Starting phenix.real_space_refine on Wed May 14 02:41:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ysz_39566/05_2025/8ysz_39566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ysz_39566/05_2025/8ysz_39566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ysz_39566/05_2025/8ysz_39566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ysz_39566/05_2025/8ysz_39566.map" model { file = "/net/cci-nas-00/data/ceres_data/8ysz_39566/05_2025/8ysz_39566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ysz_39566/05_2025/8ysz_39566.cif" } resolution = 3.38 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= 0.006 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 77 5.16 5 C 7081 2.51 5 N 1922 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11170 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 244 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain breaks: 1 Chain: "A" Number of atoms: 6408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6408 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 41, 'TRANS': 755} Chain breaks: 9 Chain: "B" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3874 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 25, 'TRANS': 451} Chain breaks: 10 Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain breaks: 1 Chain: "E" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain breaks: 1 Time building chain proxies: 9.34, per 1000 atoms: 0.84 Number of scatterers: 11170 At special positions: 0 Unit cell: (90.42, 114.84, 173.58, 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 77 16.00 O 2090 8.00 N 1922 7.00 C 7081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 60 " distance=2.04 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 215 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.04 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 24 sheets defined 16.5% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'D' and resid 11 through 22 removed outlier: 4.140A pdb=" N LEU D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.930A pdb=" N ARG A 46 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.682A pdb=" N ILE A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.644A pdb=" N CYS A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.537A pdb=" N ILE A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 891 through 896 removed outlier: 4.204A pdb=" N GLU A 896 " --> pdb=" O HIS A 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.543A pdb=" N LEU B 357 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 386 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.473A pdb=" N PHE B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 462 through 473 removed outlier: 3.501A pdb=" N LYS B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 4.309A pdb=" N GLN B 479 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 721 through 741 removed outlier: 3.651A pdb=" N PHE B 741 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 895 removed outlier: 3.888A pdb=" N ALA B 894 " --> pdb=" O LYS B 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.741A pdb=" N VAL C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.528A pdb=" N LEU C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 52 through 57 removed outlier: 3.528A pdb=" N LEU E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 41 removed outlier: 7.247A pdb=" N GLU A 33 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 56 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS A 35 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY A 58 " --> pdb=" O CYS A 35 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 37 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 60 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A 39 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 62 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG A 41 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 41 removed outlier: 7.247A pdb=" N GLU A 33 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 56 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS A 35 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY A 58 " --> pdb=" O CYS A 35 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 37 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 60 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A 39 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 62 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG A 41 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 87 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A 58 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N LEU A 89 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 60 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE A 91 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 62 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 88 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE A 123 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 90 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ARG A 145 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 121 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 147 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE A 123 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 144 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL A 173 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 146 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 243 removed outlier: 7.170A pdb=" N ASN A 242 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N CYS A 252 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 281 removed outlier: 6.377A pdb=" N HIS A 274 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 348 removed outlier: 6.249A pdb=" N LYS A 346 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE A 454 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 428 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N HIS A 456 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 430 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 453 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 502 through 507 Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 561 Processing sheet with id=AB1, first strand: chain 'A' and resid 557 through 561 Processing sheet with id=AB2, first strand: chain 'A' and resid 626 through 634 removed outlier: 5.222A pdb=" N ASP A 627 " --> pdb=" O LYS A 643 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 643 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN A 633 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 789 removed outlier: 3.833A pdb=" N GLU A 787 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 657 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 871 through 872 removed outlier: 3.685A pdb=" N LEU A 871 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 874 through 875 Processing sheet with id=AB6, first strand: chain 'A' and resid 907 through 911 Processing sheet with id=AB7, first strand: chain 'B' and resid 338 through 346 removed outlier: 7.457A pdb=" N VAL B 362 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS B 340 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN B 364 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 342 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N SER B 366 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY B 344 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 390 through 393 removed outlier: 7.103A pdb=" N ILE B 391 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 395 through 398 removed outlier: 5.497A pdb=" N LYS B 452 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 427 " --> pdb=" O LYS B 452 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 502 through 506 Processing sheet with id=AC2, first strand: chain 'B' and resid 557 through 561 removed outlier: 3.614A pdb=" N GLY B 529 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 629 through 634 removed outlier: 6.193A pdb=" N GLN B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 638 " --> pdb=" O ILE B 797 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 786 through 789 removed outlier: 4.619A pdb=" N ALA B 812 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 823 " --> pdb=" O ALA B 812 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 786 through 789 Processing sheet with id=AC6, first strand: chain 'B' and resid 845 through 849 removed outlier: 3.517A pdb=" N THR B 846 " --> pdb=" O MET B 858 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 648 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: 4.13 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2008 1.32 - 1.45: 3019 1.45 - 1.57: 6297 1.57 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 11417 Sorted by residual: bond pdb=" CA PRO B 576 " pdb=" C PRO B 576 " ideal model delta sigma weight residual 1.521 1.470 0.051 1.19e-02 7.06e+03 1.87e+01 bond pdb=" N PRO B 576 " pdb=" CA PRO B 576 " ideal model delta sigma weight residual 1.466 1.421 0.044 1.21e-02 6.83e+03 1.34e+01 bond pdb=" C PRO B 576 " pdb=" O PRO B 576 " ideal model delta sigma weight residual 1.233 1.199 0.034 1.21e-02 6.83e+03 7.96e+00 bond pdb=" N GLY A 27 " pdb=" CA GLY A 27 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.11e+00 bond pdb=" CA PRO B 576 " pdb=" CB PRO B 576 " ideal model delta sigma weight residual 1.533 1.500 0.033 1.47e-02 4.63e+03 4.98e+00 ... (remaining 11412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 14935 1.62 - 3.23: 442 3.23 - 4.85: 56 4.85 - 6.47: 9 6.47 - 8.08: 1 Bond angle restraints: 15443 Sorted by residual: angle pdb=" CA PRO B 576 " pdb=" C PRO B 576 " pdb=" O PRO B 576 " ideal model delta sigma weight residual 121.95 116.02 5.93 1.25e+00 6.40e-01 2.25e+01 angle pdb=" CA PRO B 576 " pdb=" C PRO B 576 " pdb=" N GLY B 577 " ideal model delta sigma weight residual 115.04 121.39 -6.35 1.35e+00 5.49e-01 2.21e+01 angle pdb=" N TYR A 806 " pdb=" CA TYR A 806 " pdb=" C TYR A 806 " ideal model delta sigma weight residual 108.34 113.50 -5.16 1.31e+00 5.83e-01 1.55e+01 angle pdb=" N ASN A 42 " pdb=" CA ASN A 42 " pdb=" CB ASN A 42 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N LYS B 511 " pdb=" CA LYS B 511 " pdb=" C LYS B 511 " ideal model delta sigma weight residual 109.06 115.25 -6.19 1.70e+00 3.46e-01 1.32e+01 ... (remaining 15438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6197 17.92 - 35.83: 529 35.83 - 53.75: 115 53.75 - 71.67: 32 71.67 - 89.58: 14 Dihedral angle restraints: 6887 sinusoidal: 2864 harmonic: 4023 Sorted by residual: dihedral pdb=" CB CYS D 21 " pdb=" SG CYS D 21 " pdb=" SG CYS D 60 " pdb=" CB CYS D 60 " ideal model delta sinusoidal sigma weight residual 93.00 13.23 79.77 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS A 268 " pdb=" SG CYS A 268 " pdb=" SG CYS A 280 " pdb=" CB CYS A 280 " ideal model delta sinusoidal sigma weight residual 93.00 168.88 -75.88 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS A 286 " pdb=" SG CYS A 286 " pdb=" SG CYS A 311 " pdb=" CB CYS A 311 " ideal model delta sinusoidal sigma weight residual -86.00 -148.08 62.08 1 1.00e+01 1.00e-02 5.10e+01 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1006 0.029 - 0.058: 459 0.058 - 0.087: 97 0.087 - 0.116: 94 0.116 - 0.146: 26 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 84 " pdb=" N ILE A 84 " pdb=" C ILE A 84 " pdb=" CB ILE A 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 122 " pdb=" N ILE A 122 " pdb=" C ILE A 122 " pdb=" CB ILE A 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1679 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 520 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 521 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 873 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" CD GLU B 873 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU B 873 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU B 873 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 575 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO B 576 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 576 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 576 " -0.016 5.00e-02 4.00e+02 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 143 2.59 - 3.17: 10336 3.17 - 3.75: 16465 3.75 - 4.32: 23790 4.32 - 4.90: 38241 Nonbonded interactions: 88975 Sorted by model distance: nonbonded pdb=" O ARG A 604 " pdb=" OG1 THR A 605 " model vdw 2.017 3.040 nonbonded pdb=" O GLU A 883 " pdb=" OE1 GLU A 883 " model vdw 2.128 3.040 nonbonded pdb=" N GLU A 130 " pdb=" OE1 GLU A 130 " model vdw 2.136 3.120 nonbonded pdb=" NH1 ARG B 801 " pdb=" OE2 GLU B 864 " model vdw 2.198 3.120 nonbonded pdb=" N GLU C 12 " pdb=" OE1 GLU C 12 " model vdw 2.206 3.120 ... (remaining 88970 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: 11.220 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: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.910 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.003 0.051 11441 Z= 0.163 Angle : 0.659 8.084 15491 Z= 0.384 Chirality : 0.041 0.146 1682 Planarity : 0.003 0.034 1991 Dihedral : 14.547 89.585 4211 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.72 % Allowed : 12.36 % Favored : 86.92 % 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: -1.65 (0.23), residues: 1336 helix: -0.64 (0.43), residues: 150 sheet: -1.13 (0.34), residues: 244 loop : -1.21 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.007 0.001 HIS A 892 PHE 0.009 0.001 PHE E 19 TYR 0.010 0.001 TYR A 606 ARG 0.004 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.23438 ( 243) hydrogen bonds : angle 9.77880 ( 648) SS BOND : bond 0.00263 ( 24) SS BOND : angle 0.79591 ( 48) covalent geometry : bond 0.00300 (11417) covalent geometry : angle 0.65805 (15443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9294 (pp) cc_final: 0.9059 (mp) REVERT: A 321 MET cc_start: 0.8330 (pmm) cc_final: 0.8096 (pmm) REVERT: B 469 MET cc_start: 0.8630 (tpt) cc_final: 0.8291 (tpp) outliers start: 9 outliers final: 2 residues processed: 78 average time/residue: 0.2335 time to fit residues: 27.0993 Evaluate side-chains 60 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 384 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 482 ASN B 458 ASN B 467 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.084791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058466 restraints weight = 44160.465| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 4.31 r_work: 0.3022 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11441 Z= 0.273 Angle : 0.730 10.855 15491 Z= 0.379 Chirality : 0.047 0.174 1682 Planarity : 0.004 0.030 1991 Dihedral : 6.023 23.528 1506 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.98 % Favored : 90.94 % Rotamer: Outliers : 2.17 % Allowed : 13.48 % Favored : 84.35 % 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: -1.79 (0.22), residues: 1336 helix: -0.87 (0.40), residues: 160 sheet: -1.48 (0.31), residues: 265 loop : -1.18 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 439 HIS 0.010 0.001 HIS A 802 PHE 0.019 0.002 PHE A 803 TYR 0.018 0.002 TYR A 428 ARG 0.004 0.001 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 243) hydrogen bonds : angle 7.48286 ( 648) SS BOND : bond 0.00389 ( 24) SS BOND : angle 0.97058 ( 48) covalent geometry : bond 0.00614 (11417) covalent geometry : angle 0.72865 (15443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9399 (pp) cc_final: 0.9095 (mp) REVERT: A 431 ASP cc_start: 0.8401 (t0) cc_final: 0.8072 (t0) REVERT: A 601 ASP cc_start: 0.8851 (p0) cc_final: 0.8296 (t0) REVERT: B 543 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 892 HIS cc_start: 0.9351 (OUTLIER) cc_final: 0.8959 (t-170) REVERT: C 17 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8473 (tt) outliers start: 27 outliers final: 11 residues processed: 84 average time/residue: 0.1771 time to fit residues: 24.5555 Evaluate side-chains 65 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain C residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 112 optimal weight: 0.0070 chunk 57 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.086402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.060379 restraints weight = 44979.781| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.34 r_work: 0.3075 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11441 Z= 0.114 Angle : 0.604 10.351 15491 Z= 0.314 Chirality : 0.043 0.143 1682 Planarity : 0.003 0.032 1991 Dihedral : 5.509 23.048 1502 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 2.33 % Allowed : 14.45 % Favored : 83.23 % 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: -1.62 (0.23), residues: 1336 helix: -0.60 (0.40), residues: 160 sheet: -1.30 (0.32), residues: 253 loop : -1.12 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.014 0.001 PHE A 258 TYR 0.013 0.001 TYR B 876 ARG 0.003 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 243) hydrogen bonds : angle 6.83867 ( 648) SS BOND : bond 0.00179 ( 24) SS BOND : angle 0.77770 ( 48) covalent geometry : bond 0.00246 (11417) covalent geometry : angle 0.60309 (15443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9382 (pp) cc_final: 0.9115 (mp) REVERT: D 18 GLN cc_start: 0.9514 (tp40) cc_final: 0.9273 (mt0) REVERT: A 277 ASP cc_start: 0.8677 (t0) cc_final: 0.8234 (t0) REVERT: A 431 ASP cc_start: 0.8378 (t0) cc_final: 0.8066 (t0) REVERT: A 534 TYR cc_start: 0.8398 (p90) cc_final: 0.8182 (p90) REVERT: A 601 ASP cc_start: 0.8801 (p0) cc_final: 0.8303 (t0) REVERT: B 382 GLU cc_start: 0.8579 (tp30) cc_final: 0.8054 (mm-30) REVERT: B 892 HIS cc_start: 0.9361 (OUTLIER) cc_final: 0.9121 (t-170) outliers start: 29 outliers final: 12 residues processed: 88 average time/residue: 0.2069 time to fit residues: 28.3891 Evaluate side-chains 72 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 892 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 133 optimal weight: 0.0040 chunk 119 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN B 458 ASN ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.086711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.060580 restraints weight = 45059.539| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 4.32 r_work: 0.3114 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11441 Z= 0.108 Angle : 0.578 9.352 15491 Z= 0.301 Chirality : 0.043 0.153 1682 Planarity : 0.003 0.037 1991 Dihedral : 5.243 21.119 1502 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 2.01 % Allowed : 14.61 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.22), residues: 1336 helix: -0.68 (0.39), residues: 172 sheet: -1.21 (0.32), residues: 260 loop : -1.14 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.016 0.001 PHE B 409 TYR 0.008 0.001 TYR A 606 ARG 0.004 0.000 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 243) hydrogen bonds : angle 6.52578 ( 648) SS BOND : bond 0.00139 ( 24) SS BOND : angle 0.69703 ( 48) covalent geometry : bond 0.00239 (11417) covalent geometry : angle 0.57748 (15443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9376 (pp) cc_final: 0.9099 (mp) REVERT: D 18 GLN cc_start: 0.9478 (tp-100) cc_final: 0.9265 (mt0) REVERT: A 277 ASP cc_start: 0.8631 (t0) cc_final: 0.8208 (t0) REVERT: A 431 ASP cc_start: 0.8302 (t0) cc_final: 0.8002 (t0) REVERT: A 601 ASP cc_start: 0.8717 (p0) cc_final: 0.8243 (t0) REVERT: A 629 ILE cc_start: 0.9169 (mm) cc_final: 0.8850 (pt) REVERT: A 856 HIS cc_start: 0.9323 (OUTLIER) cc_final: 0.9113 (t-90) REVERT: B 382 GLU cc_start: 0.8501 (tp30) cc_final: 0.8023 (mm-30) outliers start: 25 outliers final: 12 residues processed: 85 average time/residue: 0.1936 time to fit residues: 25.9875 Evaluate side-chains 70 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 639 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 128 optimal weight: 10.0000 chunk 17 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 802 HIS B 847 HIS B 892 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.084852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.058574 restraints weight = 45215.218| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.30 r_work: 0.3058 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11441 Z= 0.226 Angle : 0.634 11.952 15491 Z= 0.328 Chirality : 0.044 0.160 1682 Planarity : 0.004 0.038 1991 Dihedral : 5.361 20.614 1502 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.54 % Rotamer: Outliers : 2.49 % Allowed : 14.61 % Favored : 82.91 % 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: -1.75 (0.22), residues: 1336 helix: -0.69 (0.39), residues: 173 sheet: -1.42 (0.31), residues: 267 loop : -1.20 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 859 HIS 0.009 0.001 HIS A 654 PHE 0.017 0.002 PHE A 408 TYR 0.015 0.002 TYR A 428 ARG 0.008 0.000 ARG B 603 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 243) hydrogen bonds : angle 6.58210 ( 648) SS BOND : bond 0.00343 ( 24) SS BOND : angle 0.76610 ( 48) covalent geometry : bond 0.00515 (11417) covalent geometry : angle 0.63307 (15443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9389 (pp) cc_final: 0.9085 (mp) REVERT: D 18 GLN cc_start: 0.9466 (tp-100) cc_final: 0.9240 (mm-40) REVERT: A 277 ASP cc_start: 0.8693 (t0) cc_final: 0.8247 (t0) REVERT: A 431 ASP cc_start: 0.8355 (t0) cc_final: 0.8073 (t0) REVERT: A 534 TYR cc_start: 0.8441 (p90) cc_final: 0.8237 (p90) REVERT: A 601 ASP cc_start: 0.8753 (p0) cc_final: 0.8227 (t0) outliers start: 31 outliers final: 18 residues processed: 85 average time/residue: 0.1962 time to fit residues: 26.6241 Evaluate side-chains 72 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 857 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 56 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 ASN B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.086013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.059983 restraints weight = 45224.412| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.30 r_work: 0.3103 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11441 Z= 0.106 Angle : 0.573 10.711 15491 Z= 0.297 Chirality : 0.043 0.165 1682 Planarity : 0.003 0.036 1991 Dihedral : 5.137 20.370 1502 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.81 % Rotamer: Outliers : 2.01 % Allowed : 15.25 % Favored : 82.74 % 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: -1.72 (0.22), residues: 1336 helix: -0.78 (0.38), residues: 180 sheet: -1.37 (0.31), residues: 267 loop : -1.16 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 924 HIS 0.018 0.001 HIS A 856 PHE 0.015 0.001 PHE B 509 TYR 0.009 0.001 TYR A 87 ARG 0.006 0.000 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 243) hydrogen bonds : angle 6.33073 ( 648) SS BOND : bond 0.00155 ( 24) SS BOND : angle 0.65900 ( 48) covalent geometry : bond 0.00233 (11417) covalent geometry : angle 0.57294 (15443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9357 (pp) cc_final: 0.9043 (mp) REVERT: D 18 GLN cc_start: 0.9460 (tp-100) cc_final: 0.9250 (mm-40) REVERT: A 431 ASP cc_start: 0.8308 (t0) cc_final: 0.8042 (t0) REVERT: A 601 ASP cc_start: 0.8696 (p0) cc_final: 0.8205 (t0) REVERT: A 629 ILE cc_start: 0.9088 (mm) cc_final: 0.8848 (pt) outliers start: 25 outliers final: 18 residues processed: 87 average time/residue: 0.1764 time to fit residues: 24.8484 Evaluate side-chains 73 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 845 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 107 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 ASN B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.085849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059828 restraints weight = 45579.668| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.35 r_work: 0.3100 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11441 Z= 0.120 Angle : 0.566 10.163 15491 Z= 0.293 Chirality : 0.042 0.158 1682 Planarity : 0.003 0.038 1991 Dihedral : 5.049 19.834 1502 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.34 % Favored : 92.59 % Rotamer: Outliers : 2.49 % Allowed : 15.17 % Favored : 82.34 % 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: -1.65 (0.23), residues: 1336 helix: -0.55 (0.40), residues: 173 sheet: -1.31 (0.32), residues: 262 loop : -1.16 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 924 HIS 0.009 0.001 HIS A 654 PHE 0.014 0.001 PHE B 509 TYR 0.009 0.001 TYR A 534 ARG 0.005 0.000 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 243) hydrogen bonds : angle 6.26829 ( 648) SS BOND : bond 0.00179 ( 24) SS BOND : angle 0.85537 ( 48) covalent geometry : bond 0.00270 (11417) covalent geometry : angle 0.56500 (15443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9034 (mp) REVERT: D 18 GLN cc_start: 0.9453 (tp-100) cc_final: 0.9251 (mm-40) REVERT: A 321 MET cc_start: 0.8494 (pmm) cc_final: 0.8142 (pmm) REVERT: A 431 ASP cc_start: 0.8299 (t0) cc_final: 0.8020 (t0) REVERT: A 601 ASP cc_start: 0.8685 (p0) cc_final: 0.8205 (t0) REVERT: A 629 ILE cc_start: 0.9096 (mm) cc_final: 0.8861 (pt) REVERT: A 833 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6057 (pmm) REVERT: B 800 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7419 (pp) outliers start: 31 outliers final: 22 residues processed: 90 average time/residue: 0.2097 time to fit residues: 29.3949 Evaluate side-chains 85 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain B residue 845 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 131 optimal weight: 0.0030 chunk 105 optimal weight: 0.9990 chunk 122 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 112 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 0.4550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.086434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.060493 restraints weight = 45343.522| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.36 r_work: 0.3118 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11441 Z= 0.098 Angle : 0.563 10.000 15491 Z= 0.291 Chirality : 0.042 0.155 1682 Planarity : 0.003 0.036 1991 Dihedral : 4.947 19.654 1502 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 2.17 % Allowed : 15.81 % Favored : 82.02 % 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: -1.60 (0.23), residues: 1336 helix: -0.49 (0.40), residues: 173 sheet: -1.19 (0.31), residues: 268 loop : -1.16 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.013 0.001 PHE B 409 TYR 0.008 0.001 TYR A 87 ARG 0.005 0.000 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 243) hydrogen bonds : angle 6.15297 ( 648) SS BOND : bond 0.00145 ( 24) SS BOND : angle 0.74278 ( 48) covalent geometry : bond 0.00214 (11417) covalent geometry : angle 0.56218 (15443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9037 (mp) REVERT: D 18 GLN cc_start: 0.9447 (tp-100) cc_final: 0.9245 (mm-40) REVERT: A 321 MET cc_start: 0.8453 (pmm) cc_final: 0.8094 (pmm) REVERT: A 431 ASP cc_start: 0.8268 (t0) cc_final: 0.8005 (t0) REVERT: A 601 ASP cc_start: 0.8661 (p0) cc_final: 0.8200 (t0) REVERT: A 629 ILE cc_start: 0.9102 (mm) cc_final: 0.8803 (pt) REVERT: A 833 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6129 (pmm) REVERT: B 382 GLU cc_start: 0.8485 (tp30) cc_final: 0.7870 (mm-30) REVERT: B 800 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7433 (pp) outliers start: 27 outliers final: 20 residues processed: 87 average time/residue: 0.2019 time to fit residues: 26.7205 Evaluate side-chains 82 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 8 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 89 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 120 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.086082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.060136 restraints weight = 45165.862| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.31 r_work: 0.3108 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11441 Z= 0.119 Angle : 0.565 9.448 15491 Z= 0.292 Chirality : 0.042 0.158 1682 Planarity : 0.003 0.037 1991 Dihedral : 4.913 20.207 1502 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 2.33 % Allowed : 15.89 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1336 helix: -0.43 (0.40), residues: 173 sheet: -1.13 (0.32), residues: 276 loop : -1.12 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.011 0.001 PHE B 409 TYR 0.014 0.001 TYR B 534 ARG 0.004 0.000 ARG B 821 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 243) hydrogen bonds : angle 6.09507 ( 648) SS BOND : bond 0.00174 ( 24) SS BOND : angle 0.68084 ( 48) covalent geometry : bond 0.00269 (11417) covalent geometry : angle 0.56450 (15443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9037 (mp) REVERT: A 431 ASP cc_start: 0.8313 (t0) cc_final: 0.8031 (t0) REVERT: A 601 ASP cc_start: 0.8638 (p0) cc_final: 0.8167 (t0) REVERT: A 833 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6223 (pmm) REVERT: B 382 GLU cc_start: 0.8520 (tp30) cc_final: 0.7875 (mm-30) REVERT: B 800 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7497 (pp) outliers start: 29 outliers final: 22 residues processed: 85 average time/residue: 0.2117 time to fit residues: 28.2370 Evaluate side-chains 83 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 119 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 125 optimal weight: 0.0970 chunk 104 optimal weight: 0.3980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.086360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.060407 restraints weight = 45480.188| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 4.32 r_work: 0.3118 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11441 Z= 0.103 Angle : 0.566 9.541 15491 Z= 0.293 Chirality : 0.043 0.225 1682 Planarity : 0.004 0.064 1991 Dihedral : 4.902 20.009 1502 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 2.17 % Allowed : 15.89 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1336 helix: -0.45 (0.40), residues: 173 sheet: -1.09 (0.31), residues: 277 loop : -1.10 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 859 HIS 0.010 0.001 HIS A 654 PHE 0.017 0.001 PHE B 509 TYR 0.011 0.001 TYR B 534 ARG 0.017 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 243) hydrogen bonds : angle 6.04885 ( 648) SS BOND : bond 0.00142 ( 24) SS BOND : angle 0.64417 ( 48) covalent geometry : bond 0.00228 (11417) covalent geometry : angle 0.56587 (15443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9043 (mp) REVERT: A 321 MET cc_start: 0.8384 (pmm) cc_final: 0.8064 (pmm) REVERT: A 431 ASP cc_start: 0.8305 (t0) cc_final: 0.8026 (t0) REVERT: A 601 ASP cc_start: 0.8658 (p0) cc_final: 0.8179 (t0) REVERT: A 833 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.6178 (pmm) REVERT: B 382 GLU cc_start: 0.8501 (tp30) cc_final: 0.7870 (mm-30) REVERT: B 800 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7499 (pp) outliers start: 27 outliers final: 22 residues processed: 83 average time/residue: 0.1796 time to fit residues: 24.2045 Evaluate side-chains 85 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 831 ARG Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 ASN B 866 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.086431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.060487 restraints weight = 45143.122| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.36 r_work: 0.3120 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11441 Z= 0.104 Angle : 0.561 9.253 15491 Z= 0.288 Chirality : 0.043 0.203 1682 Planarity : 0.003 0.037 1991 Dihedral : 4.792 19.160 1502 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 2.01 % Allowed : 16.05 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.23), residues: 1336 helix: -0.33 (0.40), residues: 171 sheet: -1.10 (0.32), residues: 264 loop : -1.11 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 924 HIS 0.010 0.001 HIS A 654 PHE 0.016 0.001 PHE B 509 TYR 0.010 0.001 TYR B 534 ARG 0.009 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 243) hydrogen bonds : angle 5.95110 ( 648) SS BOND : bond 0.00155 ( 24) SS BOND : angle 0.59980 ( 48) covalent geometry : bond 0.00232 (11417) covalent geometry : angle 0.56098 (15443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7573.23 seconds wall clock time: 131 minutes 45.38 seconds (7905.38 seconds total)