Starting phenix.real_space_refine on Wed Aug 5 00:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tv0_56282/08_2026/9tv0_56282.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tv0_56282/08_2026/9tv0_56282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tv0_56282/08_2026/9tv0_56282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tv0_56282/08_2026/9tv0_56282.map" model { file = "/net/cci-nas-00/data/ceres_data/9tv0_56282/08_2026/9tv0_56282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tv0_56282/08_2026/9tv0_56282.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 74 5.16 5 C 4762 2.51 5 N 1232 2.21 5 O 1435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7503 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5168 Classifications: {'peptide': 639} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 624} Chain breaks: 5 Chain: "B" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2335 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 6, 'TRANS': 273} Chain breaks: 7 Time building chain proxies: 1.50, per 1000 atoms: 0.20 Number of scatterers: 7503 At special positions: 0 Unit cell: (99.008, 134.784, 92.352, 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 74 16.00 O 1435 8.00 N 1232 7.00 C 4762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 112 " distance=2.04 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 461 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 576 " - pdb=" SG CYS A 637 " distance=2.03 Simple disulfide: pdb=" SG CYS A 594 " - pdb=" SG CYS A 625 " distance=2.02 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 659 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS A 680 " - pdb=" SG CYS A 691 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 701 " distance=2.03 Simple disulfide: pdb=" SG CYS A 703 " - pdb=" SG CYS A 714 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 730 " distance=2.03 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 739 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 752 " distance=2.03 Simple disulfide: pdb=" SG CYS A 754 " - pdb=" SG CYS A 766 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 268 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 327 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 339.4 milliseconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1762 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 24 sheets defined 11.4% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 41 through 47 removed outlier: 4.238A pdb=" N ARG A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.683A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.636A pdb=" N ASP A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.927A pdb=" N THR A 623 " --> pdb=" O HIS A 620 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 624 " --> pdb=" O PHE A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 620 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 74 removed outlier: 5.442A pdb=" N VAL A 69 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A 152 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.555A pdb=" N ASP B 282 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY B 295 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU B 280 " --> pdb=" O GLY B 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 179 Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 226 Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 256 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA8, first strand: chain 'A' and resid 297 through 300 Processing sheet with id=AA9, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AB1, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AB2, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.509A pdb=" N ASN A 411 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A 473 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL A 409 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 475 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE A 407 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 390 through 391 removed outlier: 5.218A pdb=" N CYS A 474 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE A 381 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N ILE A 560 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS A 637 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER A 636 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE A 583 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER A 638 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE A 581 " --> pdb=" O SER A 638 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AB5, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AB6, first strand: chain 'A' and resid 648 through 653 Processing sheet with id=AB7, first strand: chain 'A' and resid 689 through 691 Processing sheet with id=AB8, first strand: chain 'A' and resid 707 through 710 Processing sheet with id=AB9, first strand: chain 'A' and resid 729 through 733 Processing sheet with id=AC1, first strand: chain 'A' and resid 746 through 748 Processing sheet with id=AC2, first strand: chain 'A' and resid 758 through 761 removed outlier: 3.805A pdb=" N ASN A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 39 through 43 removed outlier: 7.245A pdb=" N ILE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 346 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.636A pdb=" N PHE B 54 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU B 60 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 77 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP B 92 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 79 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 145 through 149 removed outlier: 6.275A pdb=" N ILE B 105 " --> pdb=" O TYR B 164 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER B 166 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 107 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 177 through 181 removed outlier: 7.153A pdb=" N GLU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 237 " --> pdb=" O CYS B 258 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.67 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: 2407 1.34 - 1.46: 1786 1.46 - 1.58: 3376 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 7652 Sorted by residual: bond pdb=" CG LEU A 138 " pdb=" CD1 LEU A 138 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB ILE B 335 " pdb=" CG2 ILE B 335 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.85e-01 bond pdb=" CB ILE A 560 " pdb=" CG2 ILE A 560 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.34e-01 bond pdb=" CB THR A 116 " pdb=" CG2 THR A 116 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.93e-01 bond pdb=" CB CYS A 299 " pdb=" SG CYS A 299 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.66e-01 ... (remaining 7647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 9960 1.28 - 2.56: 306 2.56 - 3.83: 32 3.83 - 5.11: 7 5.11 - 6.39: 3 Bond angle restraints: 10308 Sorted by residual: angle pdb=" N TYR A 139 " pdb=" CA TYR A 139 " pdb=" C TYR A 139 " ideal model delta sigma weight residual 108.20 112.11 -3.91 1.71e+00 3.42e-01 5.22e+00 angle pdb=" CA CYS A 288 " pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " ideal model delta sigma weight residual 114.40 109.65 4.75 2.30e+00 1.89e-01 4.27e+00 angle pdb=" CA CYS A 306 " pdb=" CB CYS A 306 " pdb=" SG CYS A 306 " ideal model delta sigma weight residual 114.40 118.97 -4.57 2.30e+00 1.89e-01 3.95e+00 angle pdb=" CA CYS A 680 " pdb=" CB CYS A 680 " pdb=" SG CYS A 680 " ideal model delta sigma weight residual 114.40 118.74 -4.34 2.30e+00 1.89e-01 3.56e+00 angle pdb=" CA TYR A 417 " pdb=" CB TYR A 417 " pdb=" CG TYR A 417 " ideal model delta sigma weight residual 113.90 117.21 -3.31 1.80e+00 3.09e-01 3.37e+00 ... (remaining 10303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4346 17.12 - 34.24: 286 34.24 - 51.36: 48 51.36 - 68.48: 10 68.48 - 85.60: 3 Dihedral angle restraints: 4693 sinusoidal: 1960 harmonic: 2733 Sorted by residual: dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual -86.00 -147.27 61.27 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS A 741 " pdb=" SG CYS A 741 " pdb=" SG CYS A 752 " pdb=" CB CYS A 752 " ideal model delta sinusoidal sigma weight residual 93.00 150.54 -57.54 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CB CYS A 661 " pdb=" SG CYS A 661 " pdb=" SG CYS A 674 " pdb=" CB CYS A 674 " ideal model delta sinusoidal sigma weight residual 93.00 144.18 -51.18 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 4690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 662 0.031 - 0.061: 288 0.061 - 0.092: 89 0.092 - 0.122: 65 0.122 - 0.153: 9 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CG LEU A 138 " pdb=" CB LEU A 138 " pdb=" CD1 LEU A 138 " pdb=" CD2 LEU A 138 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA PRO A 394 " pdb=" N PRO A 394 " pdb=" C PRO A 394 " pdb=" CB PRO A 394 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1110 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 339 " 0.170 9.50e-02 1.11e+02 7.69e-02 4.80e+00 pdb=" NE ARG B 339 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 339 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 339 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 339 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 316 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 317 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 36 " -0.129 9.50e-02 1.11e+02 5.85e-02 2.87e+00 pdb=" NE ARG B 36 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 36 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 36 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 36 " 0.000 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 4958 3.07 - 3.53: 7216 3.53 - 3.99: 11484 3.99 - 4.44: 13829 4.44 - 4.90: 22234 Nonbonded interactions: 59721 Sorted by model distance: nonbonded pdb=" N GLU A 171 " pdb=" O GLU A 171 " model vdw 2.613 2.496 nonbonded pdb=" N VAL A 258 " pdb=" O VAL A 258 " model vdw 2.615 2.496 nonbonded pdb=" N LYS B 262 " pdb=" O LYS B 262 " model vdw 2.626 2.496 nonbonded pdb=" N CYS A 594 " pdb=" O CYS A 594 " model vdw 2.635 2.496 nonbonded pdb=" N ASP B 297 " pdb=" O ASP B 297 " model vdw 2.636 2.496 ... (remaining 59716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.090 Find NCS groups from input model: 0.030 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7684 Z= 0.189 Angle : 0.535 6.390 10372 Z= 0.291 Chirality : 0.043 0.153 1113 Planarity : 0.004 0.077 1324 Dihedral : 11.172 85.604 2835 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.04 % Allowed : 8.58 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.28), residues: 891 helix: -0.44 (0.57), residues: 79 sheet: -0.71 (0.31), residues: 292 loop : -1.34 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG B 339 TYR 0.018 0.001 TYR A 286 PHE 0.020 0.001 PHE A 237 TRP 0.004 0.001 TRP B 87 HIS 0.008 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 7652) covalent geometry : angle 0.52750 / 0.29 (10308) SS BOND : bond 0.00357 / 0.29 ( 32) SS BOND : angle 1.27321 / 1.11 ( 64) hydrogen bonds : bond 0.15167 / 9.70 ( 232) hydrogen bonds : angle 7.06129 / 4.86 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 VAL cc_start: 0.8673 (m) cc_final: 0.8374 (p) REVERT: B 333 VAL cc_start: 0.8115 (t) cc_final: 0.7889 (m) REVERT: B 355 THR cc_start: 0.7398 (p) cc_final: 0.7159 (t) outliers start: 9 outliers final: 2 residues processed: 199 average time/residue: 0.3789 time to fit residues: 80.8739 Evaluate side-chains 93 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 323 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN A 196 ASN A 297 GLN A 577 GLN A 671 ASN A 688 ASN A 692 GLN A 727 ASN A 734 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.132056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.094192 restraints weight = 15337.143| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.31 r_work: 0.3550 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7684 Z= 0.199 Angle : 0.713 10.243 10372 Z= 0.374 Chirality : 0.048 0.346 1113 Planarity : 0.004 0.042 1324 Dihedral : 4.864 25.080 994 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.22 % Allowed : 15.55 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.28), residues: 891 helix: -0.57 (0.54), residues: 80 sheet: -0.63 (0.31), residues: 286 loop : -1.23 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 102 TYR 0.037 0.002 TYR A 669 PHE 0.026 0.002 PHE A 237 TRP 0.013 0.002 TRP B 87 HIS 0.009 0.002 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 7652) covalent geometry : angle 0.69774 / 0.37 (10308) SS BOND : bond 0.00717 / 0.42 ( 32) SS BOND : angle 1.98095 / 1.39 ( 64) hydrogen bonds : bond 0.04053 / 2.53 ( 232) hydrogen bonds : angle 5.86684 / 3.99 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 155 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8555 (mm110) REVERT: A 166 GLU cc_start: 0.8501 (tt0) cc_final: 0.8288 (tt0) REVERT: A 170 PHE cc_start: 0.8446 (p90) cc_final: 0.7952 (p90) REVERT: A 183 MET cc_start: 0.8433 (mtm) cc_final: 0.8069 (ptp) REVERT: A 408 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: A 458 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7840 (m-70) REVERT: A 573 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7981 (mmtt) REVERT: A 671 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8151 (t0) REVERT: A 692 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: A 753 ILE cc_start: 0.7086 (pp) cc_final: 0.6878 (pp) REVERT: B 38 GLU cc_start: 0.7846 (tp30) cc_final: 0.7567 (mt-10) REVERT: B 119 CYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7251 (m) REVERT: B 208 TRP cc_start: 0.4387 (m100) cc_final: 0.3782 (p90) outliers start: 45 outliers final: 10 residues processed: 145 average time/residue: 0.4513 time to fit residues: 70.0348 Evaluate side-chains 98 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS A 358 ASN A 400 GLN A 645 HIS A 692 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 235 ASN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.130374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.091889 restraints weight = 14776.477| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.27 r_work: 0.3504 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 7684 Z= 0.169 Angle : 0.667 17.018 10372 Z= 0.348 Chirality : 0.045 0.274 1113 Planarity : 0.003 0.041 1324 Dihedral : 4.506 21.392 990 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.18 % Allowed : 18.21 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.27), residues: 891 helix: -0.39 (0.56), residues: 80 sheet: -0.60 (0.32), residues: 278 loop : -1.20 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.013 0.001 TYR A 669 PHE 0.020 0.001 PHE A 237 TRP 0.011 0.002 TRP B 87 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 7652) covalent geometry : angle 0.65739 / 0.34 (10308) SS BOND : bond 0.00365 / 0.23 ( 32) SS BOND : angle 1.57689 / 1.10 ( 64) hydrogen bonds : bond 0.03797 / 2.34 ( 232) hydrogen bonds : angle 5.53448 / 3.76 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8483 (p) REVERT: A 155 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8657 (mm110) REVERT: A 170 PHE cc_start: 0.8627 (p90) cc_final: 0.7892 (p90) REVERT: A 183 MET cc_start: 0.8393 (mtm) cc_final: 0.8030 (ptp) REVERT: A 188 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8032 (mmt90) REVERT: A 379 GLU cc_start: 0.7590 (pt0) cc_final: 0.7312 (pt0) REVERT: A 458 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.8096 (m-70) REVERT: A 692 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: B 38 GLU cc_start: 0.7857 (tp30) cc_final: 0.7645 (mt-10) REVERT: B 119 CYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7152 (m) REVERT: B 208 TRP cc_start: 0.4032 (m100) cc_final: 0.3513 (p90) REVERT: B 339 ARG cc_start: 0.7500 (mtp180) cc_final: 0.7104 (ttm110) outliers start: 36 outliers final: 10 residues processed: 108 average time/residue: 0.4991 time to fit residues: 57.4141 Evaluate side-chains 81 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 331 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN A 400 GLN A 457 HIS A 692 GLN B 80 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.126606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.088030 restraints weight = 15411.221| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.23 r_work: 0.3479 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7684 Z= 0.215 Angle : 0.685 14.670 10372 Z= 0.357 Chirality : 0.046 0.170 1113 Planarity : 0.004 0.042 1324 Dihedral : 4.691 19.825 990 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.76 % Allowed : 17.98 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.27), residues: 891 helix: -0.35 (0.56), residues: 80 sheet: -0.77 (0.31), residues: 284 loop : -1.39 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.017 0.001 TYR A 413 PHE 0.024 0.002 PHE A 237 TRP 0.009 0.002 TRP B 87 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 ( 7652) covalent geometry : angle 0.67537 / 0.35 (10308) SS BOND : bond 0.00487 / 0.30 ( 32) SS BOND : angle 1.62053 / 1.12 ( 64) hydrogen bonds : bond 0.03791 / 2.32 ( 232) hydrogen bonds : angle 5.56315 / 3.77 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 39 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 170 PHE cc_start: 0.8695 (p90) cc_final: 0.7893 (p90) REVERT: A 188 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7980 (mmt90) REVERT: A 457 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.8398 (t-90) REVERT: A 458 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8181 (m-70) REVERT: A 612 GLU cc_start: 0.8753 (tt0) cc_final: 0.8476 (tp30) REVERT: A 744 ARG cc_start: 0.8330 (mpp80) cc_final: 0.7313 (mpp80) REVERT: B 119 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7642 (m) REVERT: B 139 ASN cc_start: 0.8639 (p0) cc_final: 0.8361 (t0) REVERT: B 229 ARG cc_start: 0.8257 (ptt-90) cc_final: 0.7944 (ptp-170) REVERT: B 339 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7227 (ttm110) outliers start: 41 outliers final: 15 residues processed: 99 average time/residue: 0.4353 time to fit residues: 46.1056 Evaluate side-chains 78 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 9 optimal weight: 0.0470 chunk 74 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.129371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.090022 restraints weight = 14828.859| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.34 r_work: 0.3458 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7684 Z= 0.152 Angle : 0.646 14.311 10372 Z= 0.333 Chirality : 0.045 0.164 1113 Planarity : 0.003 0.040 1324 Dihedral : 4.505 18.887 990 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.48 % Allowed : 19.84 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.27), residues: 891 helix: -0.31 (0.56), residues: 80 sheet: -0.67 (0.31), residues: 274 loop : -1.30 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.022 0.001 TYR A 152 PHE 0.022 0.001 PHE A 237 TRP 0.013 0.002 TRP B 87 HIS 0.006 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 7652) covalent geometry : angle 0.63807 / 0.33 (10308) SS BOND : bond 0.00393 / 0.21 ( 32) SS BOND : angle 1.41376 / 0.98 ( 64) hydrogen bonds : bond 0.03435 / 2.11 ( 232) hydrogen bonds : angle 5.46997 / 3.70 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 155 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8727 (mm110) REVERT: A 170 PHE cc_start: 0.8704 (p90) cc_final: 0.7691 (p90) REVERT: A 183 MET cc_start: 0.8218 (mtm) cc_final: 0.7835 (ptp) REVERT: A 188 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7937 (mmt90) REVERT: A 458 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.8324 (m-70) REVERT: A 612 GLU cc_start: 0.8856 (tt0) cc_final: 0.8516 (tp30) REVERT: A 617 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8944 (tp) REVERT: A 692 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: B 119 CYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7732 (m) REVERT: B 139 ASN cc_start: 0.8735 (p0) cc_final: 0.8447 (t0) outliers start: 30 outliers final: 12 residues processed: 87 average time/residue: 0.4268 time to fit residues: 39.6244 Evaluate side-chains 74 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 291 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN B 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.128789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.089308 restraints weight = 14967.086| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.37 r_work: 0.3449 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.7557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7684 Z= 0.173 Angle : 0.645 13.856 10372 Z= 0.338 Chirality : 0.045 0.144 1113 Planarity : 0.003 0.042 1324 Dihedral : 4.543 21.886 990 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.71 % Allowed : 19.95 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.27), residues: 891 helix: -0.23 (0.57), residues: 80 sheet: -0.76 (0.30), residues: 286 loop : -1.31 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.023 0.001 TYR A 152 PHE 0.022 0.001 PHE A 237 TRP 0.015 0.003 TRP B 208 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 7652) covalent geometry : angle 0.63776 / 0.34 (10308) SS BOND : bond 0.00368 / 0.22 ( 32) SS BOND : angle 1.40741 / 0.97 ( 64) hydrogen bonds : bond 0.03500 / 2.14 ( 232) hydrogen bonds : angle 5.43436 / 3.68 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8493 (p) REVERT: A 155 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8737 (mm110) REVERT: A 170 PHE cc_start: 0.8715 (p90) cc_final: 0.7723 (p90) REVERT: A 388 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: A 458 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8339 (m-70) REVERT: A 612 GLU cc_start: 0.8831 (tt0) cc_final: 0.8455 (tp30) REVERT: A 692 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: A 744 ARG cc_start: 0.7713 (mpp80) cc_final: 0.7335 (mpp-170) REVERT: B 119 CYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7838 (m) REVERT: B 139 ASN cc_start: 0.8796 (p0) cc_final: 0.8485 (t0) REVERT: B 229 ARG cc_start: 0.8141 (ptp-170) cc_final: 0.7891 (ptp-170) REVERT: B 239 PHE cc_start: 0.8965 (m-80) cc_final: 0.8723 (m-80) REVERT: B 352 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8288 (m110) outliers start: 32 outliers final: 13 residues processed: 88 average time/residue: 0.3978 time to fit residues: 37.6323 Evaluate side-chains 76 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 352 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 GLN A 702 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.127708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.088415 restraints weight = 15034.611| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.41 r_work: 0.3428 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.7758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7684 Z= 0.217 Angle : 0.682 13.593 10372 Z= 0.359 Chirality : 0.046 0.144 1113 Planarity : 0.003 0.044 1324 Dihedral : 4.728 21.583 990 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.48 % Allowed : 20.30 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.27), residues: 891 helix: -0.24 (0.57), residues: 80 sheet: -0.75 (0.31), residues: 282 loop : -1.33 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 102 TYR 0.024 0.001 TYR A 152 PHE 0.024 0.001 PHE A 237 TRP 0.016 0.003 TRP B 208 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 ( 7652) covalent geometry : angle 0.67327 / 0.36 (10308) SS BOND : bond 0.00374 / 0.24 ( 32) SS BOND : angle 1.52205 / 1.03 ( 64) hydrogen bonds : bond 0.03738 / 2.26 ( 232) hydrogen bonds : angle 5.52100 / 3.73 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8448 (p) REVERT: A 155 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8751 (mm110) REVERT: A 259 TYR cc_start: 0.7229 (m-80) cc_final: 0.7010 (m-80) REVERT: A 388 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: A 458 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8447 (m-70) REVERT: A 672 LYS cc_start: 0.8843 (pptt) cc_final: 0.8365 (pptt) REVERT: A 676 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.9004 (tmt170) REVERT: A 692 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: B 119 CYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7839 (m) REVERT: B 139 ASN cc_start: 0.8865 (p0) cc_final: 0.8537 (t0) REVERT: B 229 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7875 (ptp-170) REVERT: B 352 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7697 (m-40) outliers start: 30 outliers final: 13 residues processed: 82 average time/residue: 0.4342 time to fit residues: 37.8981 Evaluate side-chains 69 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 352 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.128669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.089435 restraints weight = 15043.419| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.35 r_work: 0.3457 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.7874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7684 Z= 0.156 Angle : 0.664 13.424 10372 Z= 0.346 Chirality : 0.045 0.138 1113 Planarity : 0.003 0.041 1324 Dihedral : 4.576 21.886 990 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.02 % Allowed : 20.77 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.27), residues: 891 helix: -0.39 (0.56), residues: 80 sheet: -0.66 (0.32), residues: 274 loop : -1.32 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 102 TYR 0.025 0.001 TYR A 152 PHE 0.022 0.001 PHE A 237 TRP 0.018 0.003 TRP B 208 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 7652) covalent geometry : angle 0.65690 / 0.34 (10308) SS BOND : bond 0.00348 / 0.21 ( 32) SS BOND : angle 1.41933 / 1.00 ( 64) hydrogen bonds : bond 0.03512 / 2.11 ( 232) hydrogen bonds : angle 5.42468 / 3.68 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8473 (p) REVERT: A 155 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8718 (mm110) REVERT: A 170 PHE cc_start: 0.8708 (p90) cc_final: 0.7719 (p90) REVERT: A 183 MET cc_start: 0.8168 (mtm) cc_final: 0.7787 (ptp) REVERT: A 259 TYR cc_start: 0.7231 (m-80) cc_final: 0.6997 (m-80) REVERT: A 388 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: A 458 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.8369 (m-70) REVERT: A 672 LYS cc_start: 0.8836 (pptt) cc_final: 0.8624 (pptt) REVERT: A 692 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: B 119 CYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7747 (m) REVERT: B 139 ASN cc_start: 0.8824 (p0) cc_final: 0.8486 (t0) REVERT: B 352 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7658 (m-40) outliers start: 26 outliers final: 13 residues processed: 78 average time/residue: 0.4112 time to fit residues: 34.3596 Evaluate side-chains 67 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 352 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN A 692 GLN A 702 GLN B 352 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.126869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.087433 restraints weight = 15079.957| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.35 r_work: 0.3419 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.8027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7684 Z= 0.231 Angle : 0.703 13.465 10372 Z= 0.368 Chirality : 0.046 0.141 1113 Planarity : 0.003 0.044 1324 Dihedral : 4.789 20.781 990 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.90 % Allowed : 20.19 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.27), residues: 891 helix: -0.18 (0.58), residues: 74 sheet: -0.80 (0.30), residues: 292 loop : -1.41 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 45 TYR 0.026 0.002 TYR A 152 PHE 0.024 0.001 PHE A 237 TRP 0.020 0.003 TRP B 208 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 ( 7652) covalent geometry : angle 0.69517 / 0.36 (10308) SS BOND : bond 0.00407 / 0.27 ( 32) SS BOND : angle 1.49667 / 1.03 ( 64) hydrogen bonds : bond 0.03985 / 2.34 ( 232) hydrogen bonds : angle 5.46311 / 3.71 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 155 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8772 (mm110) REVERT: A 259 TYR cc_start: 0.7251 (m-80) cc_final: 0.7019 (m-80) REVERT: A 388 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: A 458 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8425 (m-70) REVERT: A 612 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8552 (tp30) REVERT: A 672 LYS cc_start: 0.8831 (pptt) cc_final: 0.8366 (pptt) REVERT: A 692 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: B 119 CYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7707 (m) REVERT: B 139 ASN cc_start: 0.8862 (p0) cc_final: 0.8505 (t0) REVERT: B 352 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7911 (m-40) outliers start: 25 outliers final: 15 residues processed: 72 average time/residue: 0.4269 time to fit residues: 32.7003 Evaluate side-chains 70 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 352 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.0870 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.128248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088990 restraints weight = 14920.237| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.42 r_work: 0.3455 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.8132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7684 Z= 0.157 Angle : 0.677 13.360 10372 Z= 0.351 Chirality : 0.045 0.140 1113 Planarity : 0.003 0.040 1324 Dihedral : 4.615 21.272 990 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.67 % Allowed : 21.11 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.27), residues: 891 helix: -0.15 (0.57), residues: 74 sheet: -0.72 (0.31), residues: 282 loop : -1.35 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.026 0.001 TYR A 152 PHE 0.022 0.001 PHE A 237 TRP 0.024 0.004 TRP B 208 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 7652) covalent geometry : angle 0.67106 / 0.35 (10308) SS BOND : bond 0.00343 / 0.20 ( 32) SS BOND : angle 1.34311 / 0.93 ( 64) hydrogen bonds : bond 0.03613 / 2.13 ( 232) hydrogen bonds : angle 5.41725 / 3.68 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8455 (p) REVERT: A 155 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8742 (mm110) REVERT: A 170 PHE cc_start: 0.8703 (p90) cc_final: 0.7652 (p90) REVERT: A 259 TYR cc_start: 0.7297 (m-80) cc_final: 0.7034 (m-80) REVERT: A 458 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.8393 (m-70) REVERT: A 612 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8444 (tp30) REVERT: A 672 LYS cc_start: 0.8752 (pptt) cc_final: 0.8298 (pptt) REVERT: A 692 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: B 119 CYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7601 (m) REVERT: B 139 ASN cc_start: 0.8876 (p0) cc_final: 0.8518 (t0) REVERT: B 352 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7542 (m-40) outliers start: 23 outliers final: 15 residues processed: 69 average time/residue: 0.4024 time to fit residues: 29.7995 Evaluate side-chains 70 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 352 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 56 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 GLN B 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.128307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.089038 restraints weight = 14942.468| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.42 r_work: 0.3454 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7684 Z= 0.160 Angle : 0.673 13.364 10372 Z= 0.349 Chirality : 0.045 0.142 1113 Planarity : 0.003 0.040 1324 Dihedral : 4.570 20.967 990 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.55 % Allowed : 21.23 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.27), residues: 891 helix: -0.13 (0.57), residues: 74 sheet: -0.72 (0.31), residues: 279 loop : -1.32 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.025 0.001 TYR A 152 PHE 0.022 0.001 PHE A 237 TRP 0.020 0.003 TRP B 208 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 7652) covalent geometry : angle 0.66740 / 0.35 (10308) SS BOND : bond 0.00345 / 0.21 ( 32) SS BOND : angle 1.30715 / 0.91 ( 64) hydrogen bonds : bond 0.03588 / 2.11 ( 232) hydrogen bonds : angle 5.33928 / 3.63 ( 597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.36 seconds wall clock time: 42 minutes 4.30 seconds (2524.30 seconds total)