Starting phenix.real_space_refine on Sat Aug 23 02:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yyl_39675/08_2025/8yyl_39675.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yyl_39675/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yyl_39675/08_2025/8yyl_39675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yyl_39675/08_2025/8yyl_39675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yyl_39675/08_2025/8yyl_39675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yyl_39675/08_2025/8yyl_39675.map" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.40, per 1000 atoms: 0.27 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: 0.95 Conformation dependent library (CDL) restraints added in 385.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.38 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: 1.69 Time building geometry restraints manager: 1.25 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG B 416 TYR 0.028 0.002 TYR A 118 PHE 0.054 0.002 PHE A 258 TRP 0.052 0.002 TRP B 441 HIS 0.018 0.002 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9185) covalent geometry : angle 0.69970 (12423) SS BOND : bond 0.00426 ( 21) SS BOND : angle 1.03393 ( 42) hydrogen bonds : bond 0.19349 ( 219) hydrogen bonds : angle 8.25458 ( 606) *********************** 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 : 0.363 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: 0.1296 time to fit residues: 17.0903 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 : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 738 ASN B 802 HIS C 5 HIS C 10 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.105937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078505 restraints weight = 48737.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.078455 restraints weight = 40069.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.078427 restraints weight = 29858.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.078958 restraints weight = 24004.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.078846 restraints weight = 20056.787| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9206 Z= 0.162 Angle : 0.607 9.588 12465 Z= 0.316 Chirality : 0.046 0.176 1350 Planarity : 0.005 0.075 1591 Dihedral : 4.638 21.704 1205 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.25), residues: 1071 helix: -0.07 (0.46), residues: 138 sheet: 0.56 (0.32), residues: 266 loop : -0.63 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 416 TYR 0.016 0.002 TYR A 118 PHE 0.023 0.002 PHE A 258 TRP 0.025 0.002 TRP B 441 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9185) covalent geometry : angle 0.60349 (12423) SS BOND : bond 0.00393 ( 21) SS BOND : angle 1.30923 ( 42) hydrogen bonds : bond 0.03851 ( 219) hydrogen bonds : angle 6.16456 ( 606) *********************** 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 79 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.389 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: B 840 ASP cc_start: 0.8619 (m-30) cc_final: 0.8371 (p0) REVERT: B 893 PHE cc_start: 0.7658 (t80) cc_final: 0.7408 (t80) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1317 time to fit residues: 13.8132 Evaluate side-chains 55 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 0.0370 chunk 72 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 0.0170 chunk 74 optimal weight: 10.0000 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 575 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.106344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.080934 restraints weight = 51503.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.081577 restraints weight = 40128.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.081403 restraints weight = 30777.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.081499 restraints weight = 22699.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.081617 restraints weight = 21764.512| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9206 Z= 0.124 Angle : 0.531 9.919 12465 Z= 0.278 Chirality : 0.044 0.153 1350 Planarity : 0.005 0.123 1591 Dihedral : 4.525 27.332 1205 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.25), residues: 1071 helix: 0.08 (0.47), residues: 135 sheet: 0.32 (0.32), residues: 261 loop : -0.56 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 914 TYR 0.014 0.001 TYR A 118 PHE 0.015 0.001 PHE A 258 TRP 0.027 0.001 TRP B 924 HIS 0.004 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9185) covalent geometry : angle 0.52931 (12423) SS BOND : bond 0.00344 ( 21) SS BOND : angle 0.97769 ( 42) hydrogen bonds : bond 0.03430 ( 219) hydrogen bonds : angle 5.93164 ( 606) *********************** 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 75 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.490 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: 0.7928 (mpp) cc_final: 0.7719 (mpp) REVERT: B 840 ASP cc_start: 0.8639 (m-30) cc_final: 0.8429 (p0) REVERT: B 893 PHE cc_start: 0.7345 (t80) cc_final: 0.7100 (t80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1250 time to fit residues: 12.7895 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 : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN C 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.106273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.081456 restraints weight = 52077.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.082247 restraints weight = 40778.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.081790 restraints weight = 29827.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.082235 restraints weight = 24204.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.082704 restraints weight = 19787.525| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9206 Z= 0.104 Angle : 0.513 9.753 12465 Z= 0.268 Chirality : 0.044 0.185 1350 Planarity : 0.004 0.071 1591 Dihedral : 4.326 28.010 1205 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.25), residues: 1071 helix: 0.06 (0.46), residues: 138 sheet: 0.46 (0.33), residues: 242 loop : -0.60 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 399 TYR 0.014 0.001 TYR A 118 PHE 0.014 0.001 PHE A 258 TRP 0.031 0.002 TRP B 924 HIS 0.004 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9185) covalent geometry : angle 0.51119 (12423) SS BOND : bond 0.00321 ( 21) SS BOND : angle 0.92067 ( 42) hydrogen bonds : bond 0.03175 ( 219) hydrogen bonds : angle 5.55206 ( 606) *********************** 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 70 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.371 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: 0.8412 (mmt) cc_final: 0.7892 (tpp) REVERT: A 531 MET cc_start: 0.7848 (mpp) cc_final: 0.7625 (mpp) REVERT: B 840 ASP cc_start: 0.8647 (m-30) cc_final: 0.8369 (p0) REVERT: B 893 PHE cc_start: 0.7458 (t80) cc_final: 0.7175 (t80) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1296 time to fit residues: 12.2126 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 : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 HIS ** 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 = 0.4165 r_free = 0.4165 target = 0.105114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079137 restraints weight = 50455.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.079322 restraints weight = 38677.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.078879 restraints weight = 29594.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.079191 restraints weight = 25126.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.079613 restraints weight = 20515.185| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9206 Z= 0.117 Angle : 0.516 9.443 12465 Z= 0.267 Chirality : 0.044 0.187 1350 Planarity : 0.003 0.054 1591 Dihedral : 4.324 28.550 1205 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.25), residues: 1071 helix: 0.31 (0.47), residues: 135 sheet: 0.30 (0.32), residues: 256 loop : -0.60 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 399 TYR 0.014 0.001 TYR A 118 PHE 0.012 0.001 PHE A 258 TRP 0.027 0.001 TRP B 441 HIS 0.007 0.001 HIS B 737 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9185) covalent geometry : angle 0.51457 (12423) SS BOND : bond 0.00295 ( 21) SS BOND : angle 0.85037 ( 42) hydrogen bonds : bond 0.02991 ( 219) hydrogen bonds : angle 5.43284 ( 606) *********************** 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 72 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8546 (mmt) cc_final: 0.8038 (tpp) REVERT: A 396 LYS cc_start: 0.8217 (tptm) cc_final: 0.7344 (tptp) REVERT: B 810 LEU cc_start: 0.8843 (tp) cc_final: 0.8395 (pp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1166 time to fit residues: 11.5421 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 : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 11 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.105123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.079777 restraints weight = 49795.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.080147 restraints weight = 37623.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.079448 restraints weight = 26541.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.079255 restraints weight = 23021.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.079700 restraints weight = 20486.958| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9206 Z= 0.094 Angle : 0.493 9.314 12465 Z= 0.254 Chirality : 0.044 0.263 1350 Planarity : 0.003 0.046 1591 Dihedral : 4.188 27.355 1205 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.10 % Allowed : 1.00 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.25), residues: 1071 helix: 0.23 (0.46), residues: 141 sheet: 0.18 (0.32), residues: 256 loop : -0.58 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 399 TYR 0.012 0.001 TYR A 118 PHE 0.010 0.001 PHE B 455 TRP 0.024 0.001 TRP B 441 HIS 0.004 0.001 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9185) covalent geometry : angle 0.49217 (12423) SS BOND : bond 0.00260 ( 21) SS BOND : angle 0.77724 ( 42) hydrogen bonds : bond 0.02792 ( 219) hydrogen bonds : angle 5.25309 ( 606) *********************** 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 73 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8576 (mmt) cc_final: 0.8118 (tpp) REVERT: A 396 LYS cc_start: 0.7903 (tptm) cc_final: 0.7160 (tptp) REVERT: A 531 MET cc_start: 0.7797 (mpp) cc_final: 0.7566 (mpp) REVERT: A 533 PHE cc_start: 0.9144 (m-80) cc_final: 0.8931 (m-80) REVERT: B 391 ILE cc_start: 0.7800 (pt) cc_final: 0.7565 (tp) REVERT: B 810 LEU cc_start: 0.8836 (tp) cc_final: 0.8396 (pp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1139 time to fit residues: 11.3297 Evaluate side-chains 57 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.104556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.079503 restraints weight = 50201.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.079549 restraints weight = 38536.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.079815 restraints weight = 27556.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.080206 restraints weight = 22061.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.080675 restraints weight = 18705.708| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9206 Z= 0.101 Angle : 0.500 8.915 12465 Z= 0.257 Chirality : 0.044 0.257 1350 Planarity : 0.003 0.043 1591 Dihedral : 4.127 27.204 1205 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.10 % Allowed : 1.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.25), residues: 1071 helix: 0.25 (0.46), residues: 137 sheet: 0.24 (0.33), residues: 250 loop : -0.59 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 399 TYR 0.012 0.001 TYR A 118 PHE 0.011 0.001 PHE B 455 TRP 0.023 0.001 TRP B 441 HIS 0.003 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9185) covalent geometry : angle 0.49833 (12423) SS BOND : bond 0.00297 ( 21) SS BOND : angle 0.85106 ( 42) hydrogen bonds : bond 0.02749 ( 219) hydrogen bonds : angle 5.20047 ( 606) *********************** 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 73 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8557 (mmt) cc_final: 0.8097 (tpp) REVERT: A 396 LYS cc_start: 0.7972 (tptm) cc_final: 0.7290 (tptp) REVERT: A 431 ASP cc_start: 0.8382 (t0) cc_final: 0.8053 (t0) REVERT: B 380 GLU cc_start: 0.8417 (mp0) cc_final: 0.8161 (mp0) REVERT: B 810 LEU cc_start: 0.8841 (tp) cc_final: 0.8357 (pp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1148 time to fit residues: 11.5244 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 : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 18 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 100 optimal weight: 9.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN ** 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 = 0.4168 r_free = 0.4168 target = 0.105309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.081664 restraints weight = 51209.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.082329 restraints weight = 35807.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.081901 restraints weight = 27520.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.082239 restraints weight = 23083.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.082317 restraints weight = 19949.472| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9206 Z= 0.091 Angle : 0.499 8.894 12465 Z= 0.254 Chirality : 0.044 0.336 1350 Planarity : 0.003 0.048 1591 Dihedral : 4.059 26.076 1205 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.10 % Allowed : 0.50 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.25), residues: 1071 helix: 0.27 (0.46), residues: 141 sheet: 0.38 (0.34), residues: 241 loop : -0.56 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 399 TYR 0.012 0.001 TYR C 49 PHE 0.009 0.001 PHE A 258 TRP 0.022 0.001 TRP B 441 HIS 0.003 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9185) covalent geometry : angle 0.49656 (12423) SS BOND : bond 0.00271 ( 21) SS BOND : angle 0.92070 ( 42) hydrogen bonds : bond 0.02696 ( 219) hydrogen bonds : angle 5.15514 ( 606) *********************** 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 71 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.417 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: 0.8607 (mmt) cc_final: 0.8150 (tpp) REVERT: A 396 LYS cc_start: 0.7752 (tptm) cc_final: 0.7186 (tptp) REVERT: A 431 ASP cc_start: 0.8375 (t0) cc_final: 0.7957 (t0) REVERT: B 810 LEU cc_start: 0.8836 (tp) cc_final: 0.8385 (pp) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1153 time to fit residues: 11.3100 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 : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 88 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 0.0170 chunk 57 optimal weight: 4.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 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 = 0.4169 r_free = 0.4169 target = 0.105216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.081550 restraints weight = 51922.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.081837 restraints weight = 36552.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.081665 restraints weight = 29455.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.081989 restraints weight = 24457.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.081985 restraints weight = 21332.936| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9206 Z= 0.090 Angle : 0.489 7.663 12465 Z= 0.250 Chirality : 0.044 0.320 1350 Planarity : 0.003 0.052 1591 Dihedral : 3.985 26.404 1205 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.25), residues: 1071 helix: 0.17 (0.45), residues: 146 sheet: 0.32 (0.34), residues: 240 loop : -0.55 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 399 TYR 0.011 0.001 TYR A 118 PHE 0.010 0.001 PHE B 455 TRP 0.022 0.001 TRP B 441 HIS 0.003 0.000 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9185) covalent geometry : angle 0.48805 (12423) SS BOND : bond 0.00243 ( 21) SS BOND : angle 0.77738 ( 42) hydrogen bonds : bond 0.02649 ( 219) hydrogen bonds : angle 5.02805 ( 606) *********************** 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 71 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.398 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: 0.8607 (mmt) cc_final: 0.8161 (tpp) REVERT: A 396 LYS cc_start: 0.7679 (tptm) cc_final: 0.7083 (tptp) REVERT: A 431 ASP cc_start: 0.8438 (t0) cc_final: 0.7973 (t0) REVERT: B 455 PHE cc_start: 0.8860 (m-80) cc_final: 0.8645 (m-80) REVERT: B 810 LEU cc_start: 0.8932 (tp) cc_final: 0.8478 (pp) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1147 time to fit residues: 11.1479 Evaluate side-chains 54 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.0040 chunk 90 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN ** 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 = 0.4171 r_free = 0.4171 target = 0.105214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081674 restraints weight = 51866.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.081808 restraints weight = 36241.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.081732 restraints weight = 29617.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.082039 restraints weight = 23764.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.082249 restraints weight = 21223.856| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9206 Z= 0.088 Angle : 0.491 8.468 12465 Z= 0.250 Chirality : 0.044 0.308 1350 Planarity : 0.003 0.047 1591 Dihedral : 3.950 26.426 1205 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 1071 helix: 0.26 (0.46), residues: 140 sheet: 0.33 (0.34), residues: 240 loop : -0.51 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 398 TYR 0.011 0.001 TYR A 534 PHE 0.011 0.001 PHE B 455 TRP 0.021 0.001 TRP B 441 HIS 0.011 0.001 HIS B 892 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9185) covalent geometry : angle 0.48977 (12423) SS BOND : bond 0.00251 ( 21) SS BOND : angle 0.76769 ( 42) hydrogen bonds : bond 0.02581 ( 219) hydrogen bonds : angle 4.97014 ( 606) ********************** 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 71 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.391 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: 0.8515 (mmt) cc_final: 0.8039 (tpp) REVERT: A 396 LYS cc_start: 0.7696 (tptm) cc_final: 0.7139 (tptp) REVERT: A 431 ASP cc_start: 0.8414 (t0) cc_final: 0.7955 (t0) REVERT: A 533 PHE cc_start: 0.9139 (m-80) cc_final: 0.8925 (m-80) REVERT: B 455 PHE cc_start: 0.8857 (m-80) cc_final: 0.8636 (m-80) REVERT: B 810 LEU cc_start: 0.8935 (tp) cc_final: 0.8477 (pp) REVERT: B 893 PHE cc_start: 0.7522 (t80) cc_final: 0.7278 (t80) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1103 time to fit residues: 10.8850 Evaluate side-chains 59 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 96 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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** B 662 GLN C 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.101424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.076004 restraints weight = 48257.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.074714 restraints weight = 35317.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.075070 restraints weight = 32746.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.075062 restraints weight = 25191.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.075191 restraints weight = 22886.655| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9206 Z= 0.163 Angle : 0.584 9.199 12465 Z= 0.299 Chirality : 0.045 0.296 1350 Planarity : 0.004 0.056 1591 Dihedral : 4.469 25.858 1205 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.25), residues: 1071 helix: 0.55 (0.46), residues: 135 sheet: 0.44 (0.34), residues: 242 loop : -0.64 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 398 TYR 0.015 0.001 TYR C 49 PHE 0.019 0.002 PHE A 455 TRP 0.024 0.002 TRP B 441 HIS 0.005 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9185) covalent geometry : angle 0.58145 (12423) SS BOND : bond 0.00478 ( 21) SS BOND : angle 1.11503 ( 42) hydrogen bonds : bond 0.03100 ( 219) hydrogen bonds : angle 5.28189 ( 606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.67 seconds wall clock time: 35 minutes 0.95 seconds (2100.95 seconds total)