Starting phenix.real_space_refine on Fri Nov 15 10:45:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3d_35150/11_2024/8i3d_35150.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3d_35150/11_2024/8i3d_35150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3d_35150/11_2024/8i3d_35150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3d_35150/11_2024/8i3d_35150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3d_35150/11_2024/8i3d_35150.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3d_35150/11_2024/8i3d_35150.cif" } resolution = 2.81 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= 0.107 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 58 5.16 5 C 5720 2.51 5 N 1474 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8798 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4399 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 4 Restraints were copied for chains: B Time building chain proxies: 7.88, per 1000 atoms: 0.90 Number of scatterers: 8798 At special positions: 0 Unit cell: (75.53, 100.43, 123.67, 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 58 16.00 O 1546 8.00 N 1474 7.00 C 5720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.2 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 59.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.574A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.631A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 187' Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.584A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.543A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.706A pdb=" N PHE A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.529A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.632A pdb=" N THR A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 removed outlier: 3.611A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 401 removed outlier: 3.676A pdb=" N CYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.707A pdb=" N SER A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.696A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.532A pdb=" N GLN A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 462' Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.906A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.560A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.719A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 561 removed outlier: 3.640A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.000A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.558A pdb=" N VAL A 579 " --> pdb=" O MET A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 4.060A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.705A pdb=" N VAL A 625 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 659 removed outlier: 3.881A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.574A pdb=" N LEU B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.631A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 187' Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.586A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.542A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.705A pdb=" N PHE B 275 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.529A pdb=" N LEU B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.632A pdb=" N THR B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 360 removed outlier: 3.611A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 401 removed outlier: 3.677A pdb=" N CYS B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP B 386 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.707A pdb=" N SER B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.697A pdb=" N GLN B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.531A pdb=" N GLN B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 462' Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.906A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.559A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.719A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.640A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 removed outlier: 4.001A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.558A pdb=" N VAL B 579 " --> pdb=" O MET B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 4.060A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 626 removed outlier: 3.705A pdb=" N VAL B 625 " --> pdb=" O CYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 659 removed outlier: 3.881A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 6.221A pdb=" N TYR A 47 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 85 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 45 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 87 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 43 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A 89 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS A 41 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 45 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 124 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.622A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 91 removed outlier: 6.222A pdb=" N TYR B 47 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER B 85 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 45 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 87 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 43 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY B 89 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS B 41 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 45 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 124 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.623A pdb=" N PHE B 288 " --> pdb=" O LEU B 280 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2698 1.34 - 1.46: 1713 1.46 - 1.57: 4477 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8980 Sorted by residual: bond pdb=" C ALA B 350 " pdb=" N PRO B 351 " ideal model delta sigma weight residual 1.335 1.372 -0.036 1.36e-02 5.41e+03 7.13e+00 bond pdb=" C ALA A 350 " pdb=" N PRO A 351 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.36e-02 5.41e+03 7.02e+00 bond pdb=" CB VAL B 507 " pdb=" CG1 VAL B 507 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.77e+00 bond pdb=" CB VAL A 507 " pdb=" CG1 VAL A 507 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.68e+00 bond pdb=" CB GLN B 531 " pdb=" CG GLN B 531 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.29e+00 ... (remaining 8975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11563 1.98 - 3.95: 489 3.95 - 5.93: 66 5.93 - 7.90: 34 7.90 - 9.88: 14 Bond angle restraints: 12166 Sorted by residual: angle pdb=" C GLY B 605 " pdb=" N CYS B 606 " pdb=" CA CYS B 606 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C GLY A 605 " pdb=" N CYS A 606 " pdb=" CA CYS A 606 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C GLY B 597 " pdb=" N GLU B 598 " pdb=" CA GLU B 598 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY A 597 " pdb=" N GLU A 598 " pdb=" CA GLU A 598 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C CYS B 35 " pdb=" N PHE B 36 " pdb=" CA PHE B 36 " ideal model delta sigma weight residual 121.80 131.68 -9.88 2.44e+00 1.68e-01 1.64e+01 ... (remaining 12161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 4619 15.12 - 30.24: 527 30.24 - 45.36: 104 45.36 - 60.48: 22 60.48 - 75.60: 8 Dihedral angle restraints: 5280 sinusoidal: 2046 harmonic: 3234 Sorted by residual: dihedral pdb=" CA GLY B 605 " pdb=" C GLY B 605 " pdb=" N CYS B 606 " pdb=" CA CYS B 606 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLY A 605 " pdb=" C GLY A 605 " pdb=" N CYS A 606 " pdb=" CA CYS A 606 " ideal model delta harmonic sigma weight residual -180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA LYS B 285 " pdb=" C LYS B 285 " pdb=" N CYS B 286 " pdb=" CA CYS B 286 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 5277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 976 0.052 - 0.104: 382 0.104 - 0.156: 72 0.156 - 0.208: 12 0.208 - 0.260: 4 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CB VAL B 456 " pdb=" CA VAL B 456 " pdb=" CG1 VAL B 456 " pdb=" CG2 VAL B 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB VAL A 456 " pdb=" CA VAL A 456 " pdb=" CG1 VAL A 456 " pdb=" CG2 VAL A 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE A 660 " pdb=" CA ILE A 660 " pdb=" CG1 ILE A 660 " pdb=" CG2 ILE A 660 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1443 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 350 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 351 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 351 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 351 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 350 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO A 351 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 495 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A 496 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 496 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 496 " 0.034 5.00e-02 4.00e+02 ... (remaining 1491 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2948 2.84 - 3.36: 7482 3.36 - 3.87: 14139 3.87 - 4.39: 16962 4.39 - 4.90: 29567 Nonbonded interactions: 71098 Sorted by model distance: nonbonded pdb=" NH2 ARG B 436 " pdb=" O TYR B 508 " model vdw 2.328 3.120 nonbonded pdb=" O SER B 85 " pdb=" OG SER B 85 " model vdw 2.329 3.040 nonbonded pdb=" NH2 ARG A 436 " pdb=" O TYR A 508 " model vdw 2.329 3.120 nonbonded pdb=" O SER A 85 " pdb=" OG SER A 85 " model vdw 2.329 3.040 nonbonded pdb=" OG SER B 452 " pdb=" O SER B 530 " model vdw 2.337 3.040 ... (remaining 71093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.780 Find NCS groups from input model: 0.230 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.009 0.086 8980 Z= 0.597 Angle : 0.993 9.880 12166 Z= 0.534 Chirality : 0.056 0.260 1446 Planarity : 0.007 0.064 1494 Dihedral : 13.502 75.601 3204 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.83 % Allowed : 4.99 % Favored : 94.18 % Cbeta Deviations : 0.19 % 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: -5.74 (0.17), residues: 1112 helix: -4.53 (0.07), residues: 670 sheet: -0.75 (0.55), residues: 82 loop : -2.51 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 425 HIS 0.009 0.002 HIS A 662 PHE 0.021 0.002 PHE A 499 TYR 0.037 0.002 TYR A 475 ARG 0.006 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 413 GLN cc_start: 0.8309 (tt0) cc_final: 0.7968 (mt0) REVERT: A 468 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7705 (ttm170) REVERT: B 174 THR cc_start: 0.8198 (m) cc_final: 0.7961 (p) REVERT: B 283 GLU cc_start: 0.6733 (pm20) cc_final: 0.6326 (mp0) REVERT: B 304 PHE cc_start: 0.8403 (m-80) cc_final: 0.8111 (m-80) REVERT: B 326 THR cc_start: 0.5791 (OUTLIER) cc_final: 0.5543 (t) REVERT: B 338 ARG cc_start: 0.8221 (ttp80) cc_final: 0.8014 (ttp80) REVERT: B 401 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7489 (mtp-110) REVERT: B 413 GLN cc_start: 0.8154 (tt0) cc_final: 0.7872 (mt0) REVERT: B 468 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7642 (ttm170) outliers start: 8 outliers final: 2 residues processed: 169 average time/residue: 1.5786 time to fit residues: 280.7547 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 326 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 266 GLN A 531 GLN B 224 ASN B 266 GLN B 311 ASN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8980 Z= 0.168 Angle : 0.576 5.858 12166 Z= 0.303 Chirality : 0.040 0.127 1446 Planarity : 0.006 0.045 1494 Dihedral : 5.231 39.642 1227 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.22 % Allowed : 10.60 % Favored : 86.17 % 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: -2.98 (0.21), residues: 1112 helix: -1.99 (0.16), residues: 676 sheet: -0.34 (0.57), residues: 82 loop : -1.94 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.002 0.001 HIS A 434 PHE 0.009 0.001 PHE A 502 TYR 0.028 0.001 TYR A 475 ARG 0.010 0.001 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.996 Fit side-chains REVERT: A 273 GLN cc_start: 0.7864 (mm110) cc_final: 0.7489 (tp40) REVERT: A 274 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7185 (mtp) REVERT: A 413 GLN cc_start: 0.8097 (tt0) cc_final: 0.7881 (mt0) REVERT: A 468 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7417 (ttm170) REVERT: B 174 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7063 (p) REVERT: B 183 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: B 247 GLN cc_start: 0.8093 (mt0) cc_final: 0.7809 (mt0) REVERT: B 283 GLU cc_start: 0.6627 (pm20) cc_final: 0.6345 (mp0) REVERT: B 468 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7288 (ttm170) outliers start: 31 outliers final: 6 residues processed: 156 average time/residue: 1.5330 time to fit residues: 252.5081 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 462 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 0.0070 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 224 ASN A 247 GLN A 266 GLN B 154 HIS B 224 ASN B 266 GLN B 531 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8980 Z= 0.301 Angle : 0.610 5.761 12166 Z= 0.314 Chirality : 0.043 0.137 1446 Planarity : 0.005 0.049 1494 Dihedral : 4.989 24.253 1226 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.12 % Allowed : 12.68 % Favored : 84.20 % 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: -1.54 (0.24), residues: 1112 helix: -0.63 (0.19), residues: 678 sheet: -0.13 (0.57), residues: 82 loop : -1.77 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 447 HIS 0.005 0.001 HIS B 662 PHE 0.021 0.002 PHE B 502 TYR 0.029 0.002 TYR B 475 ARG 0.009 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.981 Fit side-chains REVERT: A 83 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7384 (mm) REVERT: A 273 GLN cc_start: 0.7856 (mm110) cc_final: 0.7474 (tp40) REVERT: A 274 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7232 (mtp) REVERT: A 468 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7457 (ttm170) REVERT: B 83 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7400 (mm) REVERT: B 174 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7130 (p) REVERT: B 183 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: B 247 GLN cc_start: 0.8112 (mt0) cc_final: 0.7800 (mt0) REVERT: B 256 LYS cc_start: 0.7981 (mttm) cc_final: 0.7684 (mmtt) REVERT: B 468 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7466 (ttm170) outliers start: 30 outliers final: 11 residues processed: 141 average time/residue: 1.4266 time to fit residues: 213.2014 Evaluate side-chains 124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN A 266 GLN B 224 ASN B 266 GLN B 413 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8980 Z= 0.174 Angle : 0.526 5.570 12166 Z= 0.272 Chirality : 0.040 0.126 1446 Planarity : 0.004 0.040 1494 Dihedral : 4.632 23.538 1226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.29 % Allowed : 14.76 % Favored : 82.95 % 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: -0.74 (0.25), residues: 1112 helix: 0.07 (0.20), residues: 676 sheet: -0.16 (0.56), residues: 82 loop : -1.49 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.003 0.001 HIS B 662 PHE 0.021 0.001 PHE B 502 TYR 0.025 0.001 TYR B 475 ARG 0.007 0.000 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.978 Fit side-chains REVERT: A 273 GLN cc_start: 0.7802 (mm110) cc_final: 0.7428 (tp40) REVERT: A 468 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7526 (ttm170) REVERT: B 83 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7266 (mm) REVERT: B 174 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7196 (p) REVERT: B 183 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: B 247 GLN cc_start: 0.8017 (mt0) cc_final: 0.7694 (mt0) REVERT: B 256 LYS cc_start: 0.7975 (mttm) cc_final: 0.7703 (mmtt) REVERT: B 468 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7488 (ttm170) outliers start: 22 outliers final: 8 residues processed: 136 average time/residue: 1.4274 time to fit residues: 205.4706 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN A 266 GLN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8980 Z= 0.198 Angle : 0.532 5.534 12166 Z= 0.273 Chirality : 0.041 0.130 1446 Planarity : 0.004 0.044 1494 Dihedral : 4.529 22.075 1225 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.22 % Allowed : 13.62 % Favored : 83.16 % 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: -0.41 (0.25), residues: 1112 helix: 0.38 (0.20), residues: 676 sheet: -0.23 (0.55), residues: 82 loop : -1.40 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.003 0.001 HIS A 662 PHE 0.022 0.001 PHE A 502 TYR 0.025 0.001 TYR A 475 ARG 0.007 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.128 Fit side-chains REVERT: A 83 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7294 (mm) REVERT: A 273 GLN cc_start: 0.7817 (mm110) cc_final: 0.7444 (tp40) REVERT: A 468 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7524 (ttm170) REVERT: B 83 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7313 (mm) REVERT: B 174 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7207 (p) REVERT: B 183 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: B 247 GLN cc_start: 0.8014 (mt0) cc_final: 0.7705 (mt0) REVERT: B 256 LYS cc_start: 0.7965 (mttm) cc_final: 0.7728 (mttt) REVERT: B 468 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7536 (ttm170) REVERT: B 603 MET cc_start: 0.7312 (mpt) cc_final: 0.7086 (mpt) outliers start: 31 outliers final: 15 residues processed: 137 average time/residue: 1.4346 time to fit residues: 208.2156 Evaluate side-chains 134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN A 266 GLN A 461 GLN B 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8980 Z= 0.155 Angle : 0.507 5.486 12166 Z= 0.260 Chirality : 0.040 0.125 1446 Planarity : 0.004 0.040 1494 Dihedral : 4.363 21.146 1225 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.70 % Allowed : 14.76 % Favored : 82.54 % 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: -0.02 (0.26), residues: 1112 helix: 0.75 (0.21), residues: 674 sheet: -0.18 (0.55), residues: 82 loop : -1.35 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.003 0.001 HIS B 662 PHE 0.022 0.001 PHE B 502 TYR 0.022 0.001 TYR A 475 ARG 0.009 0.000 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.994 Fit side-chains REVERT: A 273 GLN cc_start: 0.7784 (mm110) cc_final: 0.7427 (tp40) REVERT: A 314 ASP cc_start: 0.7522 (m-30) cc_final: 0.7072 (m-30) REVERT: A 468 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7553 (ttm170) REVERT: B 83 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7221 (mm) REVERT: B 174 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7206 (p) REVERT: B 183 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: B 247 GLN cc_start: 0.8014 (mt0) cc_final: 0.7690 (mt0) REVERT: B 256 LYS cc_start: 0.7959 (mttm) cc_final: 0.7716 (mttt) REVERT: B 314 ASP cc_start: 0.7453 (m-30) cc_final: 0.7031 (m-30) REVERT: B 468 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7526 (ttm170) outliers start: 26 outliers final: 13 residues processed: 146 average time/residue: 1.4673 time to fit residues: 226.6143 Evaluate side-chains 137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN A 266 GLN B 224 ASN B 484 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8980 Z= 0.185 Angle : 0.528 5.628 12166 Z= 0.271 Chirality : 0.041 0.142 1446 Planarity : 0.004 0.040 1494 Dihedral : 4.368 20.149 1225 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.70 % Allowed : 16.32 % Favored : 80.98 % 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: 0.11 (0.26), residues: 1112 helix: 0.87 (0.21), residues: 674 sheet: -0.17 (0.55), residues: 82 loop : -1.32 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 447 HIS 0.004 0.001 HIS B 662 PHE 0.024 0.001 PHE A 502 TYR 0.022 0.001 TYR B 475 ARG 0.007 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.870 Fit side-chains REVERT: A 83 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7300 (mm) REVERT: A 273 GLN cc_start: 0.7791 (mm110) cc_final: 0.7435 (tp40) REVERT: A 468 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7558 (ttm170) REVERT: B 83 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7292 (mm) REVERT: B 174 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7232 (p) REVERT: B 183 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: B 247 GLN cc_start: 0.8017 (mt0) cc_final: 0.7706 (mt0) REVERT: B 256 LYS cc_start: 0.7955 (mttm) cc_final: 0.7703 (mttt) REVERT: B 314 ASP cc_start: 0.7545 (m-30) cc_final: 0.7070 (m-30) REVERT: B 468 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7520 (ttm170) outliers start: 26 outliers final: 14 residues processed: 137 average time/residue: 1.3161 time to fit residues: 192.0189 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 GLN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8980 Z= 0.320 Angle : 0.592 5.657 12166 Z= 0.303 Chirality : 0.045 0.139 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.644 20.627 1225 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.60 % Allowed : 16.42 % Favored : 80.98 % 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: -0.08 (0.25), residues: 1112 helix: 0.74 (0.20), residues: 668 sheet: -0.22 (0.54), residues: 82 loop : -1.42 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 447 HIS 0.004 0.001 HIS A 395 PHE 0.028 0.002 PHE B 502 TYR 0.026 0.002 TYR B 475 ARG 0.010 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.056 Fit side-chains REVERT: A 83 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7349 (mm) REVERT: A 174 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7250 (p) REVERT: A 274 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7202 (mtp) REVERT: A 468 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7537 (ttm170) REVERT: B 83 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7322 (mm) REVERT: B 174 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7282 (p) REVERT: B 183 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 247 GLN cc_start: 0.8056 (mt0) cc_final: 0.7736 (mt0) REVERT: B 256 LYS cc_start: 0.7952 (mttm) cc_final: 0.7711 (mttt) REVERT: B 468 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7490 (ttm170) outliers start: 25 outliers final: 10 residues processed: 122 average time/residue: 1.3658 time to fit residues: 176.9954 Evaluate side-chains 113 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8980 Z= 0.152 Angle : 0.512 5.484 12166 Z= 0.263 Chirality : 0.040 0.153 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.370 19.302 1225 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.77 % Allowed : 16.84 % Favored : 81.39 % 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: 0.28 (0.26), residues: 1112 helix: 1.06 (0.21), residues: 668 sheet: -0.14 (0.56), residues: 82 loop : -1.33 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS B 662 PHE 0.026 0.001 PHE A 502 TYR 0.022 0.001 TYR B 475 ARG 0.007 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.894 Fit side-chains REVERT: A 83 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7285 (mm) REVERT: A 468 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7548 (ttm170) REVERT: B 83 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7269 (mm) REVERT: B 174 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7262 (p) REVERT: B 183 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: B 247 GLN cc_start: 0.7963 (mt0) cc_final: 0.7644 (mt0) REVERT: B 256 LYS cc_start: 0.7958 (mttm) cc_final: 0.7720 (mttt) REVERT: B 468 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7500 (ttm170) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 1.4116 time to fit residues: 178.2810 Evaluate side-chains 119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN B 461 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8980 Z= 0.379 Angle : 0.623 5.713 12166 Z= 0.318 Chirality : 0.047 0.149 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.709 19.831 1225 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.98 % Allowed : 17.36 % Favored : 80.67 % 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: -0.11 (0.25), residues: 1112 helix: 0.72 (0.20), residues: 668 sheet: -0.20 (0.54), residues: 82 loop : -1.46 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 447 HIS 0.005 0.001 HIS B 395 PHE 0.034 0.002 PHE B 502 TYR 0.026 0.002 TYR B 475 ARG 0.011 0.001 ARG A 463 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.952 Fit side-chains REVERT: A 83 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7392 (mm) REVERT: A 174 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7271 (p) REVERT: A 468 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7500 (ttm170) REVERT: B 83 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7408 (mm) REVERT: B 174 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7296 (p) REVERT: B 183 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: B 247 GLN cc_start: 0.8034 (mt0) cc_final: 0.7707 (mt0) REVERT: B 256 LYS cc_start: 0.7950 (mttm) cc_final: 0.7714 (mttt) REVERT: B 468 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7460 (ttm170) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 1.4095 time to fit residues: 177.8509 Evaluate side-chains 116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114731 restraints weight = 9044.051| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.18 r_work: 0.2930 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8980 Z= 0.332 Angle : 0.604 5.978 12166 Z= 0.310 Chirality : 0.045 0.142 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.724 19.844 1225 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.87 % Allowed : 18.09 % Favored : 80.04 % 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: -0.15 (0.25), residues: 1112 helix: 0.70 (0.20), residues: 666 sheet: -0.21 (0.55), residues: 82 loop : -1.49 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 447 HIS 0.004 0.001 HIS A 395 PHE 0.034 0.002 PHE A 502 TYR 0.026 0.002 TYR B 475 ARG 0.006 0.000 ARG B 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3715.08 seconds wall clock time: 67 minutes 7.82 seconds (4027.82 seconds total)