Starting phenix.real_space_refine on Tue Jul 29 04:49:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7i_9934/07_2025/6k7i_9934.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7i_9934/07_2025/6k7i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7i_9934/07_2025/6k7i_9934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7i_9934/07_2025/6k7i_9934.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7i_9934/07_2025/6k7i_9934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7i_9934/07_2025/6k7i_9934.cif" } resolution = 3.22 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= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.16, per 1000 atoms: 0.68 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.49 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: 3.90 Time building geometry restraints manager: 3.50 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 - 22.47: 6025 22.47 - 44.94: 486 44.94 - 67.40: 49 67.40 - 89.87: 15 89.87 - 112.34: 3 Dihedral angle restraints: 6578 sinusoidal: 2755 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 6575 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: 1.100 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.880 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 15.636 112.339 4103 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.97 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 (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: -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 TRP 0.025 0.004 TRP A 860 HIS 0.009 0.002 HIS A 124 PHE 0.039 0.004 PHE C 304 TYR 0.035 0.004 TYR A 59 ARG 0.016 0.001 ARG A 479 Details of bonding type rmsd link_NAG-ASN : bond 0.01642 ( 3) link_NAG-ASN : angle 6.35267 ( 9) link_ALPHA1-4 : bond 0.02046 ( 1) link_ALPHA1-4 : angle 5.35538 ( 3) link_BETA1-4 : bond 0.00421 ( 1) link_BETA1-4 : angle 2.95532 ( 3) hydrogen bonds : bond 0.14020 ( 461) hydrogen bonds : angle 7.12380 ( 1329) SS BOND : bond 0.01126 ( 3) SS BOND : angle 4.18192 ( 6) covalent geometry : bond 0.01504 (10841) covalent geometry : angle 1.31461 (14722) *********************** 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 : 1.182 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: 0.2585 time to fit residues: 50.4297 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 : 1.146 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4314 r_free = 0.4314 target = 0.213400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.187232 restraints weight = 10267.370| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.15 r_work: 0.3795 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1409 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= 0.144 Angle : 0.718 9.586 14743 Z= 0.365 Chirality : 0.048 0.463 1683 Planarity : 0.005 0.049 1832 Dihedral : 10.862 107.617 1632 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 2.26 % Allowed : 10.96 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.20), residues: 1300 helix: -1.28 (0.19), residues: 572 sheet: -1.42 (0.40), residues: 144 loop : -2.73 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.003 0.001 HIS A 682 PHE 0.023 0.001 PHE A 368 TYR 0.014 0.001 TYR A 59 ARG 0.004 0.000 ARG A 479 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 3) link_NAG-ASN : angle 4.52592 ( 9) link_ALPHA1-4 : bond 0.01569 ( 1) link_ALPHA1-4 : angle 3.97531 ( 3) link_BETA1-4 : bond 0.00100 ( 1) link_BETA1-4 : angle 0.58190 ( 3) hydrogen bonds : bond 0.04906 ( 461) hydrogen bonds : angle 5.48402 ( 1329) SS BOND : bond 0.00242 ( 3) SS BOND : angle 1.94544 ( 6) covalent geometry : bond 0.00317 (10841) covalent geometry : angle 0.70681 (14722) *********************** 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: 26 poor density : 124 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6671 (tp) REVERT: A 207 LYS cc_start: 0.5615 (mmtt) cc_final: 0.3870 (mttt) REVERT: A 390 MET cc_start: 0.7523 (ttt) cc_final: 0.7249 (ttm) REVERT: A 663 ASP cc_start: 0.8322 (t0) cc_final: 0.7956 (t0) REVERT: A 693 MET cc_start: 0.1879 (mmt) cc_final: -0.0279 (tpp) REVERT: A 831 ILE cc_start: 0.8416 (pt) cc_final: 0.8095 (mt) REVERT: A 874 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: A 1013 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8065 (pp) REVERT: C 102 CYS cc_start: 0.7050 (p) cc_final: 0.6750 (p) REVERT: C 337 PHE cc_start: 0.8160 (t80) cc_final: 0.7957 (t80) outliers start: 26 outliers final: 6 residues processed: 144 average time/residue: 0.2555 time to fit residues: 51.1291 Evaluate side-chains 113 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 57 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 813 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 = 0.4332 r_free = 0.4332 target = 0.216196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.153681 restraints weight = 10557.239| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.10 r_work: 0.3152 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1833 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= 0.126 Angle : 0.660 9.578 14743 Z= 0.332 Chirality : 0.046 0.368 1683 Planarity : 0.004 0.055 1832 Dihedral : 10.168 97.774 1626 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.00 % Allowed : 13.48 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.22), residues: 1300 helix: -0.48 (0.20), residues: 570 sheet: -1.24 (0.40), residues: 147 loop : -2.51 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.018 0.001 PHE A 368 TYR 0.012 0.001 TYR A 382 ARG 0.004 0.000 ARG A 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 3) link_NAG-ASN : angle 3.62216 ( 9) link_ALPHA1-4 : bond 0.02094 ( 1) link_ALPHA1-4 : angle 4.29281 ( 3) link_BETA1-4 : bond 0.00711 ( 1) link_BETA1-4 : angle 1.04461 ( 3) hydrogen bonds : bond 0.04333 ( 461) hydrogen bonds : angle 5.08779 ( 1329) SS BOND : bond 0.00200 ( 3) SS BOND : angle 1.51659 ( 6) covalent geometry : bond 0.00273 (10841) covalent geometry : angle 0.65053 (14722) *********************** 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 137 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7015 (tp) REVERT: A 207 LYS cc_start: 0.6312 (mmtt) cc_final: 0.4312 (mttt) REVERT: A 260 THR cc_start: 0.3490 (OUTLIER) cc_final: 0.3136 (p) REVERT: A 392 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8118 (mtt90) REVERT: A 663 ASP cc_start: 0.8469 (t0) cc_final: 0.8114 (t0) REVERT: A 693 MET cc_start: 0.1163 (mmt) cc_final: -0.0768 (tpp) REVERT: A 747 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6694 (mm) REVERT: A 874 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8152 (tp30) REVERT: A 1013 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8003 (pp) REVERT: C 42 GLN cc_start: 0.8208 (mt0) cc_final: 0.7983 (mt0) REVERT: C 102 CYS cc_start: 0.7120 (p) cc_final: 0.6832 (p) REVERT: C 337 PHE cc_start: 0.8433 (t80) cc_final: 0.8191 (t80) outliers start: 23 outliers final: 7 residues processed: 133 average time/residue: 0.2732 time to fit residues: 50.4306 Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 260 THR Chi-restraints excluded: chain A residue 747 LEU 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 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 Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN C 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.210643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.178172 restraints weight = 10474.356| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.57 r_work: 0.3601 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10849 Z= 0.187 Angle : 0.690 10.053 14743 Z= 0.348 Chirality : 0.048 0.357 1683 Planarity : 0.004 0.047 1832 Dihedral : 9.796 94.638 1625 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.61 % Allowed : 15.65 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.92 (0.22), residues: 1300 helix: -0.31 (0.21), residues: 579 sheet: -1.31 (0.39), residues: 153 loop : -2.28 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.005 0.001 HIS A 682 PHE 0.018 0.002 PHE A 368 TYR 0.016 0.002 TYR C 297 ARG 0.004 0.000 ARG A 510 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 3) link_NAG-ASN : angle 3.49617 ( 9) link_ALPHA1-4 : bond 0.01689 ( 1) link_ALPHA1-4 : angle 4.46789 ( 3) link_BETA1-4 : bond 0.00016 ( 1) link_BETA1-4 : angle 1.55618 ( 3) hydrogen bonds : bond 0.04766 ( 461) hydrogen bonds : angle 5.10103 ( 1329) SS BOND : bond 0.00324 ( 3) SS BOND : angle 1.87054 ( 6) covalent geometry : bond 0.00448 (10841) covalent geometry : angle 0.68081 (14722) *********************** 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 134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6763 (tp) REVERT: A 207 LYS cc_start: 0.5438 (mmtt) cc_final: 0.3797 (mttt) REVERT: A 644 ILE cc_start: 0.3620 (OUTLIER) cc_final: 0.3375 (pt) REVERT: A 663 ASP cc_start: 0.8289 (t0) cc_final: 0.8025 (t0) REVERT: A 693 MET cc_start: 0.1199 (mmt) cc_final: -0.0766 (tpp) REVERT: A 874 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8070 (tp30) REVERT: A 1013 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8052 (pp) REVERT: C 102 CYS cc_start: 0.7141 (p) cc_final: 0.6876 (p) REVERT: C 337 PHE cc_start: 0.8226 (t80) cc_final: 0.7945 (t80) outliers start: 30 outliers final: 13 residues processed: 128 average time/residue: 0.2533 time to fit residues: 46.3481 Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 468 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 23 optimal weight: 0.0040 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 261 GLN A 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.216366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.186641 restraints weight = 10388.672| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.36 r_work: 0.3715 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10849 Z= 0.116 Angle : 0.624 10.743 14743 Z= 0.312 Chirality : 0.044 0.265 1683 Planarity : 0.004 0.044 1832 Dihedral : 8.908 92.484 1625 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.09 % Allowed : 17.13 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.44 (0.23), residues: 1300 helix: 0.16 (0.21), residues: 576 sheet: -0.91 (0.41), residues: 152 loop : -2.15 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 682 PHE 0.015 0.001 PHE A 368 TYR 0.010 0.001 TYR C 121 ARG 0.003 0.000 ARG A 743 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 3) link_NAG-ASN : angle 3.17623 ( 9) link_ALPHA1-4 : bond 0.01893 ( 1) link_ALPHA1-4 : angle 3.97276 ( 3) link_BETA1-4 : bond 0.00417 ( 1) link_BETA1-4 : angle 0.77521 ( 3) hydrogen bonds : bond 0.03866 ( 461) hydrogen bonds : angle 4.74850 ( 1329) SS BOND : bond 0.00139 ( 3) SS BOND : angle 1.07695 ( 6) covalent geometry : bond 0.00245 (10841) covalent geometry : angle 0.61631 (14722) *********************** 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 126 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6892 (tp) REVERT: A 207 LYS cc_start: 0.5366 (mmtt) cc_final: 0.3882 (mttt) REVERT: A 663 ASP cc_start: 0.8231 (t0) cc_final: 0.7985 (t0) REVERT: A 693 MET cc_start: 0.1418 (mmt) cc_final: -0.0668 (tpp) REVERT: A 728 ILE cc_start: 0.8393 (mt) cc_final: 0.8070 (mt) REVERT: A 874 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: C 42 GLN cc_start: 0.8104 (mt0) cc_final: 0.7881 (mt0) REVERT: C 102 CYS cc_start: 0.6987 (p) cc_final: 0.6709 (p) REVERT: C 337 PHE cc_start: 0.8132 (t80) cc_final: 0.7874 (t80) outliers start: 24 outliers final: 11 residues processed: 121 average time/residue: 0.2432 time to fit residues: 42.0523 Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 261 GLN Chi-restraints excluded: chain A residue 468 MET 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 53 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 277 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.211257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.181494 restraints weight = 10601.253| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.50 r_work: 0.3624 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10849 Z= 0.175 Angle : 0.666 9.020 14743 Z= 0.333 Chirality : 0.047 0.315 1683 Planarity : 0.004 0.043 1832 Dihedral : 8.694 88.997 1623 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.91 % Allowed : 17.91 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.40 (0.23), residues: 1300 helix: 0.15 (0.21), residues: 573 sheet: -1.02 (0.40), residues: 158 loop : -2.02 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.005 0.001 HIS A 323 PHE 0.016 0.001 PHE A 368 TYR 0.014 0.001 TYR C 297 ARG 0.004 0.000 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 3) link_NAG-ASN : angle 3.34154 ( 9) link_ALPHA1-4 : bond 0.01615 ( 1) link_ALPHA1-4 : angle 4.30091 ( 3) link_BETA1-4 : bond 0.00340 ( 1) link_BETA1-4 : angle 1.28373 ( 3) hydrogen bonds : bond 0.04467 ( 461) hydrogen bonds : angle 4.87425 ( 1329) SS BOND : bond 0.00291 ( 3) SS BOND : angle 1.62061 ( 6) covalent geometry : bond 0.00417 (10841) covalent geometry : angle 0.65765 (14722) *********************** 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 123 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 207 LYS cc_start: 0.5492 (mmtt) cc_final: 0.3845 (mttt) REVERT: A 663 ASP cc_start: 0.8222 (t0) cc_final: 0.7955 (t0) REVERT: A 693 MET cc_start: 0.1171 (mmt) cc_final: -0.0769 (tpp) REVERT: A 728 ILE cc_start: 0.8505 (mt) cc_final: 0.8202 (mt) REVERT: A 874 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8043 (tp30) REVERT: C 102 CYS cc_start: 0.7108 (p) cc_final: 0.6852 (p) REVERT: C 337 PHE cc_start: 0.8211 (t80) cc_final: 0.7930 (t80) outliers start: 22 outliers final: 12 residues processed: 118 average time/residue: 0.2329 time to fit residues: 39.6477 Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 468 MET 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 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 277 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 115 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.212151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.159412 restraints weight = 10647.848| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.69 r_work: 0.3064 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10849 Z= 0.211 Angle : 0.699 9.489 14743 Z= 0.349 Chirality : 0.048 0.309 1683 Planarity : 0.004 0.044 1832 Dihedral : 8.675 87.272 1623 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.74 % Allowed : 18.17 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.48 (0.23), residues: 1300 helix: -0.01 (0.21), residues: 583 sheet: -0.99 (0.39), residues: 156 loop : -2.01 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 927 HIS 0.005 0.001 HIS A 323 PHE 0.017 0.002 PHE A 368 TYR 0.016 0.002 TYR C 122 ARG 0.004 0.000 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 3) link_NAG-ASN : angle 3.17820 ( 9) link_ALPHA1-4 : bond 0.01778 ( 1) link_ALPHA1-4 : angle 4.53866 ( 3) link_BETA1-4 : bond 0.00323 ( 1) link_BETA1-4 : angle 1.43464 ( 3) hydrogen bonds : bond 0.04764 ( 461) hydrogen bonds : angle 4.99243 ( 1329) SS BOND : bond 0.00348 ( 3) SS BOND : angle 1.91354 ( 6) covalent geometry : bond 0.00512 (10841) covalent geometry : angle 0.69103 (14722) *********************** 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 121 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7269 (tp) REVERT: A 207 LYS cc_start: 0.6212 (mmtt) cc_final: 0.4135 (mttt) REVERT: A 663 ASP cc_start: 0.8352 (t0) cc_final: 0.7995 (t0) REVERT: A 693 MET cc_start: 0.1180 (mmt) cc_final: -0.0793 (tpp) REVERT: A 728 ILE cc_start: 0.8579 (mt) cc_final: 0.8375 (mt) REVERT: A 874 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: C 102 CYS cc_start: 0.7238 (p) cc_final: 0.6957 (p) REVERT: C 337 PHE cc_start: 0.8435 (t80) cc_final: 0.8169 (t80) outliers start: 20 outliers final: 15 residues processed: 114 average time/residue: 0.3533 time to fit residues: 59.3081 Evaluate side-chains 117 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 2.349 ------------------------------------------------------------------------------- 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 468 MET 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 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 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 Chi-restraints excluded: chain C residue 277 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.214854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.186517 restraints weight = 10400.980| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.27 r_work: 0.3738 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10849 Z= 0.127 Angle : 0.627 8.621 14743 Z= 0.314 Chirality : 0.045 0.297 1683 Planarity : 0.004 0.045 1832 Dihedral : 8.319 85.291 1623 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.48 % Allowed : 18.96 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.19 (0.23), residues: 1300 helix: 0.35 (0.22), residues: 573 sheet: -0.86 (0.41), residues: 151 loop : -1.96 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.014 0.001 PHE A 368 TYR 0.011 0.001 TYR A 59 ARG 0.005 0.000 ARG A 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 3) link_NAG-ASN : angle 2.39866 ( 9) link_ALPHA1-4 : bond 0.01709 ( 1) link_ALPHA1-4 : angle 4.18896 ( 3) link_BETA1-4 : bond 0.00424 ( 1) link_BETA1-4 : angle 0.95991 ( 3) hydrogen bonds : bond 0.04004 ( 461) hydrogen bonds : angle 4.74347 ( 1329) SS BOND : bond 0.00181 ( 3) SS BOND : angle 1.16589 ( 6) covalent geometry : bond 0.00283 (10841) covalent geometry : angle 0.62069 (14722) *********************** 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 114 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7030 (tp) REVERT: A 207 LYS cc_start: 0.5578 (mmtt) cc_final: 0.3926 (mttt) REVERT: A 663 ASP cc_start: 0.8319 (t0) cc_final: 0.8102 (t0) REVERT: A 693 MET cc_start: 0.1554 (mmt) cc_final: -0.0568 (tpp) REVERT: A 728 ILE cc_start: 0.8421 (mt) cc_final: 0.8109 (mt) REVERT: A 874 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8167 (tp30) REVERT: C 102 CYS cc_start: 0.7274 (p) cc_final: 0.6998 (p) REVERT: C 337 PHE cc_start: 0.8312 (t80) cc_final: 0.8052 (t80) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.2603 time to fit residues: 40.8974 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 : 1.187 ------------------------------------------------------------------------------- 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 290 VAL Chi-restraints excluded: chain A residue 468 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.212686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.154993 restraints weight = 10615.356| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.14 r_work: 0.3092 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10849 Z= 0.175 Angle : 0.659 8.961 14743 Z= 0.330 Chirality : 0.046 0.298 1683 Planarity : 0.004 0.046 1832 Dihedral : 8.311 82.592 1623 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.83 % Allowed : 18.87 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.29 (0.23), residues: 1300 helix: 0.19 (0.21), residues: 584 sheet: -0.99 (0.39), residues: 163 loop : -1.95 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.005 0.001 HIS A 323 PHE 0.015 0.001 PHE A 368 TYR 0.014 0.001 TYR C 297 ARG 0.008 0.000 ARG A 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 3) link_NAG-ASN : angle 2.47142 ( 9) link_ALPHA1-4 : bond 0.01801 ( 1) link_ALPHA1-4 : angle 4.51640 ( 3) link_BETA1-4 : bond 0.00425 ( 1) link_BETA1-4 : angle 1.24705 ( 3) hydrogen bonds : bond 0.04459 ( 461) hydrogen bonds : angle 4.84755 ( 1329) SS BOND : bond 0.00307 ( 3) SS BOND : angle 1.67455 ( 6) covalent geometry : bond 0.00420 (10841) covalent geometry : angle 0.65225 (14722) *********************** 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 113 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6158 (mmtt) cc_final: 0.4109 (mttt) REVERT: A 663 ASP cc_start: 0.8443 (t0) cc_final: 0.8107 (t0) REVERT: A 693 MET cc_start: 0.1325 (mmt) cc_final: -0.0757 (tpp) REVERT: A 728 ILE cc_start: 0.8596 (mt) cc_final: 0.8369 (mt) REVERT: A 874 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8273 (tp30) REVERT: C 102 CYS cc_start: 0.7360 (p) cc_final: 0.7070 (p) REVERT: C 337 PHE cc_start: 0.8483 (t80) cc_final: 0.8191 (t80) outliers start: 21 outliers final: 15 residues processed: 108 average time/residue: 0.2423 time to fit residues: 38.5158 Evaluate side-chains 107 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 468 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.213411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.152691 restraints weight = 10508.210| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.38 r_work: 0.2994 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2548 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= 0.154 Angle : 0.638 9.265 14743 Z= 0.319 Chirality : 0.046 0.297 1683 Planarity : 0.004 0.047 1832 Dihedral : 8.120 78.696 1623 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.57 % Allowed : 18.96 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.22 (0.23), residues: 1300 helix: 0.29 (0.21), residues: 582 sheet: -0.88 (0.39), residues: 162 loop : -1.99 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.015 0.001 PHE A 368 TYR 0.012 0.001 TYR C 297 ARG 0.007 0.000 ARG A 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 3) link_NAG-ASN : angle 2.05533 ( 9) link_ALPHA1-4 : bond 0.01800 ( 1) link_ALPHA1-4 : angle 4.46255 ( 3) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 1.15941 ( 3) hydrogen bonds : bond 0.04232 ( 461) hydrogen bonds : angle 4.77531 ( 1329) SS BOND : bond 0.00248 ( 3) SS BOND : angle 1.45121 ( 6) covalent geometry : bond 0.00364 (10841) covalent geometry : angle 0.63188 (14722) ********************** 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: 18 poor density : 95 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6188 (mmtt) cc_final: 0.4134 (mttt) REVERT: A 663 ASP cc_start: 0.8372 (t0) cc_final: 0.8025 (t0) REVERT: A 693 MET cc_start: 0.1440 (mmt) cc_final: -0.0664 (tpp) REVERT: A 728 ILE cc_start: 0.8451 (mt) cc_final: 0.8242 (mt) REVERT: A 732 LYS cc_start: 0.7707 (tptp) cc_final: 0.7177 (ptmt) REVERT: A 874 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: C 102 CYS cc_start: 0.7302 (p) cc_final: 0.7001 (p) REVERT: C 337 PHE cc_start: 0.8510 (t80) cc_final: 0.8223 (t80) outliers start: 18 outliers final: 13 residues processed: 109 average time/residue: 0.2518 time to fit residues: 39.2045 Evaluate side-chains 108 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 378 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 38 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 1 optimal weight: 20.0000 chunk 19 optimal weight: 0.0570 chunk 120 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.219693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.190056 restraints weight = 10512.694| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.32 r_work: 0.3723 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2856 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= 0.111 Angle : 0.598 9.216 14743 Z= 0.299 Chirality : 0.044 0.303 1683 Planarity : 0.004 0.047 1832 Dihedral : 7.643 67.635 1623 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.96 % Allowed : 19.74 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1300 helix: 0.57 (0.22), residues: 579 sheet: -0.71 (0.40), residues: 161 loop : -1.93 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.002 0.001 HIS A 323 PHE 0.014 0.001 PHE A 368 TYR 0.010 0.001 TYR C 121 ARG 0.007 0.000 ARG A 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 3) link_NAG-ASN : angle 1.60970 ( 9) link_ALPHA1-4 : bond 0.01997 ( 1) link_ALPHA1-4 : angle 4.45102 ( 3) link_BETA1-4 : bond 0.00398 ( 1) link_BETA1-4 : angle 0.73606 ( 3) hydrogen bonds : bond 0.03627 ( 461) hydrogen bonds : angle 4.55117 ( 1329) SS BOND : bond 0.00127 ( 3) SS BOND : angle 0.94669 ( 6) covalent geometry : bond 0.00241 (10841) covalent geometry : angle 0.59312 (14722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5117.29 seconds wall clock time: 90 minutes 27.66 seconds (5427.66 seconds total)