Starting phenix.real_space_refine on Sat Jun 14 18:56:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxf_37905/06_2025/8wxf_37905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxf_37905/06_2025/8wxf_37905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wxf_37905/06_2025/8wxf_37905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxf_37905/06_2025/8wxf_37905.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxf_37905/06_2025/8wxf_37905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxf_37905/06_2025/8wxf_37905.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 10302 2.51 5 N 2820 2.21 5 O 3210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16380 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Chain: "B" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Chain: "C" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Time building chain proxies: 9.81, per 1000 atoms: 0.60 Number of scatterers: 16380 At special positions: 0 Unit cell: (116.16, 113.52, 146.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 3210 8.00 N 2820 7.00 C 10302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.26 Conformation dependent library (CDL) restraints added in 2.3 seconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 21 sheets defined 34.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.645A pdb=" N ALA A 81 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 82 " --> pdb=" O MET A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 82' Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.099A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 254 Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 283 through 293 removed outlier: 4.055A pdb=" N ALA A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.500A pdb=" N GLY A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.220A pdb=" N THR A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 561 through 584 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 617 through 626 Processing helix chain 'A' and resid 643 through 658 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.917A pdb=" N ALA B 82 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 225 through 254 Proline residue: B 238 - end of helix removed outlier: 3.673A pdb=" N ALA B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 283 through 292 removed outlier: 4.024A pdb=" N ALA B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 314 Processing helix chain 'B' and resid 321 through 343 Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.540A pdb=" N GLY B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 561 through 584 Processing helix chain 'B' and resid 606 through 611 removed outlier: 4.488A pdb=" N VAL B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 643 through 659 removed outlier: 3.753A pdb=" N ASN B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.617A pdb=" N ALA C 81 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 82 " --> pdb=" O MET C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 139 through 153 Processing helix chain 'C' and resid 178 through 185 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 225 through 254 Proline residue: C 238 - end of helix Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.528A pdb=" N ILE C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 4.041A pdb=" N ASP C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 344 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.640A pdb=" N THR C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 removed outlier: 3.550A pdb=" N ILE C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.646A pdb=" N GLY C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'C' and resid 561 through 584 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.539A pdb=" N ILE C 607 " --> pdb=" O PRO C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 643 through 658 Processing helix chain 'C' and resid 694 through 699 removed outlier: 4.555A pdb=" N GLY C 699 " --> pdb=" O ILE C 695 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.777A pdb=" N ILE A 17 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 25 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 52 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET A 51 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 124 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 125 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.615A pdb=" N VAL A 190 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 205 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 192 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.921A pdb=" N GLN A 380 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 457 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET A 408 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 460 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 410 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ALA A 462 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.800A pdb=" N ALA A 539 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.869A pdb=" N LEU A 499 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.344A pdb=" N MET B 51 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 124 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 125 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.997A pdb=" N PHE B 187 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 190 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 205 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 192 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 381 through 388 removed outlier: 6.721A pdb=" N MET B 408 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER B 460 " --> pdb=" O MET B 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 498 through 499 Processing sheet with id=AB4, first strand: chain 'B' and resid 539 through 540 removed outlier: 6.834A pdb=" N ALA B 539 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 removed outlier: 5.739A pdb=" N GLU C 5 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 7 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 25 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 17 " --> pdb=" O ARG C 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 7 removed outlier: 5.739A pdb=" N GLU C 5 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 7 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 30 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 52 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET C 51 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 124 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 125 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 172 through 175 removed outlier: 6.718A pdb=" N VAL C 190 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL C 205 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 192 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 380 through 388 removed outlier: 6.174A pdb=" N GLN C 380 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET C 408 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER C 460 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 498 through 500 removed outlier: 3.764A pdb=" N VAL C 519 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 539 through 540 removed outlier: 6.870A pdb=" N ALA C 539 " --> pdb=" O THR C 546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 629 through 631 removed outlier: 3.633A pdb=" N PHE C 638 " --> pdb=" O SER C 630 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 723 through 724 removed outlier: 4.114A pdb=" N ASP C 723 " --> pdb=" O SER C 731 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 731 " --> pdb=" O ASP C 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 657 hydrogen bonds defined for protein. 1878 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: 5.63 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5634 1.34 - 1.46: 3225 1.46 - 1.58: 7680 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 16626 Sorted by residual: bond pdb=" N VAL B 278 " pdb=" CA VAL B 278 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.19e+00 bond pdb=" N GLU C 77 " pdb=" CA GLU C 77 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.52e+00 bond pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.23e-02 6.61e+03 6.52e+00 bond pdb=" N LEU C 313 " pdb=" CA LEU C 313 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.17e+00 bond pdb=" N MET C 497 " pdb=" CA MET C 497 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.07e+00 ... (remaining 16621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 22045 2.05 - 4.10: 436 4.10 - 6.15: 64 6.15 - 8.20: 14 8.20 - 10.25: 7 Bond angle restraints: 22566 Sorted by residual: angle pdb=" N VAL C 186 " pdb=" CA VAL C 186 " pdb=" C VAL C 186 " ideal model delta sigma weight residual 113.47 108.80 4.67 1.01e+00 9.80e-01 2.14e+01 angle pdb=" N VAL A 510 " pdb=" CA VAL A 510 " pdb=" C VAL A 510 " ideal model delta sigma weight residual 113.71 109.59 4.12 9.50e-01 1.11e+00 1.88e+01 angle pdb=" N ASP C 47 " pdb=" CA ASP C 47 " pdb=" C ASP C 47 " ideal model delta sigma weight residual 112.86 107.89 4.97 1.22e+00 6.72e-01 1.66e+01 angle pdb=" CA GLU A 515 " pdb=" CB GLU A 515 " pdb=" CG GLU A 515 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLN A 311 " pdb=" CB GLN A 311 " pdb=" CG GLN A 311 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.37e+01 ... (remaining 22561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8590 17.48 - 34.97: 1139 34.97 - 52.45: 290 52.45 - 69.93: 51 69.93 - 87.42: 34 Dihedral angle restraints: 10104 sinusoidal: 3918 harmonic: 6186 Sorted by residual: dihedral pdb=" CA GLU B 515 " pdb=" C GLU B 515 " pdb=" N ARG B 516 " pdb=" CA ARG B 516 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU A 554 " pdb=" C LEU A 554 " pdb=" N ASP A 555 " pdb=" CA ASP A 555 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 524 " pdb=" C ILE B 524 " pdb=" N LEU B 525 " pdb=" CA LEU B 525 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 10101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1995 0.047 - 0.095: 502 0.095 - 0.142: 169 0.142 - 0.189: 8 0.189 - 0.236: 2 Chirality restraints: 2676 Sorted by residual: chirality pdb=" CB VAL B 561 " pdb=" CA VAL B 561 " pdb=" CG1 VAL B 561 " pdb=" CG2 VAL B 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL A 561 " pdb=" CA VAL A 561 " pdb=" CG1 VAL A 561 " pdb=" CG2 VAL A 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL B 278 " pdb=" N VAL B 278 " pdb=" C VAL B 278 " pdb=" CB VAL B 278 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 2673 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 557 " 0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO B 558 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 558 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 558 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 267 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO B 268 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 47 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" CG ASP B 47 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP B 47 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP B 47 " 0.019 2.00e-02 2.50e+03 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1107 2.73 - 3.27: 17011 3.27 - 3.82: 25895 3.82 - 4.36: 28346 4.36 - 4.90: 48783 Nonbonded interactions: 121142 Sorted by model distance: nonbonded pdb=" O ASP A 343 " pdb=" ND1 HIS A 344 " model vdw 2.188 3.120 nonbonded pdb=" O ASN A 655 " pdb=" NE2 GLN A 661 " model vdw 2.224 3.120 nonbonded pdb=" O ALA B 287 " pdb=" OG1 THR B 291 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG C 356 " pdb=" OD2 ASP C 523 " model vdw 2.239 3.120 nonbonded pdb=" NH1 ARG C 350 " pdb=" O GLY C 351 " model vdw 2.243 3.120 ... (remaining 121137 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.540 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.003 0.045 16626 Z= 0.164 Angle : 0.709 10.247 22566 Z= 0.386 Chirality : 0.046 0.236 2676 Planarity : 0.005 0.087 2979 Dihedral : 17.293 87.415 6138 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 0.75 % Allowed : 33.16 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2184 helix: 0.61 (0.20), residues: 693 sheet: -1.44 (0.31), residues: 325 loop : -1.55 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 173 HIS 0.003 0.001 HIS B 409 PHE 0.014 0.001 PHE C 531 TYR 0.010 0.001 TYR B 276 ARG 0.008 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.17475 ( 654) hydrogen bonds : angle 6.96870 ( 1878) covalent geometry : bond 0.00325 (16626) covalent geometry : angle 0.70893 (22566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ASP cc_start: 0.9054 (m-30) cc_final: 0.8764 (p0) REVERT: A 333 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8944 (tttt) REVERT: A 337 ARG cc_start: 0.9115 (mtp85) cc_final: 0.8662 (mtp85) REVERT: B 328 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9277 (mt) REVERT: C 208 GLU cc_start: 0.6663 (tp30) cc_final: 0.6335 (tp30) REVERT: C 249 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8224 (mt-10) REVERT: C 482 LEU cc_start: 0.8746 (mm) cc_final: 0.8314 (mm) REVERT: C 495 ILE cc_start: 0.8605 (mp) cc_final: 0.8190 (mm) REVERT: C 534 MET cc_start: 0.7696 (tpt) cc_final: 0.7452 (tpp) outliers start: 13 outliers final: 4 residues processed: 199 average time/residue: 0.2747 time to fit residues: 84.7651 Evaluate side-chains 184 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.149281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103565 restraints weight = 30872.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106557 restraints weight = 17799.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108595 restraints weight = 12478.935| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16626 Z= 0.132 Angle : 0.601 10.292 22566 Z= 0.310 Chirality : 0.044 0.201 2676 Planarity : 0.005 0.060 2979 Dihedral : 4.694 55.626 2357 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.73 % Rotamer: Outliers : 4.44 % Allowed : 28.09 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2184 helix: 0.88 (0.20), residues: 697 sheet: -1.21 (0.30), residues: 329 loop : -1.37 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 173 HIS 0.002 0.000 HIS C 694 PHE 0.018 0.001 PHE A 531 TYR 0.012 0.001 TYR B 270 ARG 0.004 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 654) hydrogen bonds : angle 5.34838 ( 1878) covalent geometry : bond 0.00302 (16626) covalent geometry : angle 0.60146 (22566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7448 (tp30) cc_final: 0.7188 (tp30) REVERT: A 333 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8821 (tttt) REVERT: A 345 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8520 (p90) REVERT: A 482 LEU cc_start: 0.9088 (mm) cc_final: 0.8597 (mm) REVERT: A 522 THR cc_start: 0.9317 (m) cc_final: 0.8852 (p) REVERT: B 389 MET cc_start: 0.8163 (mmm) cc_final: 0.7918 (mtt) REVERT: C 215 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8659 (pp20) REVERT: C 482 LEU cc_start: 0.8732 (mm) cc_final: 0.8302 (mm) outliers start: 77 outliers final: 36 residues processed: 244 average time/residue: 0.2285 time to fit residues: 89.2713 Evaluate side-chains 206 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 107 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 50 optimal weight: 0.0000 chunk 17 optimal weight: 0.0970 chunk 76 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 GLN ** 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 = 0.3938 r_free = 0.3938 target = 0.148054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106469 restraints weight = 31010.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104703 restraints weight = 22121.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105729 restraints weight = 19302.015| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16626 Z= 0.158 Angle : 0.592 12.307 22566 Z= 0.302 Chirality : 0.044 0.186 2676 Planarity : 0.005 0.057 2979 Dihedral : 4.452 53.581 2354 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.27 % Favored : 94.60 % Rotamer: Outliers : 5.42 % Allowed : 27.45 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2184 helix: 1.01 (0.20), residues: 702 sheet: -1.27 (0.29), residues: 329 loop : -1.29 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 173 HIS 0.002 0.001 HIS A 410 PHE 0.024 0.001 PHE B 345 TYR 0.012 0.002 TYR A 276 ARG 0.016 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 654) hydrogen bonds : angle 5.06529 ( 1878) covalent geometry : bond 0.00365 (16626) covalent geometry : angle 0.59160 (22566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 171 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8575 (m) REVERT: A 311 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8947 (mm-40) REVERT: A 522 THR cc_start: 0.9302 (m) cc_final: 0.8847 (p) REVERT: B 389 MET cc_start: 0.8297 (mmm) cc_final: 0.8067 (mtt) REVERT: C 30 GLU cc_start: 0.8163 (tt0) cc_final: 0.7793 (mt-10) REVERT: C 50 ASN cc_start: 0.8498 (m-40) cc_final: 0.8240 (m-40) REVERT: C 215 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8701 (pp20) REVERT: C 320 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7149 (mtm-85) outliers start: 94 outliers final: 55 residues processed: 244 average time/residue: 0.2362 time to fit residues: 93.0376 Evaluate side-chains 219 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 87 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 213 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 70 optimal weight: 0.0060 chunk 91 optimal weight: 1.9990 chunk 180 optimal weight: 0.0870 chunk 141 optimal weight: 0.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 GLN ** 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 = 0.3960 r_free = 0.3960 target = 0.149799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107182 restraints weight = 30630.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108468 restraints weight = 17841.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109525 restraints weight = 12670.091| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16626 Z= 0.111 Angle : 0.577 12.363 22566 Z= 0.289 Chirality : 0.044 0.306 2676 Planarity : 0.004 0.053 2979 Dihedral : 4.309 53.569 2354 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 4.33 % Allowed : 28.89 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2184 helix: 1.04 (0.20), residues: 701 sheet: -1.18 (0.29), residues: 330 loop : -1.18 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.004 0.000 HIS A 344 PHE 0.024 0.001 PHE A 345 TYR 0.010 0.001 TYR C 276 ARG 0.004 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 654) hydrogen bonds : angle 4.87098 ( 1878) covalent geometry : bond 0.00251 (16626) covalent geometry : angle 0.57722 (22566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 173 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8960 (mm-40) REVERT: A 482 LEU cc_start: 0.9121 (mm) cc_final: 0.8607 (mm) REVERT: A 522 THR cc_start: 0.9280 (m) cc_final: 0.8769 (p) REVERT: A 643 ASP cc_start: 0.8155 (t0) cc_final: 0.7848 (t70) REVERT: B 51 MET cc_start: 0.8396 (ttt) cc_final: 0.8116 (ttt) REVERT: B 389 MET cc_start: 0.8308 (mmm) cc_final: 0.8026 (mtt) REVERT: C 30 GLU cc_start: 0.8238 (tt0) cc_final: 0.7744 (mt-10) REVERT: C 204 MET cc_start: 0.8912 (tmm) cc_final: 0.8688 (tmm) REVERT: C 215 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8724 (pp20) REVERT: C 320 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6928 (mtm-85) outliers start: 75 outliers final: 49 residues processed: 234 average time/residue: 0.2718 time to fit residues: 104.2667 Evaluate side-chains 223 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 72 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 190 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 458 GLN ** 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 = 0.3962 r_free = 0.3962 target = 0.149955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108247 restraints weight = 31396.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106128 restraints weight = 23314.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107328 restraints weight = 18950.916| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16626 Z= 0.117 Angle : 0.573 13.336 22566 Z= 0.283 Chirality : 0.043 0.255 2676 Planarity : 0.004 0.053 2979 Dihedral : 4.199 52.283 2354 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 4.50 % Allowed : 28.78 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2184 helix: 1.05 (0.20), residues: 705 sheet: -1.13 (0.29), residues: 327 loop : -1.11 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 173 HIS 0.004 0.001 HIS A 344 PHE 0.027 0.001 PHE B 345 TYR 0.009 0.001 TYR A 80 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 654) hydrogen bonds : angle 4.77634 ( 1878) covalent geometry : bond 0.00271 (16626) covalent geometry : angle 0.57256 (22566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 177 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 THR cc_start: 0.9249 (m) cc_final: 0.8769 (p) REVERT: A 643 ASP cc_start: 0.8088 (t0) cc_final: 0.7827 (t70) REVERT: A 695 ILE cc_start: 0.1587 (OUTLIER) cc_final: 0.1359 (pt) REVERT: C 30 GLU cc_start: 0.8245 (tt0) cc_final: 0.7775 (mt-10) REVERT: C 181 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: C 215 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8737 (pp20) REVERT: C 320 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6973 (mtm-85) outliers start: 78 outliers final: 54 residues processed: 241 average time/residue: 0.2590 time to fit residues: 100.9481 Evaluate side-chains 226 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 181 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 66 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 overall best weight: 0.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108656 restraints weight = 31240.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106715 restraints weight = 23763.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107626 restraints weight = 19422.458| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16626 Z= 0.116 Angle : 0.572 13.227 22566 Z= 0.281 Chirality : 0.043 0.233 2676 Planarity : 0.004 0.053 2979 Dihedral : 3.865 51.300 2350 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 3.98 % Allowed : 29.53 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 2184 helix: 1.11 (0.20), residues: 705 sheet: -1.14 (0.29), residues: 328 loop : -1.04 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.005 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.010 0.001 TYR C 276 ARG 0.003 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 654) hydrogen bonds : angle 4.70270 ( 1878) covalent geometry : bond 0.00267 (16626) covalent geometry : angle 0.57179 (22566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 175 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8005 (t0) cc_final: 0.7781 (t0) REVERT: A 412 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8104 (m110) REVERT: A 643 ASP cc_start: 0.8097 (t0) cc_final: 0.7815 (t70) REVERT: A 695 ILE cc_start: 0.1549 (OUTLIER) cc_final: 0.1332 (pt) REVERT: B 79 MET cc_start: 0.8289 (tpp) cc_final: 0.8023 (tpp) REVERT: B 590 MET cc_start: 0.5887 (tpp) cc_final: 0.5630 (tpp) REVERT: C 30 GLU cc_start: 0.8249 (tt0) cc_final: 0.7759 (mt-10) REVERT: C 181 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: C 215 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8730 (pp20) REVERT: C 320 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6863 (mtm-85) outliers start: 69 outliers final: 57 residues processed: 231 average time/residue: 0.2471 time to fit residues: 92.6556 Evaluate side-chains 232 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 50 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 98 optimal weight: 0.0030 chunk 181 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 65 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** 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 = 0.3953 r_free = 0.3953 target = 0.149162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107899 restraints weight = 31197.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106220 restraints weight = 22479.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107281 restraints weight = 18848.090| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16626 Z= 0.129 Angle : 0.581 13.374 22566 Z= 0.285 Chirality : 0.043 0.225 2676 Planarity : 0.004 0.053 2979 Dihedral : 3.864 50.332 2350 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 4.67 % Allowed : 29.30 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 2184 helix: 1.12 (0.20), residues: 708 sheet: -1.01 (0.29), residues: 319 loop : -1.05 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.010 0.001 TYR A 80 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 654) hydrogen bonds : angle 4.67500 ( 1878) covalent geometry : bond 0.00297 (16626) covalent geometry : angle 0.58107 (22566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 171 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8022 (t0) cc_final: 0.7796 (t70) REVERT: A 303 ASP cc_start: 0.9001 (m-30) cc_final: 0.8731 (p0) REVERT: A 643 ASP cc_start: 0.8113 (t0) cc_final: 0.7877 (t70) REVERT: A 695 ILE cc_start: 0.1576 (OUTLIER) cc_final: 0.1357 (pt) REVERT: B 208 GLU cc_start: 0.7590 (tp30) cc_final: 0.7170 (tp30) REVERT: B 495 ILE cc_start: 0.8960 (mp) cc_final: 0.8634 (mm) REVERT: C 30 GLU cc_start: 0.8242 (tt0) cc_final: 0.7727 (mt-10) REVERT: C 181 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: C 215 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8736 (pp20) REVERT: C 320 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6904 (mtm-85) outliers start: 81 outliers final: 66 residues processed: 238 average time/residue: 0.3005 time to fit residues: 116.3649 Evaluate side-chains 237 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 167 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 18 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 70 optimal weight: 0.0040 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.146770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106074 restraints weight = 31160.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103730 restraints weight = 23442.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104974 restraints weight = 19615.584| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16626 Z= 0.179 Angle : 0.615 12.324 22566 Z= 0.306 Chirality : 0.044 0.269 2676 Planarity : 0.005 0.061 2979 Dihedral : 4.005 49.498 2350 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 4.79 % Allowed : 29.12 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2184 helix: 1.15 (0.20), residues: 708 sheet: -1.18 (0.29), residues: 329 loop : -1.12 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.015 0.002 TYR B 80 ARG 0.003 0.000 ARG C 367 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 654) hydrogen bonds : angle 4.75017 ( 1878) covalent geometry : bond 0.00413 (16626) covalent geometry : angle 0.61479 (22566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 172 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 695 ILE cc_start: 0.1534 (OUTLIER) cc_final: 0.1287 (pt) REVERT: B 47 ASP cc_start: 0.7913 (t70) cc_final: 0.7638 (t0) REVERT: B 389 MET cc_start: 0.8610 (mmm) cc_final: 0.8020 (mtt) REVERT: B 495 ILE cc_start: 0.8964 (mp) cc_final: 0.8726 (mp) REVERT: B 693 VAL cc_start: 0.4627 (OUTLIER) cc_final: 0.4363 (t) REVERT: C 30 GLU cc_start: 0.8179 (tt0) cc_final: 0.7771 (mt-10) REVERT: C 181 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: C 215 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8765 (pp20) REVERT: C 320 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7133 (mtm-85) REVERT: C 396 ILE cc_start: 0.8507 (pp) cc_final: 0.8290 (pt) outliers start: 83 outliers final: 69 residues processed: 236 average time/residue: 0.2479 time to fit residues: 95.2810 Evaluate side-chains 240 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 166 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 123 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 GLN ** 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 = 0.3909 r_free = 0.3909 target = 0.145743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100299 restraints weight = 30967.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103175 restraints weight = 17987.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.105128 restraints weight = 12665.891| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16626 Z= 0.172 Angle : 0.620 12.227 22566 Z= 0.307 Chirality : 0.044 0.200 2676 Planarity : 0.005 0.061 2979 Dihedral : 4.089 49.989 2350 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 4.84 % Allowed : 29.58 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2184 helix: 1.10 (0.20), residues: 710 sheet: -1.21 (0.29), residues: 331 loop : -1.13 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.005 0.001 HIS A 344 PHE 0.023 0.001 PHE A 531 TYR 0.012 0.001 TYR A 80 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 654) hydrogen bonds : angle 4.77486 ( 1878) covalent geometry : bond 0.00395 (16626) covalent geometry : angle 0.62049 (22566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 168 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8003 (mt-10) REVERT: B 47 ASP cc_start: 0.7999 (t70) cc_final: 0.7695 (t0) REVERT: B 389 MET cc_start: 0.8611 (mmm) cc_final: 0.7918 (mtt) REVERT: B 495 ILE cc_start: 0.8931 (mp) cc_final: 0.8707 (mp) REVERT: B 534 MET cc_start: 0.8220 (tpp) cc_final: 0.7869 (tpt) REVERT: B 693 VAL cc_start: 0.4587 (OUTLIER) cc_final: 0.4303 (t) REVERT: C 30 GLU cc_start: 0.8226 (tt0) cc_final: 0.7708 (mt-10) REVERT: C 181 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8450 (pm20) REVERT: C 215 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8800 (pp20) REVERT: C 320 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7185 (mtm-85) REVERT: C 396 ILE cc_start: 0.8638 (pp) cc_final: 0.8434 (pt) REVERT: C 431 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7590 (tm-30) outliers start: 84 outliers final: 72 residues processed: 237 average time/residue: 0.2355 time to fit residues: 90.3945 Evaluate side-chains 243 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 167 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 72 optimal weight: 20.0000 chunk 217 optimal weight: 30.0000 chunk 202 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** 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 = 0.3912 r_free = 0.3912 target = 0.145873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106007 restraints weight = 31195.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104582 restraints weight = 23928.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105927 restraints weight = 19253.555| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16626 Z= 0.169 Angle : 0.637 12.431 22566 Z= 0.313 Chirality : 0.045 0.207 2676 Planarity : 0.005 0.066 2979 Dihedral : 4.114 49.954 2350 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 4.27 % Allowed : 30.28 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2184 helix: 1.10 (0.20), residues: 709 sheet: -1.36 (0.28), residues: 340 loop : -1.11 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.012 0.001 TYR A 411 ARG 0.003 0.000 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 654) hydrogen bonds : angle 4.76906 ( 1878) covalent geometry : bond 0.00389 (16626) covalent geometry : angle 0.63717 (22566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 168 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7616 (mp0) cc_final: 0.7210 (mp0) REVERT: B 208 GLU cc_start: 0.7902 (tp30) cc_final: 0.7261 (tp30) REVERT: B 389 MET cc_start: 0.8587 (mmm) cc_final: 0.7489 (mmm) REVERT: B 495 ILE cc_start: 0.8975 (mp) cc_final: 0.8665 (mp) REVERT: B 534 MET cc_start: 0.8161 (tpp) cc_final: 0.7903 (tpt) REVERT: B 590 MET cc_start: 0.5806 (tpp) cc_final: 0.5443 (tpp) REVERT: C 215 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8770 (pp20) REVERT: C 320 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7231 (mtm-85) REVERT: C 396 ILE cc_start: 0.8708 (pp) cc_final: 0.8488 (pt) outliers start: 74 outliers final: 68 residues processed: 229 average time/residue: 0.2401 time to fit residues: 89.1692 Evaluate side-chains 230 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 160 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 140 optimal weight: 0.0570 chunk 4 optimal weight: 0.0370 chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 67 optimal weight: 0.0030 chunk 83 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.166228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119379 restraints weight = 30600.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123201 restraints weight = 16300.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125769 restraints weight = 10927.189| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16626 Z= 0.110 Angle : 0.612 12.188 22566 Z= 0.300 Chirality : 0.044 0.201 2676 Planarity : 0.004 0.059 2979 Dihedral : 3.964 49.412 2350 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.35 % Favored : 95.51 % Rotamer: Outliers : 3.11 % Allowed : 31.14 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2184 helix: 1.12 (0.20), residues: 707 sheet: -1.02 (0.29), residues: 326 loop : -1.02 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 173 HIS 0.004 0.000 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.008 0.001 TYR A 454 ARG 0.003 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 654) hydrogen bonds : angle 4.60523 ( 1878) covalent geometry : bond 0.00244 (16626) covalent geometry : angle 0.61221 (22566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5090.92 seconds wall clock time: 91 minutes 21.55 seconds (5481.55 seconds total)