Starting phenix.real_space_refine on Sat Jul 4 02:23:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mzd_24090/07_2026/7mzd_24090.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mzd_24090/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mzd_24090/07_2026/7mzd_24090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mzd_24090/07_2026/7mzd_24090.map" model { file = "/net/cci-nas-00/data/ceres_data/7mzd_24090/07_2026/7mzd_24090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mzd_24090/07_2026/7mzd_24090.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mzd_24090/07_2026/7mzd_24090.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mzd_24090/07_2026/7mzd_24090.cif" } 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-6108/lib/python3.11/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: 2.93, per 1000 atoms: 0.17 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: 1.09 Conformation dependent library (CDL) restraints added in 639.4 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: 0.37 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: 2.65 Time building geometry restraints manager: 1.50 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: 9983 17.95 - 35.90: 388 35.90 - 53.85: 68 53.85 - 71.80: 5 71.80 - 89.75: 11 Dihedral angle restraints: 10455 sinusoidal: 4187 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 10452 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.060 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 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 : 10.477 89.753 6428 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/Z covalent geometry : bond 0.01003 / 0.49 (17924) covalent geometry : angle 0.79052 / 0.38 (24320) SS BOND : bond 0.00190 / 0.10 ( 1) SS BOND : angle 2.14984 / 1.14 ( 2) hydrogen bonds : bond 0.11640 / 7.81 ( 1034) hydrogen bonds : angle 5.05645 / 3.53 ( 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 : 0.665 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: 0.5538 time to fit residues: 399.8591 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 : 0.652 ------------------------------------------------------------------------------- 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... 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 = 0.3545 r_free = 0.3545 target = 0.130808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.087153 restraints weight = 25815.295| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.33 r_work: 0.2754 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17925 Z= 0.165 Angle : 0.609 9.515 24322 Z= 0.314 Chirality : 0.040 0.162 2728 Planarity : 0.004 0.042 2992 Dihedral : 5.148 45.099 2376 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.34 % Allowed : 13.19 % 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: 1.89 (0.19), residues: 2120 helix: 2.57 (0.14), residues: 1280 sheet: -0.13 (0.55), residues: 76 loop : -0.98 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 491 TYR 0.012 0.001 TYR D 627 PHE 0.016 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/Z covalent geometry : bond 0.00380 / 0.16 (17924) covalent geometry : angle 0.60862 / 0.31 (24320) SS BOND : bond 0.01331 / 0.70 ( 1) SS BOND : angle 2.00374 / 1.06 ( 2) hydrogen bonds : bond 0.04341 / 2.90 ( 1034) hydrogen bonds : angle 3.92465 / 2.73 ( 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 494 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 450 time to evaluate : 0.669 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: 0.7856 (OUTLIER) cc_final: 0.7238 (mp-120) REVERT: A 246 TYR cc_start: 0.9004 (t80) cc_final: 0.8595 (t80) REVERT: A 260 GLN cc_start: 0.8095 (mt0) cc_final: 0.7679 (mt0) REVERT: A 272 TRP cc_start: 0.8011 (m-90) cc_final: 0.7573 (m-90) REVERT: A 273 GLN cc_start: 0.8356 (tp40) cc_final: 0.7910 (tp40) REVERT: A 378 HIS cc_start: 0.8134 (p-80) cc_final: 0.7832 (p90) REVERT: A 383 ASP cc_start: 0.8404 (t0) cc_final: 0.8028 (t0) REVERT: A 385 SER cc_start: 0.8742 (t) cc_final: 0.8532 (m) REVERT: A 420 ARG cc_start: 0.8906 (mmm-85) cc_final: 0.8583 (mtt90) REVERT: A 428 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8642 (ttm110) REVERT: A 572 MET cc_start: 0.9111 (tpp) cc_final: 0.8746 (tpp) REVERT: A 741 CYS cc_start: 0.8917 (m) cc_final: 0.8582 (m) REVERT: A 748 ASN cc_start: 0.9090 (t0) cc_final: 0.8709 (t0) REVERT: D 228 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7189 (mp-120) REVERT: D 246 TYR cc_start: 0.9008 (t80) cc_final: 0.8660 (t80) REVERT: D 273 GLN cc_start: 0.8192 (tp40) cc_final: 0.7693 (tp40) REVERT: D 293 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8730 (mm-30) REVERT: D 308 MET cc_start: 0.9424 (tpp) cc_final: 0.9185 (tpp) REVERT: D 405 GLU cc_start: 0.7694 (pm20) cc_final: 0.7490 (pm20) REVERT: D 471 ASP cc_start: 0.8636 (m-30) cc_final: 0.8197 (t0) REVERT: D 748 ASN cc_start: 0.9101 (t0) cc_final: 0.8702 (t0) REVERT: B 228 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7230 (mp-120) REVERT: B 246 TYR cc_start: 0.8965 (t80) cc_final: 0.8610 (t80) REVERT: B 260 GLN cc_start: 0.8209 (mt0) cc_final: 0.7725 (mt0) REVERT: B 311 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8721 (mm-30) REVERT: B 315 LEU cc_start: 0.9230 (mm) cc_final: 0.8935 (mt) REVERT: B 408 ASN cc_start: 0.8742 (m-40) cc_final: 0.8465 (m-40) REVERT: B 676 ASN cc_start: 0.9530 (m-40) cc_final: 0.8984 (m-40) REVERT: B 748 ASN cc_start: 0.9121 (t0) cc_final: 0.8717 (t0) REVERT: C 246 TYR cc_start: 0.8989 (t80) cc_final: 0.8591 (t80) REVERT: C 260 GLN cc_start: 0.8114 (mt0) cc_final: 0.7786 (mt0) REVERT: C 267 LEU cc_start: 0.9016 (mt) cc_final: 0.8812 (mp) REVERT: C 315 LEU cc_start: 0.9182 (mm) cc_final: 0.8819 (mt) REVERT: C 383 ASP cc_start: 0.8420 (t0) cc_final: 0.7990 (t0) REVERT: C 385 SER cc_start: 0.9012 (t) cc_final: 0.8803 (m) REVERT: C 406 THR cc_start: 0.8757 (m) cc_final: 0.8496 (m) REVERT: C 428 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8012 (ttm110) REVERT: C 572 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9031 (ttp) REVERT: C 741 CYS cc_start: 0.8950 (m) cc_final: 0.8644 (m) outliers start: 44 outliers final: 17 residues processed: 467 average time/residue: 0.4680 time to fit residues: 247.2516 Evaluate side-chains 410 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 389 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 108 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN B 206 HIS B 378 HIS C 206 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.089132 restraints weight = 25750.307| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.31 r_work: 0.2790 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17925 Z= 0.125 Angle : 0.576 14.655 24322 Z= 0.293 Chirality : 0.039 0.158 2728 Planarity : 0.003 0.041 2992 Dihedral : 4.870 38.299 2376 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.77 % Allowed : 15.59 % Favored : 81.65 % 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: 2.04 (0.19), residues: 2120 helix: 2.70 (0.14), residues: 1284 sheet: 0.83 (0.57), residues: 56 loop : -1.03 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 432 TYR 0.012 0.001 TYR D 374 PHE 0.014 0.001 PHE B 304 TRP 0.013 0.001 TRP B 272 HIS 0.006 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (17924) covalent geometry : angle 0.57628 / 0.29 (24320) SS BOND : bond 0.00499 / 0.26 ( 1) SS BOND : angle 1.05983 / 0.60 ( 2) hydrogen bonds : bond 0.03839 / 2.57 ( 1034) hydrogen bonds : angle 3.72379 / 2.58 ( 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 472 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 420 time to evaluate : 0.409 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 246 TYR cc_start: 0.9011 (t80) cc_final: 0.8638 (t80) REVERT: A 260 GLN cc_start: 0.8150 (mt0) cc_final: 0.7757 (mt0) REVERT: A 272 TRP cc_start: 0.8083 (m-90) cc_final: 0.7654 (m-90) REVERT: A 273 GLN cc_start: 0.8292 (tp40) cc_final: 0.7736 (tp40) REVERT: A 293 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8820 (mm-30) REVERT: A 383 ASP cc_start: 0.8410 (t0) cc_final: 0.7908 (t0) REVERT: A 385 SER cc_start: 0.8710 (t) cc_final: 0.8501 (m) REVERT: A 408 ASN cc_start: 0.8703 (m-40) cc_final: 0.8336 (m-40) REVERT: A 428 ARG cc_start: 0.8877 (ttm110) cc_final: 0.8666 (ttm110) REVERT: A 741 CYS cc_start: 0.8947 (m) cc_final: 0.8622 (m) REVERT: A 748 ASN cc_start: 0.9133 (t0) cc_final: 0.8770 (t0) REVERT: D 214 MET cc_start: 0.8213 (tpt) cc_final: 0.7739 (tpt) REVERT: D 246 TYR cc_start: 0.9006 (t80) cc_final: 0.8679 (t80) REVERT: D 273 GLN cc_start: 0.8174 (tp40) cc_final: 0.7687 (tp40) REVERT: D 293 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8745 (mm-30) REVERT: D 748 ASN cc_start: 0.9146 (t0) cc_final: 0.8756 (t0) REVERT: B 246 TYR cc_start: 0.8957 (t80) cc_final: 0.8602 (t80) REVERT: B 260 GLN cc_start: 0.8322 (mt0) cc_final: 0.7778 (mt0) REVERT: B 273 GLN cc_start: 0.8103 (tp40) cc_final: 0.7668 (tp-100) REVERT: B 293 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8721 (mm-30) REVERT: B 315 LEU cc_start: 0.9203 (mm) cc_final: 0.8893 (mt) REVERT: B 327 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8719 (mt-10) REVERT: B 405 GLU cc_start: 0.7774 (pm20) cc_final: 0.7534 (pm20) REVERT: B 748 ASN cc_start: 0.9132 (t0) cc_final: 0.8781 (t0) REVERT: C 246 TYR cc_start: 0.8986 (t80) cc_final: 0.8670 (t80) REVERT: C 260 GLN cc_start: 0.8295 (mt0) cc_final: 0.7815 (mt0) REVERT: C 267 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8867 (mp) REVERT: C 293 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8724 (mm-30) REVERT: C 315 LEU cc_start: 0.9198 (mm) cc_final: 0.8839 (mt) REVERT: C 383 ASP cc_start: 0.8364 (t0) cc_final: 0.7882 (t0) REVERT: C 385 SER cc_start: 0.8869 (t) cc_final: 0.8659 (m) REVERT: C 428 ARG cc_start: 0.8856 (ttm110) cc_final: 0.8640 (ttm110) REVERT: C 724 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8889 (tppp) REVERT: C 741 CYS cc_start: 0.8963 (m) cc_final: 0.8654 (m) outliers start: 52 outliers final: 18 residues processed: 442 average time/residue: 0.4616 time to fit residues: 230.6559 Evaluate side-chains 403 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 383 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 392 LYS 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 674 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 674 LEU 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 503 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 724 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 75 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 HIS B 228 GLN B 378 HIS C 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.089091 restraints weight = 25817.063| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.32 r_work: 0.2792 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17925 Z= 0.124 Angle : 0.561 13.704 24322 Z= 0.285 Chirality : 0.038 0.161 2728 Planarity : 0.003 0.042 2992 Dihedral : 4.686 31.650 2376 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.09 % Allowed : 16.91 % Favored : 80.00 % 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: 1.97 (0.19), residues: 2120 helix: 2.71 (0.14), residues: 1288 sheet: 0.85 (0.57), residues: 56 loop : -1.20 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 432 TYR 0.011 0.001 TYR D 374 PHE 0.014 0.001 PHE B 304 TRP 0.012 0.001 TRP D 272 HIS 0.005 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (17924) covalent geometry : angle 0.56069 / 0.28 (24320) SS BOND : bond 0.00402 / 0.21 ( 1) SS BOND : angle 2.08392 / 1.10 ( 2) hydrogen bonds : bond 0.03736 / 2.50 ( 1034) hydrogen bonds : angle 3.67673 / 2.55 ( 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 453 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 395 time to evaluate : 0.504 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 260 GLN cc_start: 0.8287 (mt0) cc_final: 0.7916 (mt0) REVERT: A 272 TRP cc_start: 0.8139 (m-90) cc_final: 0.7689 (m-90) REVERT: A 273 GLN cc_start: 0.8336 (tp40) cc_final: 0.7792 (tp40) REVERT: A 293 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8803 (mm-30) REVERT: A 383 ASP cc_start: 0.8372 (t0) cc_final: 0.7871 (t0) REVERT: A 385 SER cc_start: 0.8694 (t) cc_final: 0.8484 (m) REVERT: A 405 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 428 ARG cc_start: 0.8887 (ttm110) cc_final: 0.8677 (ttm110) REVERT: A 471 ASP cc_start: 0.8816 (m-30) cc_final: 0.8397 (t0) REVERT: A 572 MET cc_start: 0.9428 (tpp) cc_final: 0.9142 (ttp) REVERT: A 575 ARG cc_start: 0.8278 (mmp-170) cc_final: 0.7884 (mtm110) REVERT: A 741 CYS cc_start: 0.8905 (m) cc_final: 0.8653 (m) REVERT: D 214 MET cc_start: 0.8230 (tpt) cc_final: 0.7778 (tpt) REVERT: D 216 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8841 (tp) REVERT: D 246 TYR cc_start: 0.9015 (t80) cc_final: 0.8700 (t80) REVERT: D 258 THR cc_start: 0.8243 (p) cc_final: 0.7315 (p) REVERT: D 260 GLN cc_start: 0.7427 (mm110) cc_final: 0.7044 (mt0) REVERT: D 271 SER cc_start: 0.8585 (m) cc_final: 0.8114 (p) REVERT: D 272 TRP cc_start: 0.8180 (m-90) cc_final: 0.7439 (m-90) REVERT: D 273 GLN cc_start: 0.8171 (tp40) cc_final: 0.7772 (tp40) REVERT: D 293 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8768 (mm-30) REVERT: D 748 ASN cc_start: 0.9156 (t0) cc_final: 0.8762 (t0) REVERT: B 223 ASN cc_start: 0.8433 (m-40) cc_final: 0.8136 (m-40) REVERT: B 246 TYR cc_start: 0.8962 (t80) cc_final: 0.8593 (t80) REVERT: B 260 GLN cc_start: 0.8244 (mt0) cc_final: 0.7643 (mt0) REVERT: B 273 GLN cc_start: 0.8156 (tp40) cc_final: 0.7692 (tp-100) REVERT: B 293 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8790 (mm-30) REVERT: B 315 LEU cc_start: 0.9221 (mm) cc_final: 0.8867 (mt) REVERT: B 343 SER cc_start: 0.9240 (m) cc_final: 0.9001 (p) REVERT: B 748 ASN cc_start: 0.9127 (t0) cc_final: 0.8793 (t0) REVERT: C 216 LEU cc_start: 0.9152 (tt) cc_final: 0.8918 (tp) REVERT: C 246 TYR cc_start: 0.8987 (t80) cc_final: 0.8662 (t80) REVERT: C 267 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8872 (mp) REVERT: C 293 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8727 (mm-30) REVERT: C 315 LEU cc_start: 0.9202 (mm) cc_final: 0.8824 (mt) REVERT: C 383 ASP cc_start: 0.8308 (t0) cc_final: 0.7758 (t0) REVERT: C 385 SER cc_start: 0.8893 (t) cc_final: 0.8657 (m) REVERT: C 428 ARG cc_start: 0.8883 (ttm110) cc_final: 0.8681 (ttm110) REVERT: C 572 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8981 (ttp) REVERT: C 748 ASN cc_start: 0.9111 (t0) cc_final: 0.8729 (t0) outliers start: 58 outliers final: 19 residues processed: 422 average time/residue: 0.4715 time to fit residues: 224.4213 Evaluate side-chains 408 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 385 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 405 GLU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 327 GLU 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 D residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 503 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN D 228 GLN D 310 ASN B 206 HIS B 378 HIS ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.090350 restraints weight = 25572.019| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.32 r_work: 0.2811 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17925 Z= 0.115 Angle : 0.552 15.089 24322 Z= 0.279 Chirality : 0.038 0.158 2728 Planarity : 0.003 0.042 2992 Dihedral : 4.549 30.064 2376 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.14 % Allowed : 17.82 % 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: 2.03 (0.19), residues: 2120 helix: 2.76 (0.14), residues: 1288 sheet: 0.80 (0.58), residues: 56 loop : -1.19 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 432 TYR 0.014 0.001 TYR B 374 PHE 0.014 0.001 PHE B 304 TRP 0.013 0.001 TRP B 272 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17924) covalent geometry : angle 0.55176 / 0.28 (24320) SS BOND : bond 0.00494 / 0.26 ( 1) SS BOND : angle 1.45880 / 0.78 ( 2) hydrogen bonds : bond 0.03544 / 2.38 ( 1034) hydrogen bonds : angle 3.61764 / 2.50 ( 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 473 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 414 time to evaluate : 0.520 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 260 GLN cc_start: 0.8289 (mt0) cc_final: 0.7948 (mt0) REVERT: A 272 TRP cc_start: 0.8136 (m-90) cc_final: 0.7722 (m-90) REVERT: A 273 GLN cc_start: 0.8311 (tp40) cc_final: 0.7773 (tp40) REVERT: A 293 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8729 (mm-30) REVERT: A 383 ASP cc_start: 0.8343 (t0) cc_final: 0.7783 (t0) REVERT: A 385 SER cc_start: 0.8636 (t) cc_final: 0.8390 (m) REVERT: A 420 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8460 (mmm-85) REVERT: A 428 ARG cc_start: 0.8859 (ttm110) cc_final: 0.8649 (ttm110) REVERT: A 471 ASP cc_start: 0.8816 (m-30) cc_final: 0.8383 (t0) REVERT: A 575 ARG cc_start: 0.8313 (mmp-170) cc_final: 0.7914 (mtm110) REVERT: A 741 CYS cc_start: 0.8871 (m) cc_final: 0.8600 (m) REVERT: D 214 MET cc_start: 0.8105 (tpt) cc_final: 0.7651 (tpt) REVERT: D 216 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8910 (tp) REVERT: D 246 TYR cc_start: 0.9017 (t80) cc_final: 0.8695 (t80) REVERT: D 258 THR cc_start: 0.8123 (p) cc_final: 0.7900 (p) REVERT: D 271 SER cc_start: 0.8785 (m) cc_final: 0.8552 (p) REVERT: D 272 TRP cc_start: 0.7960 (m-90) cc_final: 0.7583 (m-90) REVERT: D 273 GLN cc_start: 0.8165 (tp40) cc_final: 0.7641 (tp40) REVERT: D 293 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8705 (mm-30) REVERT: D 471 ASP cc_start: 0.8841 (m-30) cc_final: 0.8421 (t0) REVERT: B 223 ASN cc_start: 0.8326 (m-40) cc_final: 0.8047 (m110) REVERT: B 246 TYR cc_start: 0.8959 (t80) cc_final: 0.8578 (t80) REVERT: B 260 GLN cc_start: 0.8248 (mt0) cc_final: 0.7864 (mt0) REVERT: B 273 GLN cc_start: 0.8183 (tp40) cc_final: 0.7674 (tp-100) REVERT: B 276 ASP cc_start: 0.8535 (t0) cc_final: 0.8309 (t0) REVERT: B 293 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8771 (mm-30) REVERT: B 331 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8781 (mmm-85) REVERT: B 471 ASP cc_start: 0.8881 (m-30) cc_final: 0.8475 (t0) REVERT: B 575 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7864 (mmt180) REVERT: C 246 TYR cc_start: 0.8979 (t80) cc_final: 0.8641 (t80) REVERT: C 267 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8908 (mp) REVERT: C 293 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8713 (mm-30) REVERT: C 315 LEU cc_start: 0.9201 (mm) cc_final: 0.8820 (mt) REVERT: C 383 ASP cc_start: 0.8227 (t0) cc_final: 0.7616 (t0) REVERT: C 385 SER cc_start: 0.8654 (t) cc_final: 0.8427 (m) REVERT: C 428 ARG cc_start: 0.8859 (ttm110) cc_final: 0.8052 (ttp-110) REVERT: C 471 ASP cc_start: 0.8869 (m-30) cc_final: 0.8453 (t0) REVERT: C 572 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8929 (ttp) REVERT: C 748 ASN cc_start: 0.9128 (t0) cc_final: 0.8746 (t0) outliers start: 59 outliers final: 25 residues processed: 436 average time/residue: 0.4569 time to fit residues: 225.6694 Evaluate side-chains 420 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 390 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 216 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 D residue 741 CYS Chi-restraints excluded: chain B residue 215 THR 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 512 SER Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 675 LEU 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 327 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 ASN D 408 ASN D 410 HIS B 206 HIS B 269 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.089471 restraints weight = 25494.027| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.32 r_work: 0.2803 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17925 Z= 0.127 Angle : 0.575 15.191 24322 Z= 0.287 Chirality : 0.038 0.160 2728 Planarity : 0.003 0.043 2992 Dihedral : 4.518 29.302 2376 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.93 % Allowed : 18.46 % Favored : 78.62 % 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: 1.95 (0.19), residues: 2120 helix: 2.70 (0.14), residues: 1288 sheet: 0.79 (0.58), residues: 56 loop : -1.22 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 432 TYR 0.013 0.001 TYR C 374 PHE 0.014 0.001 PHE B 304 TRP 0.014 0.001 TRP B 272 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17924) covalent geometry : angle 0.57537 / 0.29 (24320) SS BOND : bond 0.00421 / 0.22 ( 1) SS BOND : angle 1.16966 / 0.64 ( 2) hydrogen bonds : bond 0.03682 / 2.46 ( 1034) hydrogen bonds : angle 3.66556 / 2.54 ( 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 463 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 408 time to evaluate : 0.422 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 216 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8973 (tp) REVERT: A 260 GLN cc_start: 0.8286 (mt0) cc_final: 0.7564 (mt0) REVERT: A 273 GLN cc_start: 0.8297 (tp40) cc_final: 0.7789 (tp40) REVERT: A 293 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8731 (mm-30) REVERT: A 383 ASP cc_start: 0.8328 (t0) cc_final: 0.7752 (t0) REVERT: A 385 SER cc_start: 0.8669 (t) cc_final: 0.8399 (m) REVERT: A 420 ARG cc_start: 0.8942 (mmm-85) cc_final: 0.8475 (mmm-85) REVERT: A 428 ARG cc_start: 0.8873 (ttm110) cc_final: 0.8011 (ttm110) REVERT: A 471 ASP cc_start: 0.8844 (m-30) cc_final: 0.8421 (t0) REVERT: A 575 ARG cc_start: 0.8330 (mmp-170) cc_final: 0.7919 (mtm110) REVERT: A 741 CYS cc_start: 0.8875 (m) cc_final: 0.8563 (m) REVERT: D 214 MET cc_start: 0.8040 (tpt) cc_final: 0.7585 (tpt) REVERT: D 216 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8952 (tp) REVERT: D 246 TYR cc_start: 0.9034 (t80) cc_final: 0.8739 (t80) REVERT: D 258 THR cc_start: 0.8204 (p) cc_final: 0.7983 (p) REVERT: D 272 TRP cc_start: 0.8036 (m-90) cc_final: 0.7698 (m-90) REVERT: D 273 GLN cc_start: 0.8204 (tp40) cc_final: 0.7685 (tp40) REVERT: D 276 ASP cc_start: 0.8562 (t0) cc_final: 0.8320 (t0) REVERT: D 293 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8737 (mm-30) REVERT: D 360 PRO cc_start: 0.9229 (Cg_exo) cc_final: 0.9019 (Cg_endo) REVERT: D 471 ASP cc_start: 0.8874 (m-30) cc_final: 0.8467 (t0) REVERT: D 505 SER cc_start: 0.8259 (p) cc_final: 0.8020 (p) REVERT: B 246 TYR cc_start: 0.8967 (t80) cc_final: 0.8621 (t80) REVERT: B 260 GLN cc_start: 0.8313 (mt0) cc_final: 0.7575 (mt0) REVERT: B 273 GLN cc_start: 0.8157 (tp40) cc_final: 0.7725 (tp40) REVERT: B 276 ASP cc_start: 0.8602 (t0) cc_final: 0.8358 (t0) REVERT: B 293 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8782 (mm-30) REVERT: B 331 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8723 (mmm-85) REVERT: B 471 ASP cc_start: 0.8890 (m-30) cc_final: 0.8519 (t0) REVERT: C 246 TYR cc_start: 0.8984 (t80) cc_final: 0.8717 (t80) REVERT: C 271 SER cc_start: 0.9029 (m) cc_final: 0.8782 (p) REVERT: C 293 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8725 (mm-30) REVERT: C 315 LEU cc_start: 0.9198 (mm) cc_final: 0.8800 (mt) REVERT: C 383 ASP cc_start: 0.8276 (t0) cc_final: 0.7649 (t0) REVERT: C 389 THR cc_start: 0.8960 (t) cc_final: 0.8723 (m) REVERT: C 428 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8643 (ttm110) REVERT: C 471 ASP cc_start: 0.8879 (m-30) cc_final: 0.8493 (t0) REVERT: C 572 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8936 (ttp) REVERT: C 748 ASN cc_start: 0.9111 (t0) cc_final: 0.8717 (t0) outliers start: 55 outliers final: 26 residues processed: 432 average time/residue: 0.4678 time to fit residues: 228.3975 Evaluate side-chains 415 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 385 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 392 LYS 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 216 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 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 215 THR 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 572 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 56 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN D 410 HIS B 206 HIS B 378 HIS ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.088839 restraints weight = 25628.039| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.30 r_work: 0.2786 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17925 Z= 0.140 Angle : 0.604 15.048 24322 Z= 0.300 Chirality : 0.039 0.160 2728 Planarity : 0.003 0.044 2992 Dihedral : 4.573 29.058 2376 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.82 % Allowed : 19.52 % Favored : 77.66 % 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: 2.64 (0.14), residues: 1288 sheet: 0.69 (0.58), residues: 56 loop : -1.25 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 432 TYR 0.012 0.001 TYR D 374 PHE 0.023 0.001 PHE B 266 TRP 0.016 0.001 TRP B 272 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17924) covalent geometry : angle 0.60377 / 0.30 (24320) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 1.95550 / 1.03 ( 2) hydrogen bonds : bond 0.03804 / 2.54 ( 1034) hydrogen bonds : angle 3.71490 / 2.56 ( 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 439 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 386 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8315 (tp40) cc_final: 0.7766 (tp40) REVERT: A 293 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8746 (mm-30) REVERT: A 343 SER cc_start: 0.9257 (m) cc_final: 0.9027 (p) REVERT: A 383 ASP cc_start: 0.8327 (t0) cc_final: 0.7753 (t0) REVERT: A 385 SER cc_start: 0.8700 (t) cc_final: 0.8436 (m) REVERT: A 420 ARG cc_start: 0.8938 (mmm-85) cc_final: 0.8434 (mmm-85) REVERT: A 428 ARG cc_start: 0.8891 (ttm110) cc_final: 0.8114 (ttp-110) REVERT: A 471 ASP cc_start: 0.8849 (m-30) cc_final: 0.8429 (t0) REVERT: A 505 SER cc_start: 0.8454 (p) cc_final: 0.8196 (m) REVERT: A 575 ARG cc_start: 0.8322 (mmp-170) cc_final: 0.7909 (mtm110) REVERT: A 741 CYS cc_start: 0.8899 (m) cc_final: 0.8588 (m) REVERT: D 214 MET cc_start: 0.7999 (tpt) cc_final: 0.7573 (tpt) REVERT: D 216 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8968 (tp) REVERT: D 246 TYR cc_start: 0.9072 (t80) cc_final: 0.8785 (t80) REVERT: D 258 THR cc_start: 0.8214 (p) cc_final: 0.7986 (p) REVERT: D 273 GLN cc_start: 0.8285 (tp40) cc_final: 0.7750 (tp-100) REVERT: D 276 ASP cc_start: 0.8587 (t0) cc_final: 0.8333 (t0) REVERT: D 293 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8747 (mm-30) REVERT: D 471 ASP cc_start: 0.8875 (m-30) cc_final: 0.8484 (t0) REVERT: D 505 SER cc_start: 0.8338 (p) cc_final: 0.8092 (p) REVERT: D 738 TYR cc_start: 0.8414 (m-10) cc_final: 0.8169 (m-10) REVERT: B 214 MET cc_start: 0.8016 (tpt) cc_final: 0.7552 (tpt) REVERT: B 246 TYR cc_start: 0.8968 (t80) cc_final: 0.8606 (t80) REVERT: B 273 GLN cc_start: 0.8128 (tp40) cc_final: 0.7683 (tp40) REVERT: B 276 ASP cc_start: 0.8585 (t0) cc_final: 0.8355 (t0) REVERT: B 283 VAL cc_start: 0.9022 (t) cc_final: 0.8783 (t) REVERT: B 293 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8727 (mm-30) REVERT: B 308 MET cc_start: 0.9380 (tpp) cc_final: 0.9131 (tpp) REVERT: B 471 ASP cc_start: 0.8898 (m-30) cc_final: 0.8546 (t0) REVERT: B 505 SER cc_start: 0.8386 (p) cc_final: 0.8181 (p) REVERT: B 575 ARG cc_start: 0.8292 (mmp-170) cc_final: 0.7832 (mtm110) REVERT: B 710 LYS cc_start: 0.8978 (tppt) cc_final: 0.8659 (ttpp) REVERT: C 214 MET cc_start: 0.8158 (tpt) cc_final: 0.7678 (tpt) REVERT: C 246 TYR cc_start: 0.9034 (t80) cc_final: 0.8764 (t80) REVERT: C 271 SER cc_start: 0.9003 (m) cc_final: 0.8768 (p) REVERT: C 293 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8757 (mm-30) REVERT: C 315 LEU cc_start: 0.9213 (mm) cc_final: 0.8844 (mt) REVERT: C 428 ARG cc_start: 0.8865 (ttm110) cc_final: 0.8656 (ttm110) REVERT: C 471 ASP cc_start: 0.8870 (m-30) cc_final: 0.8494 (t0) REVERT: C 572 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8890 (ttp) REVERT: C 748 ASN cc_start: 0.9099 (t0) cc_final: 0.8737 (t0) outliers start: 53 outliers final: 27 residues processed: 411 average time/residue: 0.4608 time to fit residues: 214.4835 Evaluate side-chains 405 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 376 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 392 LYS 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 216 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 D residue 741 CYS 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 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 572 MET Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 154 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS 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 = 0.3571 r_free = 0.3571 target = 0.132647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.088884 restraints weight = 25453.231| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.31 r_work: 0.2791 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17925 Z= 0.135 Angle : 0.618 14.487 24322 Z= 0.304 Chirality : 0.039 0.160 2728 Planarity : 0.003 0.044 2992 Dihedral : 4.547 28.423 2376 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.23 % Allowed : 20.48 % Favored : 77.29 % 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 (0.19), residues: 2120 helix: 2.63 (0.14), residues: 1288 sheet: 0.61 (0.59), residues: 56 loop : -1.25 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 331 TYR 0.013 0.001 TYR C 374 PHE 0.015 0.001 PHE B 304 TRP 0.018 0.001 TRP B 272 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (17924) covalent geometry : angle 0.61790 / 0.30 (24320) SS BOND : bond 0.00466 / 0.25 ( 1) SS BOND : angle 2.03960 / 1.08 ( 2) hydrogen bonds : bond 0.03742 / 2.51 ( 1034) hydrogen bonds : angle 3.71960 / 2.57 ( 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 438 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 396 time to evaluate : 0.569 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: 0.9010 (t80) cc_final: 0.8653 (t80) REVERT: A 273 GLN cc_start: 0.8302 (tp40) cc_final: 0.7792 (tp-100) REVERT: A 293 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8761 (mm-30) REVERT: A 343 SER cc_start: 0.9269 (m) cc_final: 0.9056 (p) REVERT: A 383 ASP cc_start: 0.8335 (t0) cc_final: 0.7762 (t0) REVERT: A 385 SER cc_start: 0.8698 (t) cc_final: 0.8425 (m) REVERT: A 420 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8404 (mmm-85) REVERT: A 428 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8120 (ttp-110) REVERT: A 471 ASP cc_start: 0.8860 (m-30) cc_final: 0.8445 (t0) REVERT: A 499 ARG cc_start: 0.8740 (tpp-160) cc_final: 0.8336 (mmt-90) REVERT: A 505 SER cc_start: 0.8432 (p) cc_final: 0.8203 (m) REVERT: A 575 ARG cc_start: 0.8346 (mmp-170) cc_final: 0.7901 (mtm110) REVERT: A 682 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8062 (ttp) REVERT: A 710 LYS cc_start: 0.8964 (tppt) cc_final: 0.8656 (ttpp) REVERT: A 741 CYS cc_start: 0.8898 (m) cc_final: 0.8575 (m) REVERT: A 748 ASN cc_start: 0.9158 (t0) cc_final: 0.8648 (t0) REVERT: D 214 MET cc_start: 0.7915 (tpt) cc_final: 0.7519 (tpt) REVERT: D 246 TYR cc_start: 0.9086 (t80) cc_final: 0.8780 (t80) REVERT: D 258 THR cc_start: 0.8238 (p) cc_final: 0.8007 (p) REVERT: D 273 GLN cc_start: 0.8245 (tp40) cc_final: 0.7772 (tp40) REVERT: D 276 ASP cc_start: 0.8546 (t0) cc_final: 0.8319 (t0) REVERT: D 293 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8697 (mm-30) REVERT: D 405 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7824 (mm-30) REVERT: D 471 ASP cc_start: 0.8891 (m-30) cc_final: 0.8493 (t0) REVERT: D 505 SER cc_start: 0.8286 (p) cc_final: 0.7735 (m) REVERT: D 738 TYR cc_start: 0.8394 (m-10) cc_final: 0.8147 (m-10) REVERT: B 214 MET cc_start: 0.7917 (tpt) cc_final: 0.7434 (tpt) REVERT: B 246 TYR cc_start: 0.8945 (t80) cc_final: 0.8602 (t80) REVERT: B 273 GLN cc_start: 0.8129 (tp40) cc_final: 0.7713 (tp40) REVERT: B 276 ASP cc_start: 0.8573 (t0) cc_final: 0.8338 (t0) REVERT: B 293 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8737 (mm-30) REVERT: B 331 ARG cc_start: 0.8887 (ttm110) cc_final: 0.8482 (mtt90) REVERT: B 420 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8619 (mmm-85) REVERT: B 471 ASP cc_start: 0.8893 (m-30) cc_final: 0.8545 (t0) REVERT: B 505 SER cc_start: 0.8328 (p) cc_final: 0.7932 (m) REVERT: B 575 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7854 (mtm110) REVERT: B 710 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8664 (ttpp) REVERT: C 214 MET cc_start: 0.8134 (tpt) cc_final: 0.7653 (tpt) REVERT: C 246 TYR cc_start: 0.9057 (t80) cc_final: 0.8809 (t80) REVERT: C 271 SER cc_start: 0.9004 (m) cc_final: 0.8791 (p) REVERT: C 293 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8761 (mm-30) REVERT: C 428 ARG cc_start: 0.8877 (ttm110) cc_final: 0.8065 (ttm110) REVERT: C 471 ASP cc_start: 0.8886 (m-30) cc_final: 0.8518 (t0) REVERT: C 572 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8900 (ttp) REVERT: C 748 ASN cc_start: 0.9114 (t0) cc_final: 0.8623 (t0) outliers start: 42 outliers final: 24 residues processed: 415 average time/residue: 0.4521 time to fit residues: 212.4800 Evaluate side-chains 403 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 375 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 392 LYS 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 A residue 682 MET Chi-restraints excluded: chain D residue 304 PHE 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 D residue 741 CYS 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 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 710 LYS 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 572 MET 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: 0.9980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 148 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 410 HIS B 206 HIS B 378 HIS C 269 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.090693 restraints weight = 25632.692| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.34 r_work: 0.2821 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17925 Z= 0.119 Angle : 0.630 15.088 24322 Z= 0.305 Chirality : 0.039 0.160 2728 Planarity : 0.003 0.045 2992 Dihedral : 4.465 27.755 2376 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.07 % Allowed : 20.64 % Favored : 77.29 % 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: 1.91 (0.19), residues: 2120 helix: 2.66 (0.14), residues: 1288 sheet: 1.04 (0.61), residues: 56 loop : -1.24 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 331 TYR 0.016 0.001 TYR B 374 PHE 0.026 0.001 PHE B 266 TRP 0.018 0.001 TRP B 272 HIS 0.005 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (17924) covalent geometry : angle 0.62988 / 0.31 (24320) SS BOND : bond 0.00436 / 0.23 ( 1) SS BOND : angle 1.73066 / 0.91 ( 2) hydrogen bonds : bond 0.03549 / 2.39 ( 1034) hydrogen bonds : angle 3.69858 / 2.56 ( 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 433 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 394 time to evaluate : 0.527 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 273 GLN cc_start: 0.8259 (tp40) cc_final: 0.7665 (tp-100) REVERT: A 293 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8753 (mm-30) REVERT: A 343 SER cc_start: 0.9251 (m) cc_final: 0.9038 (p) REVERT: A 378 HIS cc_start: 0.8321 (p90) cc_final: 0.7767 (p90) REVERT: A 383 ASP cc_start: 0.8311 (t0) cc_final: 0.7621 (t0) REVERT: A 385 SER cc_start: 0.8623 (t) cc_final: 0.8381 (m) REVERT: A 405 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7850 (mm-30) REVERT: A 420 ARG cc_start: 0.8914 (mmm-85) cc_final: 0.8425 (mmm-85) REVERT: A 428 ARG cc_start: 0.8859 (ttm110) cc_final: 0.7999 (ttm110) REVERT: A 471 ASP cc_start: 0.8854 (m-30) cc_final: 0.8357 (t0) REVERT: A 505 SER cc_start: 0.8351 (p) cc_final: 0.8064 (m) REVERT: A 575 ARG cc_start: 0.8377 (mmp-170) cc_final: 0.7917 (mtm110) REVERT: A 682 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7862 (ttp) REVERT: A 710 LYS cc_start: 0.8977 (tppt) cc_final: 0.8661 (ttpp) REVERT: A 741 CYS cc_start: 0.8871 (m) cc_final: 0.8564 (m) REVERT: D 214 MET cc_start: 0.7783 (tpt) cc_final: 0.7519 (tpt) REVERT: D 246 TYR cc_start: 0.9068 (t80) cc_final: 0.8789 (t80) REVERT: D 258 THR cc_start: 0.8203 (p) cc_final: 0.7972 (p) REVERT: D 273 GLN cc_start: 0.8139 (tp40) cc_final: 0.7561 (tp-100) REVERT: D 293 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8744 (mm-30) REVERT: D 311 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8672 (mm-30) REVERT: D 405 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7815 (mm-30) REVERT: D 471 ASP cc_start: 0.8889 (m-30) cc_final: 0.8443 (t0) REVERT: D 505 SER cc_start: 0.8200 (p) cc_final: 0.7752 (m) REVERT: D 682 MET cc_start: 0.8491 (ttm) cc_final: 0.7868 (ttp) REVERT: D 738 TYR cc_start: 0.8256 (m-10) cc_final: 0.7996 (m-10) REVERT: B 214 MET cc_start: 0.7791 (tpt) cc_final: 0.7072 (tpt) REVERT: B 246 TYR cc_start: 0.8961 (t80) cc_final: 0.8608 (t80) REVERT: B 273 GLN cc_start: 0.8107 (tp40) cc_final: 0.7844 (tp40) REVERT: B 276 ASP cc_start: 0.8567 (t0) cc_final: 0.8351 (t0) REVERT: B 293 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8744 (mm-30) REVERT: B 331 ARG cc_start: 0.8894 (ttm110) cc_final: 0.8560 (mtt90) REVERT: B 391 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8291 (tm-30) REVERT: B 420 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8627 (mmm-85) REVERT: B 471 ASP cc_start: 0.8866 (m-30) cc_final: 0.8503 (t0) REVERT: B 505 SER cc_start: 0.8294 (p) cc_final: 0.7929 (m) REVERT: B 575 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7868 (mtm110) REVERT: B 682 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: B 710 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8689 (ttpp) REVERT: C 214 MET cc_start: 0.7947 (tpt) cc_final: 0.7492 (tpt) REVERT: C 246 TYR cc_start: 0.9072 (t80) cc_final: 0.8824 (t80) REVERT: C 271 SER cc_start: 0.8984 (m) cc_final: 0.8770 (p) REVERT: C 293 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8769 (mm-30) REVERT: C 428 ARG cc_start: 0.8868 (ttm110) cc_final: 0.8070 (ttm110) REVERT: C 471 ASP cc_start: 0.8871 (m-30) cc_final: 0.8503 (t0) REVERT: C 505 SER cc_start: 0.8578 (p) cc_final: 0.8205 (m) REVERT: C 572 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8954 (ttp) REVERT: C 682 MET cc_start: 0.8543 (tpp) cc_final: 0.8333 (mtp) outliers start: 39 outliers final: 22 residues processed: 409 average time/residue: 0.4384 time to fit residues: 204.0284 Evaluate side-chains 405 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 378 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 493 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 682 MET 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 D residue 741 CYS 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 575 ARG Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain B residue 710 LYS 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 512 SER Chi-restraints excluded: chain C residue 572 MET 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: 0.6980 chunk 207 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 137 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 ASN D 410 HIS ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.090732 restraints weight = 25512.266| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.33 r_work: 0.2823 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17925 Z= 0.118 Angle : 0.636 15.578 24322 Z= 0.308 Chirality : 0.039 0.161 2728 Planarity : 0.003 0.044 2992 Dihedral : 4.457 28.129 2376 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.02 % Allowed : 21.44 % 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: 1.90 (0.19), residues: 2120 helix: 2.68 (0.14), residues: 1284 sheet: 0.92 (0.64), residues: 56 loop : -1.26 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 331 TYR 0.021 0.001 TYR B 374 PHE 0.015 0.001 PHE B 304 TRP 0.030 0.001 TRP A 272 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (17924) covalent geometry : angle 0.63581 / 0.31 (24320) SS BOND : bond 0.00432 / 0.23 ( 1) SS BOND : angle 1.59536 / 0.84 ( 2) hydrogen bonds : bond 0.03505 / 2.34 ( 1034) hydrogen bonds : angle 3.68271 / 2.55 ( 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 431 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 393 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 TRP cc_start: 0.7375 (m-10) cc_final: 0.7093 (m-10) REVERT: A 273 GLN cc_start: 0.8200 (tp40) cc_final: 0.7603 (tp-100) REVERT: A 293 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8764 (mm-30) REVERT: A 383 ASP cc_start: 0.8304 (t0) cc_final: 0.7607 (t0) REVERT: A 385 SER cc_start: 0.8607 (t) cc_final: 0.8335 (m) REVERT: A 405 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7830 (mm-30) REVERT: A 420 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8423 (mmm-85) REVERT: A 428 ARG cc_start: 0.8881 (ttm110) cc_final: 0.8029 (ttm110) REVERT: A 471 ASP cc_start: 0.8845 (m-30) cc_final: 0.8342 (t0) REVERT: A 505 SER cc_start: 0.8367 (p) cc_final: 0.8102 (m) REVERT: A 575 ARG cc_start: 0.8365 (mmp-170) cc_final: 0.7901 (mtm110) REVERT: A 682 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7991 (ttp) REVERT: A 710 LYS cc_start: 0.8970 (tppt) cc_final: 0.8676 (ttpp) REVERT: A 741 CYS cc_start: 0.8868 (m) cc_final: 0.8550 (m) REVERT: D 214 MET cc_start: 0.7766 (tpt) cc_final: 0.7515 (tpt) REVERT: D 246 TYR cc_start: 0.9071 (t80) cc_final: 0.8791 (t80) REVERT: D 258 THR cc_start: 0.8199 (p) cc_final: 0.7968 (p) REVERT: D 273 GLN cc_start: 0.8131 (tp40) cc_final: 0.7731 (tp40) REVERT: D 293 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8744 (mm-30) REVERT: D 471 ASP cc_start: 0.8878 (m-30) cc_final: 0.8429 (t0) REVERT: D 505 SER cc_start: 0.8166 (p) cc_final: 0.7795 (m) REVERT: D 682 MET cc_start: 0.8466 (ttm) cc_final: 0.8069 (mtt) REVERT: D 710 LYS cc_start: 0.8956 (tppt) cc_final: 0.8649 (ttpp) REVERT: D 738 TYR cc_start: 0.8209 (m-10) cc_final: 0.7938 (m-10) REVERT: B 214 MET cc_start: 0.7809 (tpt) cc_final: 0.7432 (tpt) REVERT: B 246 TYR cc_start: 0.8957 (t80) cc_final: 0.8606 (t80) REVERT: B 273 GLN cc_start: 0.8097 (tp40) cc_final: 0.7837 (tp40) REVERT: B 276 ASP cc_start: 0.8548 (t0) cc_final: 0.8332 (t0) REVERT: B 293 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8682 (mm-30) REVERT: B 331 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8426 (mtt90) REVERT: B 420 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8651 (mmm-85) REVERT: B 471 ASP cc_start: 0.8852 (m-30) cc_final: 0.8492 (t0) REVERT: B 505 SER cc_start: 0.8251 (p) cc_final: 0.7902 (m) REVERT: B 575 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7863 (mtm110) REVERT: B 682 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7955 (ttp) REVERT: B 710 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8719 (ttpp) REVERT: C 214 MET cc_start: 0.7983 (tpt) cc_final: 0.7519 (tpt) REVERT: C 246 TYR cc_start: 0.9068 (t80) cc_final: 0.8818 (t80) REVERT: C 293 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8759 (mm-30) REVERT: C 420 ARG cc_start: 0.8781 (mtt-85) cc_final: 0.8494 (mtt90) REVERT: C 471 ASP cc_start: 0.8855 (m-30) cc_final: 0.8491 (t0) REVERT: C 505 SER cc_start: 0.8543 (p) cc_final: 0.8203 (m) REVERT: C 572 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8936 (ttp) outliers start: 38 outliers final: 23 residues processed: 408 average time/residue: 0.4559 time to fit residues: 211.4538 Evaluate side-chains 412 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 384 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 493 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 682 MET 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 D residue 741 CYS 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 575 ARG Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain B residue 710 LYS 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 512 SER Chi-restraints excluded: chain C residue 572 MET 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: 0.5980 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.0470 chunk 126 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 410 HIS ** B 206 HIS ** 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 = 0.3602 r_free = 0.3602 target = 0.135371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.091491 restraints weight = 25679.364| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.36 r_work: 0.2843 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17925 Z= 0.115 Angle : 0.644 15.616 24322 Z= 0.309 Chirality : 0.038 0.161 2728 Planarity : 0.003 0.045 2992 Dihedral : 4.432 27.656 2376 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.91 % Allowed : 21.86 % Favored : 76.22 % 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: 1.91 (0.19), residues: 2120 helix: 2.64 (0.14), residues: 1288 sheet: 1.33 (0.65), residues: 56 loop : -1.23 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 331 TYR 0.011 0.001 TYR C 374 PHE 0.028 0.001 PHE B 266 TRP 0.034 0.001 TRP A 272 HIS 0.005 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (17924) covalent geometry : angle 0.64427 / 0.31 (24320) SS BOND : bond 0.00413 / 0.22 ( 1) SS BOND : angle 1.46667 / 0.78 ( 2) hydrogen bonds : bond 0.03441 / 2.31 ( 1034) hydrogen bonds : angle 3.67088 / 2.55 ( 2991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6576.83 seconds wall clock time: 112 minutes 19.07 seconds (6739.07 seconds total)