Starting phenix.real_space_refine on Thu Feb 13 07:09:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3d_35150/02_2025/8i3d_35150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3d_35150/02_2025/8i3d_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/cci-nas-00/data/ceres_data/8i3d_35150/02_2025/8i3d_35150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3d_35150/02_2025/8i3d_35150.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3d_35150/02_2025/8i3d_35150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3d_35150/02_2025/8i3d_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-5592/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: 7.99, per 1000 atoms: 0.91 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 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: 0.89 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: 2.56 Time building geometry restraints manager: 2.49 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: 0.04 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: 1.540 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.810 Find NCS groups from input model: 0.160 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:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- 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 : 1.015 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: 1.5887 time to fit residues: 282.8656 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 : 1.002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.157277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115563 restraints weight = 9046.034| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.73 r_work: 0.3040 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.945 Fit side-chains REVERT: A 273 GLN cc_start: 0.8153 (mm110) cc_final: 0.7805 (tp40) REVERT: A 274 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7623 (mtp) REVERT: A 346 ASP cc_start: 0.7332 (m-30) cc_final: 0.7082 (m-30) REVERT: A 413 GLN cc_start: 0.8523 (tt0) cc_final: 0.8273 (mt0) REVERT: A 468 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7291 (ttm170) REVERT: B 174 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.6843 (p) REVERT: B 183 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 247 GLN cc_start: 0.8211 (mt0) cc_final: 0.7961 (mt0) REVERT: B 256 LYS cc_start: 0.7993 (mttp) cc_final: 0.7740 (mttm) REVERT: B 283 GLU cc_start: 0.6946 (pm20) cc_final: 0.6499 (mp0) REVERT: B 326 THR cc_start: 0.5892 (OUTLIER) cc_final: 0.5689 (t) REVERT: B 468 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7168 (ttm170) outliers start: 31 outliers final: 6 residues processed: 156 average time/residue: 1.5074 time to fit residues: 248.2230 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 326 THR 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 68 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110878 restraints weight = 9189.928| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.89 r_work: 0.2970 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8980 Z= 0.336 Angle : 0.623 5.852 12166 Z= 0.321 Chirality : 0.044 0.138 1446 Planarity : 0.005 0.052 1494 Dihedral : 5.077 24.374 1227 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.12 % Allowed : 12.79 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1112 helix: -0.67 (0.19), residues: 678 sheet: -0.14 (0.57), residues: 82 loop : -1.80 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 447 HIS 0.007 0.001 HIS B 662 PHE 0.021 0.002 PHE B 502 TYR 0.030 0.002 TYR B 475 ARG 0.011 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 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.034 Fit side-chains REVERT: A 83 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7189 (mm) REVERT: A 273 GLN cc_start: 0.8057 (mm110) cc_final: 0.7695 (tp40) REVERT: A 274 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7667 (mtp) REVERT: A 346 ASP cc_start: 0.7345 (m-30) cc_final: 0.7012 (m-30) REVERT: A 413 GLN cc_start: 0.8521 (tt0) cc_final: 0.8309 (mt0) REVERT: A 468 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7235 (ttm170) REVERT: A 565 TYR cc_start: 0.8828 (m-80) cc_final: 0.8605 (m-80) REVERT: B 83 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7153 (mm) REVERT: B 174 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.6864 (p) REVERT: B 183 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: B 247 GLN cc_start: 0.8120 (mt0) cc_final: 0.7818 (mt0) REVERT: B 256 LYS cc_start: 0.7878 (mttp) cc_final: 0.7607 (mttm) REVERT: B 274 MET cc_start: 0.7995 (mtp) cc_final: 0.7790 (mtp) REVERT: B 283 GLU cc_start: 0.7050 (pm20) cc_final: 0.6687 (mp0) REVERT: B 346 ASP cc_start: 0.7280 (m-30) cc_final: 0.7053 (m-30) REVERT: B 468 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7210 (ttm170) outliers start: 30 outliers final: 10 residues processed: 142 average time/residue: 1.4218 time to fit residues: 213.9227 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.156293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115320 restraints weight = 9029.221| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.02 r_work: 0.2956 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8980 Z= 0.250 Angle : 0.563 5.657 12166 Z= 0.290 Chirality : 0.042 0.131 1446 Planarity : 0.004 0.042 1494 Dihedral : 4.806 24.147 1226 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.01 % Allowed : 14.03 % 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: -0.84 (0.25), residues: 1112 helix: 0.03 (0.20), residues: 666 sheet: -0.18 (0.56), residues: 82 loop : -1.61 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 447 HIS 0.004 0.001 HIS A 662 PHE 0.023 0.002 PHE B 502 TYR 0.027 0.001 TYR A 475 ARG 0.008 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 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.005 Fit side-chains REVERT: A 83 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7137 (mm) REVERT: A 273 GLN cc_start: 0.8079 (mm110) cc_final: 0.7719 (tp40) REVERT: A 274 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7594 (mtp) REVERT: A 346 ASP cc_start: 0.7509 (m-30) cc_final: 0.7153 (m-30) REVERT: A 468 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7292 (ttm170) REVERT: A 603 MET cc_start: 0.7466 (mpt) cc_final: 0.7246 (mpt) REVERT: B 83 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7121 (mm) REVERT: B 174 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.6930 (p) REVERT: B 183 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: B 247 GLN cc_start: 0.8139 (mt0) cc_final: 0.7829 (mt0) REVERT: B 256 LYS cc_start: 0.7911 (mttp) cc_final: 0.7664 (mttm) REVERT: B 283 GLU cc_start: 0.7084 (pm20) cc_final: 0.6733 (mp0) REVERT: B 346 ASP cc_start: 0.7465 (m-30) cc_final: 0.7120 (m-30) REVERT: B 468 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7249 (ttm170) REVERT: B 603 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6996 (mpt) outliers start: 29 outliers final: 13 residues processed: 136 average time/residue: 1.4904 time to fit residues: 214.1495 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 : 1.018 ------------------------------------------------------------------------------- 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 317 LEU 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 317 LEU 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 603 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.156870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113321 restraints weight = 9175.175| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.87 r_work: 0.3064 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8980 Z= 0.246 Angle : 0.560 5.592 12166 Z= 0.287 Chirality : 0.042 0.131 1446 Planarity : 0.004 0.042 1494 Dihedral : 4.676 22.376 1225 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.22 % Allowed : 14.14 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1112 helix: 0.33 (0.20), residues: 668 sheet: -0.22 (0.55), residues: 82 loop : -1.49 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 447 HIS 0.003 0.001 HIS A 662 PHE 0.025 0.002 PHE B 502 TYR 0.027 0.001 TYR B 475 ARG 0.009 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 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.026 Fit side-chains REVERT: A 83 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6739 (mm) REVERT: A 273 GLN cc_start: 0.7694 (mm110) cc_final: 0.7335 (tp40) REVERT: A 274 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7270 (mtp) REVERT: A 346 ASP cc_start: 0.7321 (m-30) cc_final: 0.6935 (m-30) REVERT: A 468 ARG cc_start: 0.7622 (ttp80) cc_final: 0.6633 (ttm170) REVERT: B 83 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6765 (mm) REVERT: B 174 THR cc_start: 0.7047 (OUTLIER) cc_final: 0.6494 (p) REVERT: B 183 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: B 247 GLN cc_start: 0.7655 (mt0) cc_final: 0.7359 (mt0) REVERT: B 256 LYS cc_start: 0.7496 (mttp) cc_final: 0.7204 (mttm) REVERT: B 283 GLU cc_start: 0.6849 (pm20) cc_final: 0.6447 (mp0) REVERT: B 346 ASP cc_start: 0.7258 (m-30) cc_final: 0.6762 (m-30) REVERT: B 468 ARG cc_start: 0.7636 (ttp80) cc_final: 0.6640 (ttm170) REVERT: B 603 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7053 (mpt) outliers start: 31 outliers final: 14 residues processed: 139 average time/residue: 1.4871 time to fit residues: 218.4329 Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 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 462 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 603 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 484 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113609 restraints weight = 9116.586| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.87 r_work: 0.3064 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8980 Z= 0.239 Angle : 0.554 5.583 12166 Z= 0.284 Chirality : 0.042 0.130 1446 Planarity : 0.004 0.042 1494 Dihedral : 4.614 21.943 1225 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.22 % Allowed : 14.24 % 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: -0.27 (0.26), residues: 1112 helix: 0.55 (0.20), residues: 668 sheet: -0.19 (0.55), residues: 82 loop : -1.43 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 447 HIS 0.004 0.001 HIS A 662 PHE 0.013 0.001 PHE B 387 TYR 0.026 0.001 TYR A 475 ARG 0.008 0.000 ARG A 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 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.916 Fit side-chains REVERT: A 83 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6675 (mm) REVERT: A 273 GLN cc_start: 0.7690 (mm110) cc_final: 0.7332 (tp40) REVERT: A 274 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7246 (mtp) REVERT: A 346 ASP cc_start: 0.7301 (m-30) cc_final: 0.6899 (m-30) REVERT: A 468 ARG cc_start: 0.7633 (ttp80) cc_final: 0.6627 (ttm170) REVERT: B 83 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6746 (mm) REVERT: B 174 THR cc_start: 0.7047 (OUTLIER) cc_final: 0.6497 (p) REVERT: B 183 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: B 247 GLN cc_start: 0.7603 (mt0) cc_final: 0.7297 (mt0) REVERT: B 256 LYS cc_start: 0.7489 (mttp) cc_final: 0.7011 (mtpt) REVERT: B 283 GLU cc_start: 0.6803 (pm20) cc_final: 0.6404 (mp0) REVERT: B 346 ASP cc_start: 0.7254 (m-30) cc_final: 0.6729 (m-30) REVERT: B 468 ARG cc_start: 0.7669 (ttp80) cc_final: 0.6686 (ttm170) outliers start: 31 outliers final: 14 residues processed: 133 average time/residue: 1.4548 time to fit residues: 205.0661 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 221 LEU 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 462 GLU 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 68 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115038 restraints weight = 9220.894| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.92 r_work: 0.3099 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8980 Z= 0.171 Angle : 0.522 5.496 12166 Z= 0.267 Chirality : 0.040 0.127 1446 Planarity : 0.004 0.042 1494 Dihedral : 4.438 20.717 1225 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.49 % Allowed : 16.01 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1112 helix: 0.71 (0.21), residues: 680 sheet: -0.16 (0.55), residues: 82 loop : -1.34 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.002 0.001 HIS A 154 PHE 0.025 0.001 PHE A 502 TYR 0.023 0.001 TYR A 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 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.907 Fit side-chains REVERT: A 274 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7291 (mtp) REVERT: A 346 ASP cc_start: 0.7245 (m-30) cc_final: 0.6825 (m-30) REVERT: A 468 ARG cc_start: 0.7761 (ttp80) cc_final: 0.6745 (ttm170) REVERT: B 83 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6760 (mm) REVERT: B 174 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6540 (p) REVERT: B 183 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: B 247 GLN cc_start: 0.7647 (mt0) cc_final: 0.7327 (mt0) REVERT: B 256 LYS cc_start: 0.7501 (mttp) cc_final: 0.7055 (mtpt) REVERT: B 283 GLU cc_start: 0.6873 (pm20) cc_final: 0.6478 (mp0) REVERT: B 346 ASP cc_start: 0.7265 (m-30) cc_final: 0.6748 (m-30) REVERT: B 468 ARG cc_start: 0.7780 (ttp80) cc_final: 0.6761 (ttm170) outliers start: 24 outliers final: 14 residues processed: 129 average time/residue: 1.4023 time to fit residues: 191.9390 Evaluate side-chains 124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 221 LEU 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 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 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 Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 94 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.159207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115586 restraints weight = 9226.682| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.94 r_work: 0.3105 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8980 Z= 0.168 Angle : 0.512 5.501 12166 Z= 0.262 Chirality : 0.040 0.128 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.325 20.294 1225 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.49 % Allowed : 17.05 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1112 helix: 0.89 (0.21), residues: 680 sheet: -0.14 (0.53), residues: 84 loop : -1.29 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.002 0.001 HIS A 154 PHE 0.012 0.001 PHE B 499 TYR 0.022 0.001 TYR B 475 ARG 0.006 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 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.932 Fit side-chains REVERT: A 83 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6810 (mm) REVERT: A 174 THR cc_start: 0.7082 (OUTLIER) cc_final: 0.6576 (p) REVERT: A 346 ASP cc_start: 0.7214 (m-30) cc_final: 0.6623 (m-30) REVERT: A 468 ARG cc_start: 0.7782 (ttp80) cc_final: 0.6733 (ttm170) REVERT: B 83 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6772 (mm) REVERT: B 174 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6551 (p) REVERT: B 183 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 247 GLN cc_start: 0.7651 (mt0) cc_final: 0.7324 (mt0) REVERT: B 256 LYS cc_start: 0.7542 (mttp) cc_final: 0.7060 (mtpt) REVERT: B 283 GLU cc_start: 0.6819 (pm20) cc_final: 0.6475 (mp0) REVERT: B 346 ASP cc_start: 0.7244 (m-30) cc_final: 0.6702 (m-30) REVERT: B 468 ARG cc_start: 0.7810 (ttp80) cc_final: 0.6759 (ttm170) outliers start: 24 outliers final: 15 residues processed: 128 average time/residue: 1.3236 time to fit residues: 180.2777 Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 174 THR 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 660 ILE 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 193 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 108 optimal weight: 0.4980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.160583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111877 restraints weight = 9288.980| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.82 r_work: 0.3120 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8980 Z= 0.141 Angle : 0.494 5.444 12166 Z= 0.251 Chirality : 0.039 0.129 1446 Planarity : 0.004 0.041 1494 Dihedral : 4.181 19.189 1225 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.29 % Allowed : 17.67 % 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: 0.44 (0.26), residues: 1112 helix: 1.15 (0.21), residues: 674 sheet: -0.06 (0.54), residues: 84 loop : -1.25 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.002 0.001 HIS B 154 PHE 0.024 0.001 PHE A 502 TYR 0.021 0.001 TYR B 475 ARG 0.007 0.000 ARG B 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 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.998 Fit side-chains REVERT: A 174 THR cc_start: 0.6950 (OUTLIER) cc_final: 0.6427 (p) REVERT: A 346 ASP cc_start: 0.7193 (m-30) cc_final: 0.6594 (m-30) REVERT: A 468 ARG cc_start: 0.7509 (ttp80) cc_final: 0.6537 (ttm170) REVERT: B 83 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6641 (mm) REVERT: B 174 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6428 (p) REVERT: B 183 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: B 247 GLN cc_start: 0.7489 (mt0) cc_final: 0.7141 (mt0) REVERT: B 256 LYS cc_start: 0.7421 (mttp) cc_final: 0.6927 (mtpt) REVERT: B 283 GLU cc_start: 0.6681 (pm20) cc_final: 0.6370 (mp0) REVERT: B 346 ASP cc_start: 0.7206 (m-30) cc_final: 0.6640 (m-30) REVERT: B 468 ARG cc_start: 0.7526 (ttp80) cc_final: 0.6546 (ttm170) outliers start: 22 outliers final: 10 residues processed: 134 average time/residue: 1.2459 time to fit residues: 177.9354 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 221 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.158599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109788 restraints weight = 9264.381| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.81 r_work: 0.3092 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2642 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= 0.208 Angle : 0.528 5.512 12166 Z= 0.269 Chirality : 0.041 0.127 1446 Planarity : 0.004 0.039 1494 Dihedral : 4.284 18.725 1224 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.18 % Allowed : 18.40 % Favored : 79.42 % 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: 0.32 (0.26), residues: 1112 helix: 1.05 (0.21), residues: 678 sheet: -0.12 (0.54), residues: 82 loop : -1.28 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 447 HIS 0.003 0.001 HIS A 154 PHE 0.011 0.001 PHE B 499 TYR 0.022 0.001 TYR A 475 ARG 0.008 0.000 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 134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.942 Fit side-chains REVERT: A 174 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6469 (p) REVERT: A 346 ASP cc_start: 0.7185 (m-30) cc_final: 0.6618 (m-30) REVERT: A 468 ARG cc_start: 0.7638 (ttp80) cc_final: 0.6569 (ttm170) REVERT: B 83 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6693 (mm) REVERT: B 174 THR cc_start: 0.6967 (OUTLIER) cc_final: 0.6444 (p) REVERT: B 183 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: B 247 GLN cc_start: 0.7481 (mt0) cc_final: 0.7104 (mt0) REVERT: B 256 LYS cc_start: 0.7468 (mttp) cc_final: 0.6964 (mtpt) REVERT: B 283 GLU cc_start: 0.6699 (pm20) cc_final: 0.6380 (mp0) REVERT: B 346 ASP cc_start: 0.7178 (m-30) cc_final: 0.6627 (m-30) REVERT: B 468 ARG cc_start: 0.7646 (ttp80) cc_final: 0.6597 (ttm170) outliers start: 21 outliers final: 13 residues processed: 125 average time/residue: 1.3825 time to fit residues: 183.5340 Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 LEU 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 193 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.159774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111000 restraints weight = 9234.734| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.81 r_work: 0.3094 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8980 Z= 0.167 Angle : 0.511 5.473 12166 Z= 0.260 Chirality : 0.040 0.130 1446 Planarity : 0.004 0.040 1494 Dihedral : 4.207 18.363 1224 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.60 % Allowed : 18.40 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.26), residues: 1112 helix: 1.15 (0.21), residues: 678 sheet: -0.05 (0.53), residues: 84 loop : -1.29 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS A 154 PHE 0.030 0.001 PHE A 502 TYR 0.021 0.001 TYR A 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: 6573.21 seconds wall clock time: 116 minutes 36.51 seconds (6996.51 seconds total)