Starting phenix.real_space_refine on Wed Apr 30 02:18:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yyl_39675/04_2025/8yyl_39675.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yyl_39675/04_2025/8yyl_39675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yyl_39675/04_2025/8yyl_39675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yyl_39675/04_2025/8yyl_39675.map" model { file = "/net/cci-nas-00/data/ceres_data/8yyl_39675/04_2025/8yyl_39675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yyl_39675/04_2025/8yyl_39675.cif" } resolution = 4.01 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= 0.012 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 61 5.16 5 C 5710 2.51 5 N 1542 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8981 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4517 Classifications: {'peptide': 559} Link IDs: {'PTRANS': 26, 'TRANS': 532} Chain breaks: 10 Chain: "B" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4101 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 23, 'TRANS': 482} Chain breaks: 6 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain breaks: 1 Time building chain proxies: 5.67, per 1000 atoms: 0.63 Number of scatterers: 8981 At special positions: 0 Unit cell: (85.8, 139.92, 166.32, 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 61 16.00 O 1668 8.00 N 1542 7.00 C 5710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.04 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 215 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.04 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 50 " distance=2.02 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 41 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 22 sheets defined 15.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.766A pdb=" N HIS A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.569A pdb=" N CYS A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.612A pdb=" N GLU A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'B' and resid 342 through 345 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.824A pdb=" N GLU B 356 " --> pdb=" O THR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 386 removed outlier: 4.447A pdb=" N GLU B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 474 removed outlier: 3.765A pdb=" N ILE B 466 " --> pdb=" O CYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.586A pdb=" N GLN B 573 " --> pdb=" O PRO B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 718 through 741 Processing helix chain 'B' and resid 890 through 897 Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.206A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.591A pdb=" N LEU C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.018A pdb=" N GLU A 33 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE A 56 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS A 35 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 83 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.871A pdb=" N MET A 38 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU A 63 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE A 40 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET A 65 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 61 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU A 90 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 63 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG A 92 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 92 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 120 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU A 147 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 122 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 275 Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 307 Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AA8, first strand: chain 'A' and resid 338 through 348 removed outlier: 10.666A pdb=" N VAL A 362 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N LEU A 342 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N ASN A 364 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY A 344 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 338 through 348 removed outlier: 10.666A pdb=" N VAL A 362 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N LEU A 342 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N ASN A 364 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY A 344 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LYS A 396 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 367 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ARG A 398 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE A 369 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 395 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LEU A 430 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 397 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N HIS A 456 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 429 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 500 Processing sheet with id=AB2, first strand: chain 'A' and resid 502 through 507 removed outlier: 6.697A pdb=" N ARG A 515 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 505 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU A 513 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 557 through 561 Processing sheet with id=AB4, first strand: chain 'B' and resid 338 through 340 removed outlier: 6.548A pdb=" N CYS B 339 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 391 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 346 through 348 removed outlier: 3.578A pdb=" N ARG B 398 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 395 " --> pdb=" O TYR B 428 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU B 430 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 397 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N HIS B 456 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 429 " --> pdb=" O HIS B 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 499 through 500 Processing sheet with id=AB7, first strand: chain 'B' and resid 511 through 515 removed outlier: 3.694A pdb=" N ILE B 512 " --> pdb=" O MET B 580 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 580 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 557 through 561 removed outlier: 4.098A pdb=" N GLY B 529 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 626 through 634 removed outlier: 6.741A pdb=" N LYS B 641 " --> pdb=" O PRO B 628 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER B 630 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 639 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER B 632 " --> pdb=" O GLN B 637 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLN B 637 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 786 through 790 removed outlier: 4.271A pdb=" N GLN B 815 " --> pdb=" O ARG B 821 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 821 " --> pdb=" O GLN B 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 786 through 790 Processing sheet with id=AC3, first strand: chain 'B' and resid 846 through 849 Processing sheet with id=AC4, first strand: chain 'B' and resid 883 through 889 removed outlier: 3.543A pdb=" N LEU B 871 " --> pdb=" O THR B 916 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 606 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: 3.33 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2899 1.34 - 1.46: 2171 1.46 - 1.59: 4040 1.59 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 9185 Sorted by residual: bond pdb=" N GLY B 365 " pdb=" CA GLY B 365 " ideal model delta sigma weight residual 1.449 1.477 -0.028 1.45e-02 4.76e+03 3.77e+00 bond pdb=" CG1 ILE C 32 " pdb=" CD1 ILE C 32 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" C GLY B 365 " pdb=" O GLY B 365 " ideal model delta sigma weight residual 1.235 1.213 0.022 1.35e-02 5.49e+03 2.68e+00 bond pdb=" C ALA B 537 " pdb=" O ALA B 537 " ideal model delta sigma weight residual 1.244 1.230 0.014 1.00e-02 1.00e+04 1.96e+00 bond pdb=" CA GLY B 365 " pdb=" C GLY B 365 " ideal model delta sigma weight residual 1.514 1.534 -0.019 1.41e-02 5.03e+03 1.91e+00 ... (remaining 9180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12101 1.85 - 3.71: 268 3.71 - 5.56: 38 5.56 - 7.42: 11 7.42 - 9.27: 5 Bond angle restraints: 12423 Sorted by residual: angle pdb=" N THR A 68 " pdb=" CA THR A 68 " pdb=" C THR A 68 " ideal model delta sigma weight residual 110.50 117.25 -6.75 1.41e+00 5.03e-01 2.29e+01 angle pdb=" N ASN B 376 " pdb=" CA ASN B 376 " pdb=" C ASN B 376 " ideal model delta sigma weight residual 110.91 106.38 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" C ASP B 647 " pdb=" N PRO B 648 " pdb=" CA PRO B 648 " ideal model delta sigma weight residual 119.56 115.69 3.87 1.01e+00 9.80e-01 1.47e+01 angle pdb=" CA MET A 321 " pdb=" CB MET A 321 " pdb=" CG MET A 321 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.62e+00 angle pdb=" N GLY B 365 " pdb=" CA GLY B 365 " pdb=" C GLY B 365 " ideal model delta sigma weight residual 113.18 106.55 6.63 2.37e+00 1.78e-01 7.82e+00 ... (remaining 12418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4847 17.90 - 35.81: 529 35.81 - 53.71: 123 53.71 - 71.61: 24 71.61 - 89.51: 9 Dihedral angle restraints: 5532 sinusoidal: 2306 harmonic: 3226 Sorted by residual: dihedral pdb=" CB CYS A 35 " pdb=" SG CYS A 35 " pdb=" SG CYS A 53 " pdb=" CB CYS A 53 " ideal model delta sinusoidal sigma weight residual 93.00 45.30 47.70 1 1.00e+01 1.00e-02 3.14e+01 dihedral pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " pdb=" SG CYS A 215 " pdb=" CB CYS A 215 " ideal model delta sinusoidal sigma weight residual -86.00 -43.23 -42.77 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS C 19 " pdb=" SG CYS C 19 " pdb=" SG CYS C 50 " pdb=" CB CYS C 50 " ideal model delta sinusoidal sigma weight residual -86.00 -127.50 41.50 1 1.00e+01 1.00e-02 2.41e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 893 0.037 - 0.074: 298 0.074 - 0.111: 122 0.111 - 0.149: 30 0.149 - 0.186: 7 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CB ILE B 415 " pdb=" CA ILE B 415 " pdb=" CG1 ILE B 415 " pdb=" CG2 ILE B 415 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CB ILE B 369 " pdb=" CA ILE B 369 " pdb=" CG1 ILE B 369 " pdb=" CG2 ILE B 369 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB ILE B 512 " pdb=" CA ILE B 512 " pdb=" CG1 ILE B 512 " pdb=" CG2 ILE B 512 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 1347 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 517 " -0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 518 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 521 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 522 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 258 " 0.013 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE A 258 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 258 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 258 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 258 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 258 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 258 " 0.001 2.00e-02 2.50e+03 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 530 2.73 - 3.27: 8896 3.27 - 3.81: 14968 3.81 - 4.36: 18130 4.36 - 4.90: 29967 Nonbonded interactions: 72491 Sorted by model distance: nonbonded pdb=" NZ LYS A 294 " pdb=" OD1 ASN A 295 " model vdw 2.185 3.120 nonbonded pdb=" O LYS B 584 " pdb=" OG1 THR B 587 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP A 440 " pdb=" OG SER A 442 " model vdw 2.221 3.040 nonbonded pdb=" N GLU B 465 " pdb=" OE1 GLU B 465 " model vdw 2.222 3.120 nonbonded pdb=" OG SER A 244 " pdb=" O LYS A 251 " model vdw 2.234 3.040 ... (remaining 72486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 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 : 0.004 0.066 9206 Z= 0.171 Angle : 0.701 9.272 12465 Z= 0.383 Chirality : 0.046 0.186 1350 Planarity : 0.005 0.093 1591 Dihedral : 15.498 89.513 3385 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.10 % Allowed : 18.96 % Favored : 79.94 % 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: -0.66 (0.25), residues: 1071 helix: -0.36 (0.44), residues: 134 sheet: 0.12 (0.33), residues: 263 loop : -0.67 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 441 HIS 0.018 0.002 HIS C 5 PHE 0.054 0.002 PHE A 258 TYR 0.028 0.002 TYR A 118 ARG 0.007 0.001 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.19349 ( 219) hydrogen bonds : angle 8.25458 ( 606) SS BOND : bond 0.00426 ( 21) SS BOND : angle 1.03393 ( 42) covalent geometry : bond 0.00351 ( 9185) covalent geometry : angle 0.69970 (12423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8216 (tp40) REVERT: A 580 MET cc_start: 0.5289 (pmm) cc_final: 0.5062 (pmm) REVERT: B 616 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7090 (mm-40) REVERT: B 839 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5475 (m-30) REVERT: B 891 LYS cc_start: 0.5688 (mmpt) cc_final: 0.5412 (mmpt) outliers start: 11 outliers final: 3 residues processed: 100 average time/residue: 0.2664 time to fit residues: 35.3154 Evaluate side-chains 63 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS A 375 ASN B 467 HIS B 492 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 GLN B 738 ASN B 802 HIS ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.104746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.076450 restraints weight = 47992.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.076177 restraints weight = 38781.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.075186 restraints weight = 29193.008| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9206 Z= 0.198 Angle : 0.642 9.709 12465 Z= 0.333 Chirality : 0.046 0.164 1350 Planarity : 0.005 0.078 1591 Dihedral : 4.758 22.028 1205 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % 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: -0.45 (0.25), residues: 1071 helix: -0.13 (0.45), residues: 139 sheet: 0.48 (0.32), residues: 266 loop : -0.65 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 441 HIS 0.008 0.001 HIS A 274 PHE 0.021 0.002 PHE A 258 TYR 0.017 0.002 TYR A 118 ARG 0.010 0.001 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 219) hydrogen bonds : angle 6.23202 ( 606) SS BOND : bond 0.00751 ( 21) SS BOND : angle 1.35000 ( 42) covalent geometry : bond 0.00433 ( 9185) covalent geometry : angle 0.63811 (12423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.3115 time to fit residues: 33.5126 Evaluate side-chains 53 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 307 HIS ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** 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 = 0.4134 r_free = 0.4134 target = 0.103483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078293 restraints weight = 51090.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.078072 restraints weight = 43056.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.078704 restraints weight = 30118.621| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9206 Z= 0.194 Angle : 0.599 10.170 12465 Z= 0.313 Chirality : 0.045 0.193 1350 Planarity : 0.005 0.124 1591 Dihedral : 4.847 28.086 1205 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 (0.25), residues: 1071 helix: -0.04 (0.46), residues: 135 sheet: 0.22 (0.32), residues: 253 loop : -0.67 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 924 HIS 0.005 0.001 HIS B 467 PHE 0.017 0.002 PHE A 258 TYR 0.016 0.002 TYR A 118 ARG 0.017 0.001 ARG B 914 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 219) hydrogen bonds : angle 6.12765 ( 606) SS BOND : bond 0.00423 ( 21) SS BOND : angle 1.12433 ( 42) covalent geometry : bond 0.00430 ( 9185) covalent geometry : angle 0.59690 (12423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 MET cc_start: 0.7843 (mpp) cc_final: 0.7639 (mpp) REVERT: B 810 LEU cc_start: 0.8945 (tp) cc_final: 0.8470 (pp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2460 time to fit residues: 23.4916 Evaluate side-chains 49 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.102920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.077500 restraints weight = 50337.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.077127 restraints weight = 40798.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.077610 restraints weight = 30451.839| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9206 Z= 0.158 Angle : 0.572 9.853 12465 Z= 0.295 Chirality : 0.044 0.150 1350 Planarity : 0.004 0.061 1591 Dihedral : 4.689 23.066 1205 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -0.56 (0.25), residues: 1071 helix: -0.02 (0.46), residues: 135 sheet: 0.33 (0.33), residues: 240 loop : -0.70 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 441 HIS 0.005 0.001 HIS A 274 PHE 0.015 0.001 PHE A 258 TYR 0.014 0.001 TYR A 118 ARG 0.007 0.001 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 219) hydrogen bonds : angle 5.83594 ( 606) SS BOND : bond 0.00386 ( 21) SS BOND : angle 1.04206 ( 42) covalent geometry : bond 0.00352 ( 9185) covalent geometry : angle 0.56953 (12423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7584 (tt0) cc_final: 0.7220 (mt-10) REVERT: A 137 MET cc_start: 0.8708 (mmt) cc_final: 0.8239 (tpp) REVERT: B 810 LEU cc_start: 0.8903 (tp) cc_final: 0.8436 (pp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2276 time to fit residues: 21.3522 Evaluate side-chains 51 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS C 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.102608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.077113 restraints weight = 50177.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.076885 restraints weight = 39090.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.076878 restraints weight = 31805.541| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9206 Z= 0.132 Angle : 0.537 9.677 12465 Z= 0.278 Chirality : 0.044 0.273 1350 Planarity : 0.003 0.049 1591 Dihedral : 4.547 21.546 1205 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -0.56 (0.25), residues: 1071 helix: 0.00 (0.46), residues: 138 sheet: 0.32 (0.34), residues: 234 loop : -0.68 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 441 HIS 0.004 0.001 HIS A 274 PHE 0.010 0.001 PHE A 258 TYR 0.014 0.001 TYR A 118 ARG 0.007 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 219) hydrogen bonds : angle 5.57106 ( 606) SS BOND : bond 0.00486 ( 21) SS BOND : angle 0.98787 ( 42) covalent geometry : bond 0.00298 ( 9185) covalent geometry : angle 0.53526 (12423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8726 (mmt) cc_final: 0.8249 (tpp) REVERT: B 810 LEU cc_start: 0.8939 (tp) cc_final: 0.8469 (pp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2615 time to fit residues: 23.6986 Evaluate side-chains 52 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 85 optimal weight: 0.0770 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.101786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.076171 restraints weight = 49806.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.075345 restraints weight = 36153.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.074434 restraints weight = 32219.474| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9206 Z= 0.149 Angle : 0.553 9.424 12465 Z= 0.284 Chirality : 0.044 0.207 1350 Planarity : 0.003 0.051 1591 Dihedral : 4.565 21.610 1205 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -0.59 (0.25), residues: 1071 helix: 0.39 (0.47), residues: 132 sheet: 0.21 (0.34), residues: 229 loop : -0.76 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 441 HIS 0.004 0.001 HIS A 274 PHE 0.018 0.001 PHE A 455 TYR 0.011 0.001 TYR A 457 ARG 0.007 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 219) hydrogen bonds : angle 5.63113 ( 606) SS BOND : bond 0.00335 ( 21) SS BOND : angle 1.04507 ( 42) covalent geometry : bond 0.00337 ( 9185) covalent geometry : angle 0.55045 (12423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8645 (mmt) cc_final: 0.8155 (tpp) REVERT: B 810 LEU cc_start: 0.8817 (tp) cc_final: 0.8294 (pp) REVERT: C 45 GLN cc_start: 0.9204 (mp10) cc_final: 0.8945 (mp10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2271 time to fit residues: 21.2500 Evaluate side-chains 50 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 16 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.101369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.076347 restraints weight = 50233.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.074984 restraints weight = 36056.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.075149 restraints weight = 33209.018| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9206 Z= 0.139 Angle : 0.547 9.372 12465 Z= 0.280 Chirality : 0.044 0.146 1350 Planarity : 0.003 0.048 1591 Dihedral : 4.536 21.641 1205 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -0.61 (0.25), residues: 1071 helix: 0.31 (0.46), residues: 134 sheet: 0.17 (0.34), residues: 239 loop : -0.76 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 441 HIS 0.004 0.001 HIS A 274 PHE 0.009 0.001 PHE A 258 TYR 0.013 0.001 TYR A 118 ARG 0.007 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 219) hydrogen bonds : angle 5.46077 ( 606) SS BOND : bond 0.00326 ( 21) SS BOND : angle 1.01646 ( 42) covalent geometry : bond 0.00314 ( 9185) covalent geometry : angle 0.54473 (12423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8673 (mmt) cc_final: 0.8156 (tpp) REVERT: A 533 PHE cc_start: 0.9158 (m-80) cc_final: 0.8912 (m-80) REVERT: B 810 LEU cc_start: 0.8938 (tp) cc_final: 0.8420 (pp) REVERT: B 869 ILE cc_start: 0.7804 (mm) cc_final: 0.7592 (tp) REVERT: C 45 GLN cc_start: 0.9186 (mp10) cc_final: 0.8925 (mp10) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2855 time to fit residues: 26.2264 Evaluate side-chains 53 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 99 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.101457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.076242 restraints weight = 52250.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.075825 restraints weight = 38890.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.074835 restraints weight = 27207.561| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9206 Z= 0.126 Angle : 0.550 9.183 12465 Z= 0.280 Chirality : 0.045 0.307 1350 Planarity : 0.006 0.199 1591 Dihedral : 4.579 20.801 1205 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -0.64 (0.25), residues: 1071 helix: 0.21 (0.46), residues: 139 sheet: 0.20 (0.34), residues: 229 loop : -0.77 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 441 HIS 0.003 0.001 HIS A 274 PHE 0.013 0.001 PHE A 455 TYR 0.011 0.001 TYR A 457 ARG 0.020 0.001 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 219) hydrogen bonds : angle 5.27680 ( 606) SS BOND : bond 0.00325 ( 21) SS BOND : angle 0.94538 ( 42) covalent geometry : bond 0.00284 ( 9185) covalent geometry : angle 0.54824 (12423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8720 (mmt) cc_final: 0.8244 (tpp) REVERT: B 810 LEU cc_start: 0.8899 (tp) cc_final: 0.8353 (pp) REVERT: C 45 GLN cc_start: 0.9186 (mp10) cc_final: 0.8897 (mp10) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2088 time to fit residues: 20.4141 Evaluate side-chains 52 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 51 optimal weight: 0.0970 chunk 101 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.101957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.077023 restraints weight = 51633.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.076661 restraints weight = 39670.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075738 restraints weight = 27489.750| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9206 Z= 0.104 Angle : 0.530 8.916 12465 Z= 0.269 Chirality : 0.045 0.383 1350 Planarity : 0.004 0.090 1591 Dihedral : 4.381 18.389 1205 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.60 (0.25), residues: 1071 helix: 0.38 (0.46), residues: 137 sheet: 0.20 (0.34), residues: 225 loop : -0.76 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 441 HIS 0.003 0.000 HIS A 274 PHE 0.007 0.001 PHE A 205 TYR 0.011 0.001 TYR A 118 ARG 0.012 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 219) hydrogen bonds : angle 5.16843 ( 606) SS BOND : bond 0.00278 ( 21) SS BOND : angle 0.87312 ( 42) covalent geometry : bond 0.00238 ( 9185) covalent geometry : angle 0.52877 (12423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8728 (mmt) cc_final: 0.8237 (tpp) REVERT: A 533 PHE cc_start: 0.9106 (m-80) cc_final: 0.8876 (m-80) REVERT: A 580 MET cc_start: 0.4994 (pmm) cc_final: 0.4792 (pmm) REVERT: B 810 LEU cc_start: 0.8901 (tp) cc_final: 0.8410 (pp) REVERT: C 45 GLN cc_start: 0.9171 (mp10) cc_final: 0.8883 (mp10) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2216 time to fit residues: 22.9802 Evaluate side-chains 56 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 85 optimal weight: 0.0000 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.100558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.075464 restraints weight = 50039.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.074329 restraints weight = 36006.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.074700 restraints weight = 32965.065| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9206 Z= 0.146 Angle : 0.555 8.745 12465 Z= 0.285 Chirality : 0.044 0.190 1350 Planarity : 0.004 0.063 1591 Dihedral : 4.535 18.930 1205 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.80 % 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 (0.25), residues: 1071 helix: 0.37 (0.46), residues: 138 sheet: 0.11 (0.33), residues: 239 loop : -0.76 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 441 HIS 0.004 0.001 HIS B 340 PHE 0.015 0.001 PHE A 455 TYR 0.011 0.001 TYR C 49 ARG 0.008 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 219) hydrogen bonds : angle 5.23560 ( 606) SS BOND : bond 0.00350 ( 21) SS BOND : angle 1.05251 ( 42) covalent geometry : bond 0.00327 ( 9185) covalent geometry : angle 0.55298 (12423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8670 (mmt) cc_final: 0.8171 (tpp) REVERT: A 533 PHE cc_start: 0.9123 (m-80) cc_final: 0.8860 (m-80) REVERT: B 387 LEU cc_start: 0.9533 (mm) cc_final: 0.9257 (tp) REVERT: B 810 LEU cc_start: 0.8881 (tp) cc_final: 0.8335 (pp) REVERT: B 893 PHE cc_start: 0.7709 (t80) cc_final: 0.7430 (t80) REVERT: C 45 GLN cc_start: 0.9193 (mp10) cc_final: 0.8896 (mp10) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.3194 time to fit residues: 31.7414 Evaluate side-chains 56 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 444 HIS B 649 ASN C 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.100957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.075184 restraints weight = 50790.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.073897 restraints weight = 40502.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.073000 restraints weight = 28510.913| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9206 Z= 0.120 Angle : 0.539 8.900 12465 Z= 0.274 Chirality : 0.044 0.175 1350 Planarity : 0.004 0.080 1591 Dihedral : 4.469 18.743 1205 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % 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: -0.61 (0.25), residues: 1071 helix: 0.20 (0.45), residues: 145 sheet: 0.21 (0.35), residues: 223 loop : -0.75 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 441 HIS 0.003 0.001 HIS A 274 PHE 0.010 0.001 PHE A 455 TYR 0.011 0.001 TYR A 118 ARG 0.018 0.001 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 219) hydrogen bonds : angle 5.17133 ( 606) SS BOND : bond 0.00310 ( 21) SS BOND : angle 0.90304 ( 42) covalent geometry : bond 0.00273 ( 9185) covalent geometry : angle 0.53762 (12423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.44 seconds wall clock time: 62 minutes 57.69 seconds (3777.69 seconds total)