Starting phenix.real_space_refine on Fri Sep 11 18:48:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k7i_9934/09_2026/6k7i_9934.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7i_9934/09_2026/6k7i_9934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k7i_9934/09_2026/6k7i_9934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7i_9934/09_2026/6k7i_9934.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6k7i_9934/09_2026/6k7i_9934.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k7i_9934/09_2026/6k7i_9934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k7i_9934/09_2026/6k7i_9934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7i_9934/09_2026/6k7i_9934.map" } resolution = 3.22 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= 0.004 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 56 5.16 5 C 6857 2.51 5 N 1753 2.21 5 O 1921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10590 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7853 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 30, 'TRANS': 955} Chain breaks: 3 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.41, per 1000 atoms: 0.23 Number of scatterers: 10590 At special positions: 0 Unit cell: (72.21, 112.88, 168.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 3 15.00 O 1921 8.00 N 1753 7.00 C 6857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 361.4 milliseconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 47.8% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.628A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.525A pdb=" N ALA A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 401 removed outlier: 4.213A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.361A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.850A pdb=" N ARG A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 600 through 617 removed outlier: 4.617A pdb=" N SER A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.575A pdb=" N LEU A 622 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 681 removed outlier: 4.490A pdb=" N ASN A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 762 through 777 removed outlier: 3.585A pdb=" N GLN A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 833 removed outlier: 4.349A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 856 removed outlier: 4.092A pdb=" N ASN A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.699A pdb=" N TRP A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.185A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.650A pdb=" N THR A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.419A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 4.066A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 4.942A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix removed outlier: 3.520A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 89 through 95 removed outlier: 4.002A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 95 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.639A pdb=" N GLU A 144 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN A 136 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 169 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.554A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 780 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 425 removed outlier: 6.101A pdb=" N VAL A 418 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A 647 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU A 638 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 596 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY A 640 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 544 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN A 530 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.621A pdb=" N PHE A 507 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 517 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 509 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.715A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.473A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.503A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1329 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: 1.92 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1784 1.32 - 1.44: 2914 1.44 - 1.57: 6050 1.57 - 1.69: 6 1.69 - 1.82: 87 Bond restraints: 10841 Sorted by residual: bond pdb=" O2B ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.507 1.614 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" O3A ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.698 1.603 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4 ACP A1201 " pdb=" C5 ACP A1201 " ideal model delta sigma weight residual 1.386 1.469 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3G ACP A1201 " pdb=" PG ACP A1201 " ideal model delta sigma weight residual 1.532 1.607 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 ACP A1201 " pdb=" C6 ACP A1201 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 10836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 14080 2.90 - 5.81: 552 5.81 - 8.71: 69 8.71 - 11.61: 17 11.61 - 14.52: 4 Bond angle restraints: 14722 Sorted by residual: angle pdb=" C LEU A 687 " pdb=" N LYS A 688 " pdb=" CA LYS A 688 " ideal model delta sigma weight residual 121.54 134.13 -12.59 1.91e+00 2.74e-01 4.34e+01 angle pdb=" C SER A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 120.97 135.49 -14.52 2.84e+00 1.24e-01 2.61e+01 angle pdb=" C PRO A 384 " pdb=" N THR A 385 " pdb=" CA THR A 385 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C LYS A 688 " pdb=" N LYS A 689 " pdb=" CA LYS A 689 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C ALA A 57 " pdb=" N LYS A 58 " pdb=" CA LYS A 58 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 ... (remaining 14717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5632 17.91 - 35.82: 638 35.82 - 53.73: 102 53.73 - 71.64: 12 71.64 - 89.55: 5 Dihedral angle restraints: 6389 sinusoidal: 2566 harmonic: 3823 Sorted by residual: dihedral pdb=" CA ARG A 510 " pdb=" C ARG A 510 " pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta harmonic sigma weight residual 180.00 144.75 35.25 0 5.00e+00 4.00e-02 4.97e+01 dihedral pdb=" CA HIS A 682 " pdb=" C HIS A 682 " pdb=" N SER A 683 " pdb=" CA SER A 683 " ideal model delta harmonic sigma weight residual 180.00 147.44 32.56 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA PHE A 534 " pdb=" C PHE A 534 " pdb=" N THR A 535 " pdb=" CA THR A 535 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 6386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1415 0.100 - 0.199: 244 0.199 - 0.298: 19 0.298 - 0.398: 3 0.398 - 0.497: 2 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CB THR A 511 " pdb=" CA THR A 511 " pdb=" OG1 THR A 511 " pdb=" CG2 THR A 511 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 1680 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.356 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.254 2.00e-02 2.50e+03 2.11e-01 5.58e+02 pdb=" C7 NAG C 402 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.351 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.167 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" C7 NAG C 401 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.225 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.019 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2461 2.78 - 3.31: 9477 3.31 - 3.84: 17662 3.84 - 4.37: 21051 4.37 - 4.90: 36325 Nonbonded interactions: 86976 Sorted by model distance: nonbonded pdb=" O ASP A 409 " pdb=" OG1 THR A 413 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR A 670 " pdb=" N GLY A 671 " model vdw 2.309 3.120 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.310 3.040 nonbonded pdb=" O TYR A 573 " pdb=" OG1 THR A 577 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 394 " pdb=" ND2 ASN A 397 " model vdw 2.316 3.120 ... (remaining 86971 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: 1.260 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.000 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.015 0.128 10849 Z= 0.613 Angle : 1.329 16.326 14743 Z= 0.695 Chirality : 0.076 0.497 1683 Planarity : 0.013 0.306 1832 Dihedral : 14.932 89.553 3914 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.92 % Favored : 90.69 % Rotamer: Outliers : 0.78 % Allowed : 8.43 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.41 (0.18), residues: 1300 helix: -2.90 (0.15), residues: 587 sheet: -1.92 (0.38), residues: 149 loop : -3.13 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 479 TYR 0.035 0.004 TYR A 59 PHE 0.039 0.004 PHE C 304 TRP 0.025 0.004 TRP A 860 HIS 0.009 0.002 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.01504 / 0.61 (10841) covalent geometry : angle 1.31461 / 0.69 (14722) SS BOND : bond 0.01126 / 0.55 ( 3) SS BOND : angle 4.18192 / 2.01 ( 6) hydrogen bonds : bond 0.14020 / 8.37 ( 461) hydrogen bonds : angle 7.12380 / 4.99 ( 1329) link_ALPHA1-4 : bond 0.02046 / 1.08 ( 1) link_ALPHA1-4 : angle 5.35538 / 2.80 ( 3) link_BETA1-4 : bond 0.00421 / 0.22 ( 1) link_BETA1-4 : angle 2.95532 / 1.56 ( 3) link_NAG-ASN : bond 0.01642 / 0.80 ( 3) link_NAG-ASN : angle 6.35267 / 2.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6687 (mmtt) cc_final: 0.4681 (mttm) REVERT: A 392 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7326 (mtt-85) REVERT: A 663 ASP cc_start: 0.7688 (t70) cc_final: 0.7299 (t0) REVERT: A 693 MET cc_start: 0.1202 (mmt) cc_final: -0.0638 (tpp) REVERT: A 727 LEU cc_start: 0.6848 (mp) cc_final: 0.6625 (mt) REVERT: A 732 LYS cc_start: 0.7982 (mttm) cc_final: 0.7328 (tptp) REVERT: A 1013 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8018 (pp) REVERT: C 151 LEU cc_start: 0.8640 (mt) cc_final: 0.8423 (mt) REVERT: C 184 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8052 (mt-10) REVERT: C 337 PHE cc_start: 0.8131 (t80) cc_final: 0.7924 (t80) outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.1170 time to fit residues: 23.1037 Evaluate side-chains 114 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 124 HIS A 134 GLN A 279 ASN A 320 ASN A 381 HIS A 434 ASN A 679 ASN A 813 ASN C 36 GLN C 131 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.213624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.161207 restraints weight = 10458.928| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.61 r_work: 0.3084 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10849 Z= 0.156 Angle : 0.726 10.069 14743 Z= 0.371 Chirality : 0.049 0.495 1683 Planarity : 0.005 0.052 1832 Dihedral : 7.364 57.082 1443 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.31 % Rotamer: Outliers : 2.35 % Allowed : 11.04 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -2.97 (0.20), residues: 1300 helix: -1.33 (0.19), residues: 577 sheet: -1.44 (0.40), residues: 144 loop : -2.75 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 479 TYR 0.015 0.001 TYR A 59 PHE 0.024 0.001 PHE A 368 TRP 0.018 0.001 TRP A 927 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (10841) covalent geometry : angle 0.71436 / 0.37 (14722) SS BOND : bond 0.00911 / 0.48 ( 3) SS BOND : angle 2.21087 / 1.13 ( 6) hydrogen bonds : bond 0.05093 / 3.16 ( 461) hydrogen bonds : angle 5.55606 / 3.88 ( 1329) link_ALPHA1-4 : bond 0.01267 / 0.67 ( 1) link_ALPHA1-4 : angle 2.55465 / 1.33 ( 3) link_BETA1-4 : bond 0.00330 / 0.17 ( 1) link_BETA1-4 : angle 0.76895 / 0.40 ( 3) link_NAG-ASN : bond 0.00865 / 0.43 ( 3) link_NAG-ASN : angle 4.68474 / 2.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7154 (tp) REVERT: A 207 LYS cc_start: 0.6329 (mmtt) cc_final: 0.4163 (mttt) REVERT: A 390 MET cc_start: 0.7978 (ttt) cc_final: 0.7654 (ttm) REVERT: A 663 ASP cc_start: 0.8461 (t0) cc_final: 0.8063 (t0) REVERT: A 693 MET cc_start: 0.1480 (mmt) cc_final: -0.0497 (tpp) REVERT: A 732 LYS cc_start: 0.7955 (mttm) cc_final: 0.7461 (tptp) REVERT: A 747 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6735 (mm) REVERT: A 874 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: A 1013 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8073 (pp) REVERT: C 102 CYS cc_start: 0.7111 (p) cc_final: 0.6786 (p) REVERT: C 184 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8667 (mt-10) outliers start: 27 outliers final: 6 residues processed: 143 average time/residue: 0.1213 time to fit residues: 24.1017 Evaluate side-chains 114 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 65 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 0.0010 chunk 34 optimal weight: 10.0000 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 813 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.214635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.185186 restraints weight = 10365.689| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.41 r_work: 0.3719 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10849 Z= 0.127 Angle : 0.658 9.657 14743 Z= 0.334 Chirality : 0.046 0.453 1683 Planarity : 0.004 0.055 1832 Dihedral : 6.802 59.341 1437 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.00 % Allowed : 13.65 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -2.25 (0.22), residues: 1300 helix: -0.53 (0.20), residues: 575 sheet: -1.31 (0.40), residues: 148 loop : -2.54 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 540 TYR 0.012 0.001 TYR A 382 PHE 0.019 0.001 PHE A 368 TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (10841) covalent geometry : angle 0.64908 / 0.33 (14722) SS BOND : bond 0.00170 / 0.08 ( 3) SS BOND : angle 1.51050 / 0.76 ( 6) hydrogen bonds : bond 0.04385 / 2.74 ( 461) hydrogen bonds : angle 5.13782 / 3.58 ( 1329) link_ALPHA1-4 : bond 0.00853 / 0.45 ( 1) link_ALPHA1-4 : angle 2.47773 / 1.28 ( 3) link_BETA1-4 : bond 0.00365 / 0.19 ( 1) link_BETA1-4 : angle 0.86172 / 0.47 ( 3) link_NAG-ASN : bond 0.00923 / 0.46 ( 3) link_NAG-ASN : angle 3.99109 / 1.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6796 (tp) REVERT: A 207 LYS cc_start: 0.5693 (mmtt) cc_final: 0.3952 (mttt) REVERT: A 663 ASP cc_start: 0.8359 (t0) cc_final: 0.8042 (t0) REVERT: A 693 MET cc_start: 0.1508 (mmt) cc_final: -0.0585 (tpp) REVERT: A 874 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: A 1013 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8043 (pp) REVERT: C 102 CYS cc_start: 0.7090 (p) cc_final: 0.6812 (p) outliers start: 23 outliers final: 7 residues processed: 127 average time/residue: 0.1123 time to fit residues: 20.3957 Evaluate side-chains 103 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.0270 chunk 86 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 ASN C 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.215072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.183076 restraints weight = 10630.826| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.56 r_work: 0.3618 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10849 Z= 0.113 Angle : 0.615 8.957 14743 Z= 0.312 Chirality : 0.046 0.458 1683 Planarity : 0.004 0.045 1832 Dihedral : 6.372 54.635 1436 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.09 % Allowed : 16.09 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.70 (0.22), residues: 1300 helix: -0.01 (0.21), residues: 578 sheet: -1.18 (0.39), residues: 160 loop : -2.32 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 392 TYR 0.011 0.001 TYR A 59 PHE 0.016 0.001 PHE A 368 TRP 0.014 0.001 TRP A 927 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10841) covalent geometry : angle 0.60750 / 0.31 (14722) SS BOND : bond 0.00153 / 0.08 ( 3) SS BOND : angle 1.15448 / 0.58 ( 6) hydrogen bonds : bond 0.03962 / 2.48 ( 461) hydrogen bonds : angle 4.82925 / 3.37 ( 1329) link_ALPHA1-4 : bond 0.00708 / 0.37 ( 1) link_ALPHA1-4 : angle 2.20922 / 1.14 ( 3) link_BETA1-4 : bond 0.00346 / 0.18 ( 1) link_BETA1-4 : angle 0.73893 / 0.39 ( 3) link_NAG-ASN : bond 0.00941 / 0.47 ( 3) link_NAG-ASN : angle 3.57613 / 1.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.431 Fit side-chains REVERT: A 60 ASN cc_start: 0.7462 (t0) cc_final: 0.7254 (t0) REVERT: A 159 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7022 (tp) REVERT: A 207 LYS cc_start: 0.5524 (mmtt) cc_final: 0.3835 (mttt) REVERT: A 644 ILE cc_start: 0.3432 (OUTLIER) cc_final: 0.3151 (pt) REVERT: A 663 ASP cc_start: 0.8346 (t0) cc_final: 0.8062 (t0) REVERT: A 693 MET cc_start: 0.1249 (mmt) cc_final: -0.0738 (tpp) REVERT: A 728 ILE cc_start: 0.8538 (mt) cc_final: 0.8310 (mt) REVERT: A 830 MET cc_start: 0.8248 (mmm) cc_final: 0.8009 (mtt) REVERT: A 874 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: C 102 CYS cc_start: 0.6992 (p) cc_final: 0.6727 (p) outliers start: 24 outliers final: 8 residues processed: 130 average time/residue: 0.1050 time to fit residues: 19.8361 Evaluate side-chains 109 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.207775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.175836 restraints weight = 10522.701| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.66 r_work: 0.3580 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10849 Z= 0.207 Angle : 0.683 10.055 14743 Z= 0.347 Chirality : 0.049 0.450 1683 Planarity : 0.004 0.046 1832 Dihedral : 6.467 54.629 1434 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.17 % Allowed : 16.96 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.23), residues: 1300 helix: -0.07 (0.21), residues: 574 sheet: -1.22 (0.38), residues: 163 loop : -2.09 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 540 TYR 0.017 0.002 TYR C 122 PHE 0.017 0.002 PHE A 368 TRP 0.013 0.002 TRP A 927 HIS 0.005 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (10841) covalent geometry : angle 0.67331 / 0.35 (14722) SS BOND : bond 0.00366 / 0.18 ( 3) SS BOND : angle 1.92952 / 0.93 ( 6) hydrogen bonds : bond 0.04780 / 2.98 ( 461) hydrogen bonds : angle 5.03063 / 3.50 ( 1329) link_ALPHA1-4 : bond 0.00942 / 0.50 ( 1) link_ALPHA1-4 : angle 2.94396 / 1.52 ( 3) link_BETA1-4 : bond 0.00245 / 0.13 ( 1) link_BETA1-4 : angle 1.37847 / 0.72 ( 3) link_NAG-ASN : bond 0.00991 / 0.49 ( 3) link_NAG-ASN : angle 4.12427 / 1.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.379 Fit side-chains REVERT: A 60 ASN cc_start: 0.7688 (t0) cc_final: 0.7462 (t0) REVERT: A 159 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6852 (tp) REVERT: A 207 LYS cc_start: 0.5609 (mmtt) cc_final: 0.3882 (mttt) REVERT: A 644 ILE cc_start: 0.3554 (OUTLIER) cc_final: 0.3247 (pt) REVERT: A 663 ASP cc_start: 0.8320 (t0) cc_final: 0.8038 (t0) REVERT: A 693 MET cc_start: 0.1053 (mmt) cc_final: -0.0857 (tpp) REVERT: A 830 MET cc_start: 0.8394 (mmm) cc_final: 0.8155 (mtt) REVERT: A 874 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: A 1013 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7999 (pp) REVERT: C 102 CYS cc_start: 0.7176 (p) cc_final: 0.6911 (p) outliers start: 25 outliers final: 12 residues processed: 120 average time/residue: 0.0975 time to fit residues: 17.2322 Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 3.9990 chunk 119 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.214499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.179684 restraints weight = 10563.561| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.60 r_work: 0.3505 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10849 Z= 0.131 Angle : 0.621 9.066 14743 Z= 0.313 Chirality : 0.046 0.456 1683 Planarity : 0.004 0.044 1832 Dihedral : 6.217 54.777 1434 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.83 % Allowed : 17.74 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.38 (0.23), residues: 1300 helix: 0.20 (0.21), residues: 574 sheet: -0.97 (0.41), residues: 153 loop : -2.06 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 540 TYR 0.011 0.001 TYR A 59 PHE 0.015 0.001 PHE A 368 TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10841) covalent geometry : angle 0.61289 / 0.31 (14722) SS BOND : bond 0.00209 / 0.10 ( 3) SS BOND : angle 1.25528 / 0.62 ( 6) hydrogen bonds : bond 0.04084 / 2.54 ( 461) hydrogen bonds : angle 4.80089 / 3.34 ( 1329) link_ALPHA1-4 : bond 0.00807 / 0.42 ( 1) link_ALPHA1-4 : angle 2.32255 / 1.20 ( 3) link_BETA1-4 : bond 0.00341 / 0.18 ( 1) link_BETA1-4 : angle 0.97631 / 0.51 ( 3) link_NAG-ASN : bond 0.00930 / 0.46 ( 3) link_NAG-ASN : angle 3.65909 / 1.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.352 Fit side-chains REVERT: A 159 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7159 (tp) REVERT: A 207 LYS cc_start: 0.5610 (mmtt) cc_final: 0.3855 (mttt) REVERT: A 663 ASP cc_start: 0.8476 (t0) cc_final: 0.8179 (t0) REVERT: A 693 MET cc_start: 0.1586 (mmt) cc_final: -0.0620 (tpp) REVERT: A 874 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: C 102 CYS cc_start: 0.7199 (p) cc_final: 0.6940 (p) outliers start: 21 outliers final: 13 residues processed: 117 average time/residue: 0.1041 time to fit residues: 17.7365 Evaluate side-chains 113 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 0.3980 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 30.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.215918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.187679 restraints weight = 10524.194| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.34 r_work: 0.3758 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10849 Z= 0.117 Angle : 0.614 10.048 14743 Z= 0.307 Chirality : 0.046 0.454 1683 Planarity : 0.004 0.045 1832 Dihedral : 6.033 54.312 1434 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.57 % Allowed : 18.52 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.12 (0.23), residues: 1300 helix: 0.44 (0.22), residues: 576 sheet: -0.81 (0.41), residues: 153 loop : -1.98 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 262 TYR 0.012 0.001 TYR C 82 PHE 0.014 0.001 PHE A 368 TRP 0.014 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10841) covalent geometry : angle 0.60663 / 0.31 (14722) SS BOND : bond 0.00172 / 0.09 ( 3) SS BOND : angle 1.06709 / 0.53 ( 6) hydrogen bonds : bond 0.03826 / 2.39 ( 461) hydrogen bonds : angle 4.64822 / 3.23 ( 1329) link_ALPHA1-4 : bond 0.00850 / 0.45 ( 1) link_ALPHA1-4 : angle 2.21959 / 1.15 ( 3) link_BETA1-4 : bond 0.00363 / 0.19 ( 1) link_BETA1-4 : angle 0.79539 / 0.42 ( 3) link_NAG-ASN : bond 0.00923 / 0.46 ( 3) link_NAG-ASN : angle 3.53919 / 1.63 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.408 Fit side-chains REVERT: A 159 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.6939 (tp) REVERT: A 207 LYS cc_start: 0.5411 (mmtt) cc_final: 0.3857 (mttt) REVERT: A 663 ASP cc_start: 0.8317 (t0) cc_final: 0.8064 (t0) REVERT: A 693 MET cc_start: 0.1570 (mmt) cc_final: -0.0586 (tpp) REVERT: A 874 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: C 102 CYS cc_start: 0.7225 (p) cc_final: 0.6956 (p) outliers start: 18 outliers final: 11 residues processed: 112 average time/residue: 0.1001 time to fit residues: 16.5071 Evaluate side-chains 106 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.219133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.188951 restraints weight = 10512.149| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.41 r_work: 0.3674 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10849 Z= 0.118 Angle : 0.604 8.922 14743 Z= 0.303 Chirality : 0.046 0.455 1683 Planarity : 0.004 0.046 1832 Dihedral : 5.928 54.987 1434 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.39 % Allowed : 18.78 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.01 (0.23), residues: 1300 helix: 0.56 (0.22), residues: 576 sheet: -0.92 (0.40), residues: 164 loop : -1.91 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 262 TYR 0.012 0.001 TYR A 59 PHE 0.013 0.001 PHE A 368 TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10841) covalent geometry : angle 0.59678 / 0.30 (14722) SS BOND : bond 0.00189 / 0.09 ( 3) SS BOND : angle 1.13333 / 0.56 ( 6) hydrogen bonds : bond 0.03788 / 2.36 ( 461) hydrogen bonds : angle 4.55964 / 3.18 ( 1329) link_ALPHA1-4 : bond 0.00708 / 0.37 ( 1) link_ALPHA1-4 : angle 2.18250 / 1.13 ( 3) link_BETA1-4 : bond 0.00305 / 0.16 ( 1) link_BETA1-4 : angle 0.80828 / 0.43 ( 3) link_NAG-ASN : bond 0.00924 / 0.46 ( 3) link_NAG-ASN : angle 3.53128 / 1.63 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6965 (tp) REVERT: A 207 LYS cc_start: 0.5379 (mmtt) cc_final: 0.3839 (mttt) REVERT: A 326 LYS cc_start: 0.8718 (mttt) cc_final: 0.8356 (mtmt) REVERT: A 663 ASP cc_start: 0.8232 (t0) cc_final: 0.8013 (t0) REVERT: A 693 MET cc_start: 0.1613 (mmt) cc_final: -0.0544 (tpp) REVERT: A 728 ILE cc_start: 0.8402 (mt) cc_final: 0.8200 (mt) REVERT: A 874 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7938 (tp30) REVERT: C 102 CYS cc_start: 0.7098 (p) cc_final: 0.6819 (p) REVERT: C 152 ASN cc_start: 0.7743 (t0) cc_final: 0.7478 (t0) outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.1076 time to fit residues: 16.7904 Evaluate side-chains 107 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 127 optimal weight: 0.8980 chunk 117 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.214120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.186342 restraints weight = 10487.339| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.37 r_work: 0.3653 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10849 Z= 0.140 Angle : 0.621 9.158 14743 Z= 0.312 Chirality : 0.046 0.451 1683 Planarity : 0.004 0.047 1832 Dihedral : 5.979 56.471 1434 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.48 % Allowed : 19.13 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.04 (0.23), residues: 1300 helix: 0.50 (0.22), residues: 577 sheet: -0.90 (0.39), residues: 163 loop : -1.90 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 262 TYR 0.012 0.001 TYR C 297 PHE 0.014 0.001 PHE A 368 TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10841) covalent geometry : angle 0.61289 / 0.31 (14722) SS BOND : bond 0.00253 / 0.12 ( 3) SS BOND : angle 1.41869 / 0.69 ( 6) hydrogen bonds : bond 0.04028 / 2.50 ( 461) hydrogen bonds : angle 4.63101 / 3.22 ( 1329) link_ALPHA1-4 : bond 0.00833 / 0.44 ( 1) link_ALPHA1-4 : angle 2.41957 / 1.25 ( 3) link_BETA1-4 : bond 0.00237 / 0.12 ( 1) link_BETA1-4 : angle 0.99556 / 0.52 ( 3) link_NAG-ASN : bond 0.00934 / 0.47 ( 3) link_NAG-ASN : angle 3.64765 / 1.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6937 (tp) REVERT: A 207 LYS cc_start: 0.5347 (mmtt) cc_final: 0.3805 (mttt) REVERT: A 663 ASP cc_start: 0.8232 (t0) cc_final: 0.7990 (t0) REVERT: A 693 MET cc_start: 0.1541 (mmt) cc_final: -0.0617 (tpp) REVERT: A 728 ILE cc_start: 0.8456 (mt) cc_final: 0.8250 (mt) REVERT: A 874 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: C 102 CYS cc_start: 0.7094 (p) cc_final: 0.6815 (p) outliers start: 17 outliers final: 11 residues processed: 105 average time/residue: 0.1065 time to fit residues: 16.3813 Evaluate side-chains 105 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.0070 chunk 57 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 0.0470 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.0030 chunk 20 optimal weight: 20.0000 overall best weight: 0.3908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 HIS C 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.218007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.182405 restraints weight = 10422.754| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.38 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10849 Z= 0.104 Angle : 0.583 8.658 14743 Z= 0.292 Chirality : 0.045 0.457 1683 Planarity : 0.004 0.047 1832 Dihedral : 5.745 57.780 1434 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.39 % Allowed : 19.22 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -0.89 (0.23), residues: 1300 helix: 0.72 (0.22), residues: 578 sheet: -0.82 (0.40), residues: 163 loop : -1.94 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 262 TYR 0.010 0.001 TYR C 121 PHE 0.013 0.001 PHE A 368 TRP 0.014 0.001 TRP A 860 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (10841) covalent geometry : angle 0.57634 / 0.29 (14722) SS BOND : bond 0.00111 / 0.06 ( 3) SS BOND : angle 0.84515 / 0.43 ( 6) hydrogen bonds : bond 0.03440 / 2.15 ( 461) hydrogen bonds : angle 4.43158 / 3.09 ( 1329) link_ALPHA1-4 : bond 0.00834 / 0.44 ( 1) link_ALPHA1-4 : angle 1.90312 / 0.99 ( 3) link_BETA1-4 : bond 0.00261 / 0.14 ( 1) link_BETA1-4 : angle 0.65225 / 0.35 ( 3) link_NAG-ASN : bond 0.00915 / 0.46 ( 3) link_NAG-ASN : angle 3.27288 / 1.51 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6676 (tp) REVERT: A 207 LYS cc_start: 0.4950 (mmtt) cc_final: 0.3753 (mttt) REVERT: A 326 LYS cc_start: 0.8514 (mttt) cc_final: 0.8229 (mtmt) REVERT: A 693 MET cc_start: 0.1299 (mmt) cc_final: -0.0673 (tpp) REVERT: A 778 LYS cc_start: 0.7656 (mmtm) cc_final: 0.7448 (mttp) REVERT: A 874 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7905 (tp30) REVERT: C 102 CYS cc_start: 0.6334 (p) cc_final: 0.6053 (p) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.1020 time to fit residues: 16.7907 Evaluate side-chains 105 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.213915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.184751 restraints weight = 10592.678| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.36 r_work: 0.3715 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10849 Z= 0.157 Angle : 0.631 9.244 14743 Z= 0.317 Chirality : 0.047 0.450 1683 Planarity : 0.004 0.046 1832 Dihedral : 5.873 59.150 1433 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.13 % Allowed : 19.74 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -0.89 (0.23), residues: 1300 helix: 0.60 (0.22), residues: 578 sheet: -0.78 (0.40), residues: 162 loop : -1.81 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 262 TYR 0.013 0.001 TYR C 297 PHE 0.014 0.001 PHE C 214 TRP 0.013 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10841) covalent geometry : angle 0.62266 / 0.31 (14722) SS BOND : bond 0.00268 / 0.13 ( 3) SS BOND : angle 1.52949 / 0.74 ( 6) hydrogen bonds : bond 0.04113 / 2.55 ( 461) hydrogen bonds : angle 4.59793 / 3.20 ( 1329) link_ALPHA1-4 : bond 0.00732 / 0.39 ( 1) link_ALPHA1-4 : angle 2.45392 / 1.27 ( 3) link_BETA1-4 : bond 0.00203 / 0.11 ( 1) link_BETA1-4 : angle 1.10581 / 0.58 ( 3) link_NAG-ASN : bond 0.00943 / 0.47 ( 3) link_NAG-ASN : angle 3.66927 / 1.70 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.87 seconds wall clock time: 38 minutes 52.36 seconds (2332.36 seconds total)