219 (tp40) cc_final: 0.7669 (tp40) REVERT: D 293 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8731 (mm-30) REVERT: D 360 PRO cc_start: 0.9171 (Cg_exo) cc_final: 0.8939 (Cg_endo) REVERT: D 748 ASN cc_start: 0.9131 (t0) cc_final: 0.8748 (t0) REVERT: B 246 TYR cc_start: 0.8961 (t80) cc_final: 0.8595 (t80) REVERT: B 260 GLN cc_start: 0.8242 (mt0) cc_final: 0.7643 (mt0) REVERT: B 273 GLN cc_start: 0.8174 (tp40) cc_final: 0.7713 (tp-100) REVERT: B 276 ASP cc_start: 0.8634 (t0) cc_final: 0.8375 (t0) REVERT: B 293 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8780 (mm-30) REVERT: B 315 LEU cc_start: 0.9212 (mm) cc_final: 0.8861 (mt) REVERT: B 324 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8349 (mtmm) REVERT: B 327 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8752 (mt-10) REVERT: B 343 SER cc_start: 0.9213 (m) cc_final: 0.8971 (p) REVERT: B 360 PRO cc_start: 0.9145 (Cg_exo) cc_final: 0.8943 (Cg_endo) REVERT: B 460 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8299 (mt) REVERT: B 748 ASN cc_start: 0.9119 (t0) cc_final: 0.8776 (t0) REVERT: C 246 TYR cc_start: 0.8995 (t80) cc_final: 0.8658 (t80) REVERT: C 273 GLN cc_start: 0.8090 (tp40) cc_final: 0.7858 (tp40) REVERT: C 293 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8743 (mm-30) REVERT: C 315 LEU cc_start: 0.9200 (mm) cc_final: 0.8831 (mt) REVERT: C 324 LYS cc_start: 0.8597 (mttp) cc_final: 0.8388 (mtmm) REVERT: C 327 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8656 (mt-10) REVERT: C 383 ASP cc_start: 0.8197 (t0) cc_final: 0.7869 (t0) REVERT: C 428 ARG cc_start: 0.8874 (ttm110) cc_final: 0.8671 (ttm110) REVERT: C 471 ASP cc_start: 0.8358 (m-30) cc_final: 0.8144 (t0) REVERT: C 741 CYS cc_start: 0.8954 (m) cc_final: 0.8674 (m) REVERT: C 748 ASN cc_start: 0.9104 (t0) cc_final: 0.8702 (t0) outliers start: 45 outliers final: 12 residues processed: 444 average time/residue: 0.5559 time to fit residues: 277.9106 Evaluate side-chains 400 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 386 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 80 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 676 ASN B 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.088157 restraints weight = 25639.609| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.30 r_work: 0.2771 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17925 Z= 0.143 Angle : 0.572 8.963 24322 Z= 0.291 Chirality : 0.039 0.148 2728 Planarity : 0.003 0.042 2992 Dihedral : 6.776 59.868 2720 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.71 % Allowed : 18.40 % Favored : 78.88 % 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: 1.89 (0.19), residues: 2120 helix: 2.67 (0.14), residues: 1288 sheet: 0.59 (0.57), residues: 56 loop : -1.27 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.012 0.001 TYR D 374 PHE 0.014 0.001 PHE B 304 TRP 0.014 0.001 TRP A 272 HIS 0.005 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00325 (17924) covalent geometry : angle 0.57159 (24320) SS BOND : bond 0.00554 ( 1) SS BOND : angle 1.02860 ( 2) hydrogen bonds : bond 0.03886 ( 1034) hydrogen bonds : angle 3.70714 ( 2991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 399 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 TYR cc_start: 0.9006 (t80) cc_final: 0.8624 (t80) REVERT: A 260 GLN cc_start: 0.8216 (mt0) cc_final: 0.7547 (mt0) REVERT: A 273 GLN cc_start: 0.8323 (tp40) cc_final: 0.7842 (tp40) REVERT: A 293 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8819 (mm-30) REVERT: A 383 ASP cc_start: 0.8329 (t0) cc_final: 0.7789 (t0) REVERT: A 385 SER cc_start: 0.8754 (t) cc_final: 0.8504 (m) REVERT: A 428 ARG cc_start: 0.8888 (ttm110) cc_final: 0.8016 (ttm110) REVERT: A 471 ASP cc_start: 0.8866 (m-30) cc_final: 0.8441 (t0) REVERT: A 572 MET cc_start: 0.9398 (tpp) cc_final: 0.9038 (ttp) REVERT: A 741 CYS cc_start: 0.8962 (m) cc_final: 0.8672 (m) REVERT: A 748 ASN cc_start: 0.9134 (t0) cc_final: 0.8748 (t0) REVERT: D 214 MET cc_start: 0.8272 (tpt) cc_final: 0.7766 (tpt) REVERT: D 246 TYR cc_start: 0.9098 (t80) cc_final: 0.8820 (t80) REVERT: D 271 SER cc_start: 0.8848 (m) cc_final: 0.8603 (p) REVERT: D 273 GLN cc_start: 0.8177 (tp40) cc_final: 0.7620 (tp-100) REVERT: D 293 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8756 (mm-30) REVERT: D 360 PRO cc_start: 0.9222 (Cg_exo) cc_final: 0.9012 (Cg_endo) REVERT: D 471 ASP cc_start: 0.8862 (m-30) cc_final: 0.8448 (t0) REVERT: D 748 ASN cc_start: 0.9140 (t0) cc_final: 0.8767 (t0) REVERT: B 214 MET cc_start: 0.8197 (tpt) cc_final: 0.7654 (tpt) REVERT: B 246 TYR cc_start: 0.8963 (t80) cc_final: 0.8617 (t80) REVERT: B 260 GLN cc_start: 0.8217 (mt0) cc_final: 0.7625 (mt0) REVERT: B 273 GLN cc_start: 0.8155 (tp40) cc_final: 0.7715 (tp40) REVERT: B 276 ASP cc_start: 0.8682 (t0) cc_final: 0.8403 (t0) REVERT: B 293 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8779 (mm-30) REVERT: B 324 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8362 (mtmm) REVERT: B 327 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8749 (mt-10) REVERT: B 331 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8767 (mmm-85) REVERT: B 471 ASP cc_start: 0.8877 (m-30) cc_final: 0.8487 (t0) REVERT: C 222 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: C 246 TYR cc_start: 0.9031 (t80) cc_final: 0.8753 (t80) REVERT: C 293 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8758 (mm-30) REVERT: C 315 LEU cc_start: 0.9226 (mm) cc_final: 0.8824 (mt) REVERT: C 327 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8679 (mt-10) REVERT: C 383 ASP cc_start: 0.8258 (t0) cc_final: 0.7958 (t0) REVERT: C 428 ARG cc_start: 0.8878 (ttm110) cc_final: 0.8046 (ttm110) REVERT: C 741 CYS cc_start: 0.8982 (m) cc_final: 0.8663 (m) outliers start: 51 outliers final: 19 residues processed: 423 average time/residue: 0.5661 time to fit residues: 269.7982 Evaluate side-chains 400 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 379 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 25 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.088722 restraints weight = 25535.880| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.29 r_work: 0.2783 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17925 Z= 0.132 Angle : 0.573 14.325 24322 Z= 0.289 Chirality : 0.039 0.155 2728 Planarity : 0.003 0.043 2992 Dihedral : 6.326 59.824 2720 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.45 % Allowed : 18.51 % Favored : 79.04 % 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: 1.86 (0.18), residues: 2120 helix: 2.65 (0.14), residues: 1288 sheet: 0.55 (0.58), residues: 56 loop : -1.30 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 420 TYR 0.013 0.001 TYR C 374 PHE 0.015 0.001 PHE B 304 TRP 0.023 0.001 TRP A 272 HIS 0.005 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00298 (17924) covalent geometry : angle 0.57261 (24320) SS BOND : bond 0.00412 ( 1) SS BOND : angle 1.20088 ( 2) hydrogen bonds : bond 0.03756 ( 1034) hydrogen bonds : angle 3.70535 ( 2991) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 410 time to evaluate : 0.705 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 216 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8923 (tp) REVERT: A 246 TYR cc_start: 0.9008 (t80) cc_final: 0.8699 (t80) REVERT: A 273 GLN cc_start: 0.8236 (tp40) cc_final: 0.7643 (tp40) REVERT: A 293 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8769 (mm-30) REVERT: A 383 ASP cc_start: 0.8355 (t0) cc_final: 0.7826 (t0) REVERT: A 385 SER cc_start: 0.8755 (t) cc_final: 0.8511 (m) REVERT: A 428 ARG cc_start: 0.8894 (ttm110) cc_final: 0.8116 (ttp-110) REVERT: A 471 ASP cc_start: 0.8864 (m-30) cc_final: 0.8467 (t0) REVERT: A 499 ARG cc_start: 0.8767 (tpp-160) cc_final: 0.8300 (mmt-90) REVERT: A 572 MET cc_start: 0.9398 (tpp) cc_final: 0.9012 (ttp) REVERT: A 741 CYS cc_start: 0.8911 (m) cc_final: 0.8608 (m) REVERT: D 214 MET cc_start: 0.8219 (tpt) cc_final: 0.7784 (tpt) REVERT: D 246 TYR cc_start: 0.9108 (t80) cc_final: 0.8796 (t80) REVERT: D 273 GLN cc_start: 0.8136 (tp40) cc_final: 0.7692 (tp40) REVERT: D 293 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8768 (mm-30) REVERT: D 471 ASP cc_start: 0.8880 (m-30) cc_final: 0.8478 (t0) REVERT: D 738 TYR cc_start: 0.8519 (m-10) cc_final: 0.8282 (m-10) REVERT: B 214 MET cc_start: 0.8133 (tpt) cc_final: 0.7584 (tpt) REVERT: B 223 ASN cc_start: 0.8581 (m-40) cc_final: 0.8364 (m-40) REVERT: B 246 TYR cc_start: 0.8975 (t80) cc_final: 0.8647 (t80) REVERT: B 273 GLN cc_start: 0.8187 (tp40) cc_final: 0.7978 (tp40) REVERT: B 276 ASP cc_start: 0.8704 (t0) cc_final: 0.8406 (t0) REVERT: B 293 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8754 (mm-30) REVERT: B 331 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8722 (mmm-85) REVERT: B 471 ASP cc_start: 0.8877 (m-30) cc_final: 0.8523 (t0) REVERT: C 214 MET cc_start: 0.8142 (tpt) cc_final: 0.7643 (tpt) REVERT: C 246 TYR cc_start: 0.9084 (t80) cc_final: 0.8773 (t80) REVERT: C 293 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8769 (mm-30) REVERT: C 428 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8047 (ttm110) REVERT: C 471 ASP cc_start: 0.8692 (m-30) cc_final: 0.8296 (t0) REVERT: C 741 CYS cc_start: 0.8798 (m) cc_final: 0.8550 (m) REVERT: C 748 ASN cc_start: 0.9115 (t0) cc_final: 0.8731 (t0) outliers start: 46 outliers final: 19 residues processed: 430 average time/residue: 0.5669 time to fit residues: 274.5956 Evaluate side-chains 403 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 382 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 56 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 378 HIS C 269 GLN C 676 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.086015 restraints weight = 25713.410| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.29 r_work: 0.2737 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17925 Z= 0.195 Angle : 0.635 14.402 24322 Z= 0.318 Chirality : 0.041 0.162 2728 Planarity : 0.003 0.043 2992 Dihedral : 6.400 57.970 2720 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.55 % Allowed : 19.41 % Favored : 78.03 % 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: 1.64 (0.18), residues: 2120 helix: 2.46 (0.14), residues: 1288 sheet: 0.35 (0.58), residues: 56 loop : -1.34 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 420 TYR 0.014 0.002 TYR B 374 PHE 0.014 0.001 PHE B 304 TRP 0.017 0.001 TRP A 272 HIS 0.006 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00455 (17924) covalent geometry : angle 0.63442 (24320) SS BOND : bond 0.01076 ( 1) SS BOND : angle 2.29110 ( 2) hydrogen bonds : bond 0.04295 ( 1034) hydrogen bonds : angle 3.86353 ( 2991) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 381 time to evaluate : 0.771 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 246 TYR cc_start: 0.9037 (t80) cc_final: 0.8655 (t80) REVERT: A 273 GLN cc_start: 0.8172 (tp40) cc_final: 0.7648 (tp40) REVERT: A 293 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8753 (mm-30) REVERT: A 383 ASP cc_start: 0.8332 (t0) cc_final: 0.7780 (t0) REVERT: A 385 SER cc_start: 0.8852 (t) cc_final: 0.8564 (m) REVERT: A 420 ARG cc_start: 0.8906 (mtt90) cc_final: 0.8692 (mtt90) REVERT: A 428 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8035 (ttm110) REVERT: A 471 ASP cc_start: 0.8865 (m-30) cc_final: 0.8476 (t0) REVERT: A 499 ARG cc_start: 0.8742 (tpp-160) cc_final: 0.8319 (mmt-90) REVERT: A 741 CYS cc_start: 0.8962 (m) cc_final: 0.8641 (m) REVERT: D 214 MET cc_start: 0.8131 (tpt) cc_final: 0.7727 (tpt) REVERT: D 246 TYR cc_start: 0.9074 (t80) cc_final: 0.8719 (t80) REVERT: D 273 GLN cc_start: 0.8209 (tp40) cc_final: 0.7685 (tp40) REVERT: D 293 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8764 (mm-30) REVERT: D 471 ASP cc_start: 0.8896 (m-30) cc_final: 0.8512 (t0) REVERT: D 738 TYR cc_start: 0.8583 (m-10) cc_final: 0.8327 (m-10) REVERT: B 214 MET cc_start: 0.8061 (tpt) cc_final: 0.7554 (tpt) REVERT: B 246 TYR cc_start: 0.9031 (t80) cc_final: 0.8701 (t80) REVERT: B 273 GLN cc_start: 0.8149 (tp40) cc_final: 0.7865 (tp40) REVERT: B 276 ASP cc_start: 0.8764 (t0) cc_final: 0.8420 (t0) REVERT: B 293 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8774 (mm-30) REVERT: B 391 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8410 (tm-30) REVERT: B 471 ASP cc_start: 0.8878 (m-30) cc_final: 0.8546 (t0) REVERT: C 214 MET cc_start: 0.8091 (tpt) cc_final: 0.7561 (tpt) REVERT: C 246 TYR cc_start: 0.9089 (t80) cc_final: 0.8754 (t80) REVERT: C 293 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8740 (mm-30) REVERT: C 405 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 428 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8036 (ttm110) REVERT: C 471 ASP cc_start: 0.8718 (m-30) cc_final: 0.8279 (t0) REVERT: C 725 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9095 (mp) REVERT: C 741 CYS cc_start: 0.8926 (m) cc_final: 0.8603 (m) outliers start: 48 outliers final: 26 residues processed: 404 average time/residue: 0.5634 time to fit residues: 256.5544 Evaluate side-chains 397 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 370 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 725 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 154 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.087043 restraints weight = 25547.821| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.30 r_work: 0.2755 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17925 Z= 0.165 Angle : 0.627 14.400 24322 Z= 0.311 Chirality : 0.040 0.158 2728 Planarity : 0.003 0.043 2992 Dihedral : 6.196 55.721 2720 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.45 % Allowed : 19.84 % Favored : 77.71 % 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: 1.66 (0.18), residues: 2120 helix: 2.47 (0.14), residues: 1288 sheet: 0.67 (0.60), residues: 56 loop : -1.34 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 432 TYR 0.012 0.001 TYR D 374 PHE 0.028 0.001 PHE C 730 TRP 0.021 0.001 TRP B 272 HIS 0.006 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00384 (17924) covalent geometry : angle 0.62689 (24320) SS BOND : bond 0.00520 ( 1) SS BOND : angle 2.20413 ( 2) hydrogen bonds : bond 0.04069 ( 1034) hydrogen bonds : angle 3.85092 ( 2991) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 382 time to evaluate : 0.670 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: 0.8222 (tpt) cc_final: 0.7713 (tpt) REVERT: A 228 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7031 (mp-120) REVERT: A 246 TYR cc_start: 0.9039 (t80) cc_final: 0.8718 (t80) REVERT: A 273 GLN cc_start: 0.8147 (tp40) cc_final: 0.7476 (tp-100) REVERT: A 293 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8748 (mm-30) REVERT: A 378 HIS cc_start: 0.8262 (p90) cc_final: 0.7777 (p90) REVERT: A 383 ASP cc_start: 0.8365 (t0) cc_final: 0.7813 (t0) REVERT: A 385 SER cc_start: 0.8816 (t) cc_final: 0.8526 (m) REVERT: A 420 ARG cc_start: 0.8874 (mtt90) cc_final: 0.8660 (mmt90) REVERT: A 471 ASP cc_start: 0.8859 (m-30) cc_final: 0.8466 (t0) REVERT: A 575 ARG cc_start: 0.8266 (mmp-170) cc_final: 0.7816 (mtm110) REVERT: A 710 LYS cc_start: 0.8936 (tppt) cc_final: 0.8644 (ttpp) REVERT: A 741 CYS cc_start: 0.8909 (m) cc_final: 0.8644 (m) REVERT: D 214 MET cc_start: 0.7993 (tpt) cc_final: 0.7622 (tpt) REVERT: D 246 TYR cc_start: 0.9067 (t80) cc_final: 0.8711 (t80) REVERT: D 273 GLN cc_start: 0.8121 (tp40) cc_final: 0.7547 (tp40) REVERT: D 293 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8764 (mm-30) REVERT: D 471 ASP cc_start: 0.8890 (m-30) cc_final: 0.8470 (t0) REVERT: D 738 TYR cc_start: 0.8567 (m-10) cc_final: 0.8280 (m-10) REVERT: B 214 MET cc_start: 0.8003 (tpt) cc_final: 0.7516 (tpt) REVERT: B 246 TYR cc_start: 0.8998 (t80) cc_final: 0.8656 (t80) REVERT: B 273 GLN cc_start: 0.8194 (tp40) cc_final: 0.7916 (tp40) REVERT: B 276 ASP cc_start: 0.8787 (t0) cc_final: 0.8435 (t0) REVERT: B 293 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8774 (mm-30) REVERT: B 331 ARG cc_start: 0.8884 (ttm110) cc_final: 0.8655 (mmm-85) REVERT: B 343 SER cc_start: 0.9248 (m) cc_final: 0.9022 (p) REVERT: B 391 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8400 (tm-30) REVERT: B 471 ASP cc_start: 0.8869 (m-30) cc_final: 0.8524 (t0) REVERT: B 710 LYS cc_start: 0.8939 (tppt) cc_final: 0.8633 (ttpp) REVERT: C 214 MET cc_start: 0.8044 (tpt) cc_final: 0.7556 (tpt) REVERT: C 246 TYR cc_start: 0.9077 (t80) cc_final: 0.8709 (t80) REVERT: C 293 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8739 (mm-30) REVERT: C 405 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8095 (mm-30) REVERT: C 428 ARG cc_start: 0.8926 (ttm110) cc_final: 0.8035 (ttm110) REVERT: C 471 ASP cc_start: 0.8721 (m-30) cc_final: 0.8285 (t0) REVERT: C 741 CYS cc_start: 0.8868 (m) cc_final: 0.8613 (m) outliers start: 46 outliers final: 29 residues processed: 407 average time/residue: 0.5633 time to fit residues: 258.2430 Evaluate side-chains 400 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 370 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 145 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 4 optimal weight: 0.0870 chunk 148 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.090409 restraints weight = 25568.284| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.33 r_work: 0.2811 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17925 Z= 0.118 Angle : 0.624 15.111 24322 Z= 0.305 Chirality : 0.039 0.203 2728 Planarity : 0.003 0.044 2992 Dihedral : 5.347 47.085 2720 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.65 % Allowed : 20.85 % Favored : 77.50 % 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: 1.85 (0.19), residues: 2120 helix: 2.64 (0.14), residues: 1288 sheet: 0.71 (0.63), residues: 56 loop : -1.31 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 432 TYR 0.009 0.001 TYR A 309 PHE 0.027 0.001 PHE C 266 TRP 0.022 0.001 TRP B 272 HIS 0.005 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00261 (17924) covalent geometry : angle 0.62389 (24320) SS BOND : bond 0.00455 ( 1) SS BOND : angle 1.85782 ( 2) hydrogen bonds : bond 0.03572 ( 1034) hydrogen bonds : angle 3.73852 ( 2991) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 405 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8165 (tpt) cc_final: 0.7669 (tpt) REVERT: A 228 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7064 (mp-120) REVERT: A 246 TYR cc_start: 0.8988 (t80) cc_final: 0.8666 (t80) REVERT: A 273 GLN cc_start: 0.8086 (tp40) cc_final: 0.7419 (tp-100) REVERT: A 293 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8737 (mm-30) REVERT: A 343 SER cc_start: 0.9267 (m) cc_final: 0.9030 (p) REVERT: A 383 ASP cc_start: 0.8399 (t0) cc_final: 0.7714 (t0) REVERT: A 385 SER cc_start: 0.8684 (t) cc_final: 0.8432 (m) REVERT: A 420 ARG cc_start: 0.8839 (mtt90) cc_final: 0.8617 (mmt90) REVERT: A 471 ASP cc_start: 0.8831 (m-30) cc_final: 0.8234 (t0) REVERT: A 499 ARG cc_start: 0.8788 (tpp-160) cc_final: 0.8385 (mmt-90) REVERT: A 575 ARG cc_start: 0.8317 (mmp-170) cc_final: 0.7845 (mtm110) REVERT: A 682 MET cc_start: 0.8592 (tpp) cc_final: 0.8357 (ttp) REVERT: A 710 LYS cc_start: 0.8941 (tppt) cc_final: 0.8639 (ttpp) REVERT: A 741 CYS cc_start: 0.8871 (m) cc_final: 0.8565 (m) REVERT: D 214 MET cc_start: 0.7972 (tpt) cc_final: 0.7538 (tpt) REVERT: D 246 TYR cc_start: 0.9048 (t80) cc_final: 0.8685 (t80) REVERT: D 273 GLN cc_start: 0.8152 (tp40) cc_final: 0.7655 (tp40) REVERT: D 293 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8719 (mm-30) REVERT: D 460 LEU cc_start: 0.8767 (mm) cc_final: 0.8337 (mt) REVERT: D 471 ASP cc_start: 0.8872 (m-30) cc_final: 0.8448 (t0) REVERT: D 710 LYS cc_start: 0.8955 (tppt) cc_final: 0.8647 (ttpp) REVERT: D 738 TYR cc_start: 0.8333 (m-10) cc_final: 0.8024 (m-10) REVERT: B 214 MET cc_start: 0.7912 (tpt) cc_final: 0.7464 (tpt) REVERT: B 246 TYR cc_start: 0.8946 (t80) cc_final: 0.8626 (t80) REVERT: B 273 GLN cc_start: 0.8174 (tp40) cc_final: 0.7881 (tp40) REVERT: B 276 ASP cc_start: 0.8749 (t0) cc_final: 0.8417 (t0) REVERT: B 293 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8775 (mm-30) REVERT: B 331 ARG cc_start: 0.8933 (ttm110) cc_final: 0.8343 (mmm-85) REVERT: B 378 HIS cc_start: 0.7388 (p-80) cc_final: 0.7135 (p90) REVERT: B 391 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8367 (tm-30) REVERT: B 420 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8607 (mmm-85) REVERT: B 429 PHE cc_start: 0.8329 (t80) cc_final: 0.8118 (t80) REVERT: B 471 ASP cc_start: 0.8831 (m-30) cc_final: 0.8467 (t0) REVERT: B 505 SER cc_start: 0.8062 (p) cc_final: 0.7830 (m) REVERT: B 575 ARG cc_start: 0.8317 (mmp-170) cc_final: 0.7834 (mtm110) REVERT: B 682 MET cc_start: 0.8442 (mtp) cc_final: 0.7721 (mtp) REVERT: B 710 LYS cc_start: 0.8969 (tppt) cc_final: 0.8665 (ttpp) REVERT: C 214 MET cc_start: 0.7888 (tpt) cc_final: 0.7487 (tpt) REVERT: C 246 TYR cc_start: 0.9069 (t80) cc_final: 0.8805 (t80) REVERT: C 293 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8725 (mm-30) REVERT: C 377 VAL cc_start: 0.8701 (p) cc_final: 0.8497 (p) REVERT: C 405 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7823 (mm-30) REVERT: C 460 LEU cc_start: 0.8752 (mm) cc_final: 0.8322 (mt) REVERT: C 471 ASP cc_start: 0.8692 (m-30) cc_final: 0.8268 (t0) REVERT: C 505 SER cc_start: 0.8358 (p) cc_final: 0.7964 (m) REVERT: C 741 CYS cc_start: 0.8809 (m) cc_final: 0.8523 (m) outliers start: 31 outliers final: 22 residues processed: 420 average time/residue: 0.5632 time to fit residues: 266.5543 Evaluate side-chains 413 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 390 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 83 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.090142 restraints weight = 25358.745| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.31 r_work: 0.2808 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17925 Z= 0.125 Angle : 0.642 15.720 24322 Z= 0.310 Chirality : 0.039 0.207 2728 Planarity : 0.003 0.045 2992 Dihedral : 5.036 36.715 2720 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.44 % Allowed : 21.91 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2120 helix: 2.60 (0.14), residues: 1288 sheet: 1.14 (0.65), residues: 56 loop : -1.29 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 432 TYR 0.010 0.001 TYR C 374 PHE 0.020 0.001 PHE C 730 TRP 0.021 0.001 TRP B 272 HIS 0.005 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00283 (17924) covalent geometry : angle 0.64150 (24320) SS BOND : bond 0.00451 ( 1) SS BOND : angle 1.68874 ( 2) hydrogen bonds : bond 0.03679 ( 1034) hydrogen bonds : angle 3.76445 ( 2991) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 398 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8120 (tpt) cc_final: 0.7637 (tpt) REVERT: A 228 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7085 (mp-120) REVERT: A 246 TYR cc_start: 0.8991 (t80) cc_final: 0.8656 (t80) REVERT: A 273 GLN cc_start: 0.8114 (tp40) cc_final: 0.7568 (tp40) REVERT: A 293 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8762 (mm-30) REVERT: A 383 ASP cc_start: 0.8360 (t0) cc_final: 0.7808 (t0) REVERT: A 385 SER cc_start: 0.8691 (t) cc_final: 0.8405 (m) REVERT: A 420 ARG cc_start: 0.8843 (mtt90) cc_final: 0.8604 (mmt90) REVERT: A 428 ARG cc_start: 0.8986 (ttm-80) cc_final: 0.8261 (mtm110) REVERT: A 471 ASP cc_start: 0.8840 (m-30) cc_final: 0.8268 (t0) REVERT: A 575 ARG cc_start: 0.8365 (mmp-170) cc_final: 0.7867 (mtm110) REVERT: A 710 LYS cc_start: 0.8957 (tppt) cc_final: 0.8661 (ttpp) REVERT: A 741 CYS cc_start: 0.8910 (m) cc_final: 0.8597 (m) REVERT: D 214 MET cc_start: 0.7917 (tpt) cc_final: 0.7527 (tpt) REVERT: D 246 TYR cc_start: 0.9056 (t80) cc_final: 0.8764 (t80) REVERT: D 273 GLN cc_start: 0.8155 (tp40) cc_final: 0.7752 (tp40) REVERT: D 293 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8742 (mm-30) REVERT: D 378 HIS cc_start: 0.8207 (p90) cc_final: 0.7699 (p90) REVERT: D 471 ASP cc_start: 0.8877 (m-30) cc_final: 0.8401 (t0) REVERT: D 505 SER cc_start: 0.7993 (p) cc_final: 0.7784 (m) REVERT: D 710 LYS cc_start: 0.8950 (tppt) cc_final: 0.8647 (ttpp) REVERT: D 716 MET cc_start: 0.4560 (mmp) cc_final: 0.4003 (mmt) REVERT: D 738 TYR cc_start: 0.8314 (m-10) cc_final: 0.8010 (m-10) REVERT: B 214 MET cc_start: 0.7857 (tpt) cc_final: 0.7410 (tpt) REVERT: B 246 TYR cc_start: 0.8956 (t80) cc_final: 0.8618 (t80) REVERT: B 273 GLN cc_start: 0.8152 (tp40) cc_final: 0.7858 (tp40) REVERT: B 276 ASP cc_start: 0.8728 (t0) cc_final: 0.8384 (t0) REVERT: B 293 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8786 (mm-30) REVERT: B 331 ARG cc_start: 0.8903 (ttm110) cc_final: 0.8412 (mmm-85) REVERT: B 405 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 420 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8625 (mmm-85) REVERT: B 429 PHE cc_start: 0.8329 (t80) cc_final: 0.8120 (t80) REVERT: B 471 ASP cc_start: 0.8825 (m-30) cc_final: 0.8468 (t0) REVERT: B 505 SER cc_start: 0.8071 (p) cc_final: 0.7815 (m) REVERT: B 575 ARG cc_start: 0.8327 (mmp-170) cc_final: 0.7822 (mtm110) REVERT: B 644 MET cc_start: 0.9554 (mmm) cc_final: 0.8691 (mmm) REVERT: B 710 LYS cc_start: 0.8971 (tppt) cc_final: 0.8675 (ttpp) REVERT: C 214 MET cc_start: 0.7873 (tpt) cc_final: 0.7441 (tpt) REVERT: C 246 TYR cc_start: 0.9084 (t80) cc_final: 0.8817 (t80) REVERT: C 293 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8780 (mm-30) REVERT: C 405 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 460 LEU cc_start: 0.8779 (mm) cc_final: 0.8361 (mt) REVERT: C 471 ASP cc_start: 0.8693 (m-30) cc_final: 0.8239 (t0) REVERT: C 505 SER cc_start: 0.8333 (p) cc_final: 0.7991 (m) REVERT: C 682 MET cc_start: 0.8333 (ttm) cc_final: 0.7763 (mtp) REVERT: C 741 CYS cc_start: 0.8795 (m) cc_final: 0.8530 (m) outliers start: 27 outliers final: 22 residues processed: 413 average time/residue: 0.5360 time to fit residues: 250.2375 Evaluate side-chains 413 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 390 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 0.0000 chunk 126 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.091412 restraints weight = 25500.392| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.34 r_work: 0.2829 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17925 Z= 0.116 Angle : 0.638 15.487 24322 Z= 0.309 Chirality : 0.039 0.207 2728 Planarity : 0.004 0.060 2992 Dihedral : 4.763 28.197 2720 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.70 % Allowed : 21.76 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.19), residues: 2120 helix: 2.64 (0.14), residues: 1288 sheet: 1.23 (0.69), residues: 56 loop : -1.28 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 721 TYR 0.011 0.001 TYR C 374 PHE 0.028 0.001 PHE B 266 TRP 0.020 0.001 TRP B 272 HIS 0.004 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00258 (17924) covalent geometry : angle 0.63796 (24320) SS BOND : bond 0.00490 ( 1) SS BOND : angle 1.53153 ( 2) hydrogen bonds : bond 0.03518 ( 1034) hydrogen bonds : angle 3.72937 ( 2991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7919.63 seconds wall clock time: 135 minutes 8.86 seconds (8108.86 seconds total)