Starting phenix.real_space_refine on Sun Sep 13 05:38:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9roa_54114/09_2026/9roa_54114_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9roa_54114/09_2026/9roa_54114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9roa_54114/09_2026/9roa_54114_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9roa_54114/09_2026/9roa_54114_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9roa_54114/09_2026/9roa_54114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9roa_54114/09_2026/9roa_54114.map" } resolution = 3.08 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= 0.021 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: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 60 5.16 5 Na 3 4.78 5 C 6539 2.51 5 N 1680 2.21 5 O 1922 1.98 5 H 10016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 20224 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 15038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 15038 Classifications: {'peptide': 969} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 927} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4436 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 253} Chain breaks: 1 Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 115 Unusual residues: {' MG': 1, ' NA': 3, 'ADP': 1, 'CLR': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.23, per 1000 atoms: 0.16 Number of scatterers: 20224 At special positions: 0 Unit cell: (95.6494, 80.743, 182.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 60 16.00 P 3 15.00 Mg 1 11.99 Na 3 11.00 O 1922 8.00 N 1680 7.00 C 6539 6.00 H 10016 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 401 " - " ASN B 193 " " NAG D 1 " - " ASN B 226 " " NAG E 1 " - " ASN B 158 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 455.8 milliseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 12 sheets defined 51.8% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.891A pdb=" N TYR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 90 through 112 removed outlier: 4.662A pdb=" N GLY A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 154 removed outlier: 3.509A pdb=" N LYS A 152 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 272 through 304 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.168A pdb=" N GLU A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.568A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 456 through 464 Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.511A pdb=" N ARG A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.611A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 657 through 663 removed outlier: 4.012A pdb=" N ASP A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 674 Processing helix chain 'A' and resid 684 through 698 Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 745 through 772 removed outlier: 4.120A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 813 removed outlier: 3.661A pdb=" N ILE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.965A pdb=" N ARG A 824 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'A' and resid 846 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 897 through 928 removed outlier: 4.138A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.673A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.003A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.396A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 removed outlier: 6.598A pdb=" N ASN B 158 " --> pdb=" O TRP B 155 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.125A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 183 removed outlier: 6.310A pdb=" N ASP A 179 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 248 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 188 removed outlier: 5.142A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.139A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 365 removed outlier: 5.954A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 606 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER A 365 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS A 653 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ALA A 681 " --> pdb=" O CYS A 653 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 655 " --> pdb=" O ALA A 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.925A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 543 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER A 580 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG A 541 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 480 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU A 469 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 482 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.925A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N CYS A 508 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE A 575 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 510 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLY A 577 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N LEU A 512 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N MET A 579 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.661A pdb=" N VAL A 422 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AB1, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 124 536 hydrogen bonds defined for protein. 1515 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: 5.38 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9990 1.03 - 1.23: 36 1.23 - 1.42: 4206 1.42 - 1.62: 6115 1.62 - 1.81: 88 Bond restraints: 20435 Sorted by residual: bond pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 1.816 1.558 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" CG PHD A 366 " pdb=" OD1 PHD A 366 " ideal model delta sigma weight residual 1.300 1.248 0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" CG PHD A 366 " pdb=" OD2 PHD A 366 " ideal model delta sigma weight residual 1.218 1.249 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.34e+00 ... (remaining 20430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.40: 36955 8.40 - 16.79: 0 16.79 - 25.19: 1 25.19 - 33.58: 1 33.58 - 41.98: 1 Bond angle restraints: 36958 Sorted by residual: angle pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " pdb=" OP3 PHD A 366 " ideal model delta sigma weight residual 102.98 144.96 -41.98 3.00e+00 1.11e-01 1.96e+02 angle pdb=" CG PHD A 366 " pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 125.58 98.98 26.60 3.00e+00 1.11e-01 7.86e+01 angle pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " pdb=" OP2 PHD A 366 " ideal model delta sigma weight residual 103.47 78.34 25.13 3.00e+00 1.11e-01 7.02e+01 angle pdb=" OP2 PHD A 366 " pdb=" P PHD A 366 " pdb=" OP3 PHD A 366 " ideal model delta sigma weight residual 116.75 109.12 7.63 3.00e+00 1.11e-01 6.47e+00 angle pdb=" C5 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 111.70 104.24 7.46 3.00e+00 1.11e-01 6.18e+00 ... (remaining 36953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.92: 9089 22.92 - 45.83: 538 45.83 - 68.75: 168 68.75 - 91.66: 42 91.66 - 114.58: 12 Dihedral angle restraints: 9849 sinusoidal: 5568 harmonic: 4281 Sorted by residual: dihedral pdb=" C2 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sinusoidal sigma weight residual 175.11 60.53 114.58 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" O3 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sinusoidal sigma weight residual -64.55 -178.71 114.16 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA ARG B 217 " pdb=" C ARG B 217 " pdb=" N ASP B 218 " pdb=" CA ASP B 218 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1623 0.151 - 0.303: 3 0.303 - 0.454: 0 0.454 - 0.606: 0 0.606 - 0.757: 1 Chirality restraints: 1627 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 226 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1624 not shown) Planarity restraints: 3002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 390 " -0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C ALA A 390 " 0.082 2.00e-02 2.50e+03 pdb=" O ALA A 390 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP A 391 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 56 " -0.024 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C LEU C 56 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU C 56 " -0.031 2.00e-02 2.50e+03 pdb=" N SER C 57 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 470 " 0.041 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO A 471 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 471 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 471 " 0.034 5.00e-02 4.00e+02 ... (remaining 2999 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 262 2.04 - 2.68: 31539 2.68 - 3.32: 61183 3.32 - 3.96: 77693 3.96 - 4.60: 120946 Nonbonded interactions: 291623 Sorted by model distance: nonbonded pdb=" OE1 GLN A 920 " pdb="NA NA A1107 " model vdw 1.404 2.350 nonbonded pdb=" HG1 THR A 368 " pdb=" O3B ADP A1101 " model vdw 1.500 2.450 nonbonded pdb=" O ILE A 430 " pdb="HH21 ARG A 435 " model vdw 1.544 2.450 nonbonded pdb=" OE1 GLU A 324 " pdb=" H GLU A 324 " model vdw 1.562 2.450 nonbonded pdb=" H ILE A 726 " pdb=" OD1 ASP A 743 " model vdw 1.596 2.450 ... (remaining 291618 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.00 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: 0.650 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: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.490 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.005 0.258 10429 Z= 0.234 Angle : 0.753 41.977 14170 Z= 0.319 Chirality : 0.045 0.757 1627 Planarity : 0.004 0.061 1790 Dihedral : 17.317 114.579 4130 Min Nonbonded Distance : 1.404 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.46 % Allowed : 13.88 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.76 (0.24), residues: 1262 helix: 1.32 (0.22), residues: 589 sheet: -0.28 (0.43), residues: 141 loop : -0.08 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 830 TYR 0.015 0.001 TYR A 859 PHE 0.014 0.001 PHE A 472 TRP 0.005 0.001 TRP A 79 HIS 0.004 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (10419) covalent geometry : angle 0.73877 / 0.32 (14143) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 0.28016 / 0.14 ( 6) hydrogen bonds : bond 0.13457 / 9.53 ( 524) hydrogen bonds : angle 6.35141 / 4.59 ( 1515) link_BETA1-4 : bond 0.01062 / 0.54 ( 4) link_BETA1-4 : angle 3.38758 / 1.46 ( 12) link_NAG-ASN : bond 0.00724 / 0.36 ( 3) link_NAG-ASN : angle 4.46381 / 2.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 0.2304 time to fit residues: 31.0387 Evaluate side-chains 93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069625 restraints weight = 64319.318| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.03 r_work: 0.2916 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10429 Z= 0.152 Angle : 0.574 9.698 14170 Z= 0.281 Chirality : 0.042 0.328 1627 Planarity : 0.004 0.080 1790 Dihedral : 11.382 102.849 1731 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.37 % Allowed : 13.70 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.19 (0.25), residues: 1262 helix: 1.90 (0.22), residues: 580 sheet: -0.50 (0.41), residues: 153 loop : 0.04 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.016 0.001 TYR A 859 PHE 0.009 0.001 PHE A 783 TRP 0.004 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (10419) covalent geometry : angle 0.55597 / 0.28 (14143) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 0.29391 / 0.15 ( 6) hydrogen bonds : bond 0.04340 / 2.98 ( 524) hydrogen bonds : angle 4.82564 / 3.49 ( 1515) link_BETA1-4 : bond 0.00653 / 0.33 ( 4) link_BETA1-4 : angle 3.38067 / 1.50 ( 12) link_NAG-ASN : bond 0.00746 / 0.37 ( 3) link_NAG-ASN : angle 4.20735 / 2.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7998 (pmm) cc_final: 0.7748 (pmm) REVERT: B 184 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8752 (tt) REVERT: B 285 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8221 (m-80) outliers start: 15 outliers final: 9 residues processed: 106 average time/residue: 0.2238 time to fit residues: 34.3450 Evaluate side-chains 101 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 0.0050 chunk 37 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 113 optimal weight: 0.0060 overall best weight: 1.6016 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.098125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.069900 restraints weight = 64553.324| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.05 r_work: 0.2921 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10429 Z= 0.151 Angle : 0.551 9.168 14170 Z= 0.265 Chirality : 0.042 0.357 1627 Planarity : 0.004 0.064 1790 Dihedral : 9.428 94.778 1729 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.64 % Allowed : 13.15 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.32 (0.25), residues: 1262 helix: 2.05 (0.22), residues: 580 sheet: -0.46 (0.42), residues: 146 loop : 0.04 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 830 TYR 0.017 0.001 TYR A 859 PHE 0.009 0.001 PHE A 297 TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10419) covalent geometry : angle 0.53348 / 0.26 (14143) SS BOND : bond 0.00138 / 0.07 ( 3) SS BOND : angle 0.24825 / 0.12 ( 6) hydrogen bonds : bond 0.03720 / 2.54 ( 524) hydrogen bonds : angle 4.53018 / 3.28 ( 1515) link_BETA1-4 : bond 0.00502 / 0.25 ( 4) link_BETA1-4 : angle 3.27993 / 1.45 ( 12) link_NAG-ASN : bond 0.00707 / 0.36 ( 3) link_NAG-ASN : angle 4.02242 / 2.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7982 (pmm) cc_final: 0.7730 (pmm) REVERT: B 184 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8760 (tp) REVERT: B 285 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8231 (m-80) outliers start: 18 outliers final: 11 residues processed: 104 average time/residue: 0.2224 time to fit residues: 33.1734 Evaluate side-chains 100 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.097311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.069187 restraints weight = 64868.817| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.02 r_work: 0.2902 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10429 Z= 0.205 Angle : 0.564 8.813 14170 Z= 0.276 Chirality : 0.042 0.319 1627 Planarity : 0.004 0.064 1790 Dihedral : 8.795 87.744 1729 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.19 % Allowed : 13.52 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.28 (0.25), residues: 1262 helix: 2.06 (0.22), residues: 576 sheet: -0.69 (0.41), residues: 152 loop : 0.06 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.019 0.001 TYR A 859 PHE 0.010 0.001 PHE A 297 TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (10419) covalent geometry : angle 0.54903 / 0.27 (14143) SS BOND : bond 0.00226 / 0.12 ( 3) SS BOND : angle 0.25664 / 0.13 ( 6) hydrogen bonds : bond 0.03685 / 2.49 ( 524) hydrogen bonds : angle 4.48199 / 3.25 ( 1515) link_BETA1-4 : bond 0.00442 / 0.22 ( 4) link_BETA1-4 : angle 3.05215 / 1.37 ( 12) link_NAG-ASN : bond 0.00678 / 0.34 ( 3) link_NAG-ASN : angle 3.86009 / 2.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8022 (pmm) cc_final: 0.7760 (pmm) REVERT: A 776 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 154 GLU cc_start: 0.8994 (mp0) cc_final: 0.8789 (mp0) REVERT: B 184 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8785 (tt) REVERT: B 285 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8245 (m-80) outliers start: 24 outliers final: 15 residues processed: 110 average time/residue: 0.2286 time to fit residues: 36.4009 Evaluate side-chains 106 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 889 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.098252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.070081 restraints weight = 64177.275| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.03 r_work: 0.2920 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10429 Z= 0.125 Angle : 0.535 8.668 14170 Z= 0.258 Chirality : 0.041 0.320 1627 Planarity : 0.004 0.061 1790 Dihedral : 8.400 84.057 1729 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.83 % Allowed : 13.33 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.40 (0.25), residues: 1262 helix: 2.18 (0.22), residues: 576 sheet: -0.70 (0.41), residues: 152 loop : 0.13 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 830 TYR 0.015 0.001 TYR A 859 PHE 0.010 0.001 PHE B 108 TRP 0.006 0.001 TRP A 79 HIS 0.004 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10419) covalent geometry : angle 0.51970 / 0.25 (14143) SS BOND : bond 0.00129 / 0.07 ( 3) SS BOND : angle 0.27866 / 0.14 ( 6) hydrogen bonds : bond 0.03493 / 2.37 ( 524) hydrogen bonds : angle 4.33602 / 3.15 ( 1515) link_BETA1-4 : bond 0.00522 / 0.26 ( 4) link_BETA1-4 : angle 3.01654 / 1.36 ( 12) link_NAG-ASN : bond 0.00619 / 0.31 ( 3) link_NAG-ASN : angle 3.85557 / 2.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8015 (pmm) cc_final: 0.7760 (pmm) REVERT: A 889 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8809 (tt0) REVERT: B 184 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8738 (tt) REVERT: B 285 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8239 (m-80) outliers start: 20 outliers final: 13 residues processed: 110 average time/residue: 0.2251 time to fit residues: 35.8465 Evaluate side-chains 105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 889 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.097552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.069274 restraints weight = 64239.891| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.02 r_work: 0.2908 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10429 Z= 0.179 Angle : 0.550 8.442 14170 Z= 0.268 Chirality : 0.042 0.329 1627 Planarity : 0.004 0.065 1790 Dihedral : 8.163 79.825 1729 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.92 % Allowed : 13.15 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.37 (0.25), residues: 1262 helix: 2.16 (0.22), residues: 576 sheet: -0.71 (0.41), residues: 152 loop : 0.11 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 830 TYR 0.018 0.001 TYR A 859 PHE 0.010 0.001 PHE A 297 TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (10419) covalent geometry : angle 0.53531 / 0.27 (14143) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 0.25154 / 0.13 ( 6) hydrogen bonds : bond 0.03510 / 2.37 ( 524) hydrogen bonds : angle 4.34943 / 3.16 ( 1515) link_BETA1-4 : bond 0.00461 / 0.23 ( 4) link_BETA1-4 : angle 2.81700 / 1.28 ( 12) link_NAG-ASN : bond 0.00630 / 0.32 ( 3) link_NAG-ASN : angle 3.84472 / 2.03 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8006 (pmm) cc_final: 0.7724 (pmm) REVERT: A 842 MET cc_start: 0.8882 (tpt) cc_final: 0.8656 (tpp) REVERT: B 184 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8765 (tt) REVERT: B 268 MET cc_start: 0.9211 (mmm) cc_final: 0.8418 (mmm) REVERT: B 285 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8241 (m-80) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.2192 time to fit residues: 33.8980 Evaluate side-chains 105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 3 optimal weight: 0.0030 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.099100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.070881 restraints weight = 63815.265| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.05 r_work: 0.2940 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10429 Z= 0.094 Angle : 0.522 8.349 14170 Z= 0.249 Chirality : 0.041 0.315 1627 Planarity : 0.004 0.060 1790 Dihedral : 7.766 75.567 1729 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.37 % Allowed : 13.79 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.25), residues: 1262 helix: 2.31 (0.22), residues: 576 sheet: -0.72 (0.43), residues: 142 loop : 0.22 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 830 TYR 0.013 0.001 TYR A 859 PHE 0.011 0.001 PHE B 108 TRP 0.006 0.001 TRP A 79 HIS 0.004 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (10419) covalent geometry : angle 0.50649 / 0.25 (14143) SS BOND : bond 0.00087 / 0.04 ( 3) SS BOND : angle 0.31497 / 0.16 ( 6) hydrogen bonds : bond 0.03282 / 2.23 ( 524) hydrogen bonds : angle 4.16261 / 3.02 ( 1515) link_BETA1-4 : bond 0.00550 / 0.28 ( 4) link_BETA1-4 : angle 2.89351 / 1.32 ( 12) link_NAG-ASN : bond 0.00539 / 0.27 ( 3) link_NAG-ASN : angle 3.76943 / 2.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7996 (pmm) cc_final: 0.7702 (pmm) REVERT: A 472 PHE cc_start: 0.8636 (t80) cc_final: 0.8347 (t80) REVERT: A 799 CYS cc_start: 0.9291 (m) cc_final: 0.9038 (m) REVERT: A 842 MET cc_start: 0.8879 (tpt) cc_final: 0.8651 (tpp) REVERT: B 184 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8717 (tt) REVERT: B 268 MET cc_start: 0.9196 (mmm) cc_final: 0.8417 (mmm) REVERT: B 285 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8137 (m-80) outliers start: 15 outliers final: 12 residues processed: 109 average time/residue: 0.2314 time to fit residues: 36.4102 Evaluate side-chains 109 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.098636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.070458 restraints weight = 64248.426| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.03 r_work: 0.2930 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10429 Z= 0.129 Angle : 0.528 8.313 14170 Z= 0.253 Chirality : 0.041 0.326 1627 Planarity : 0.004 0.057 1790 Dihedral : 7.593 72.295 1729 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.64 % Allowed : 14.06 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.54 (0.25), residues: 1262 helix: 2.33 (0.22), residues: 576 sheet: -0.72 (0.43), residues: 142 loop : 0.15 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.016 0.001 TYR A 859 PHE 0.010 0.001 PHE B 108 TRP 0.006 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10419) covalent geometry : angle 0.51372 / 0.25 (14143) SS BOND : bond 0.00137 / 0.07 ( 3) SS BOND : angle 0.24646 / 0.13 ( 6) hydrogen bonds : bond 0.03260 / 2.20 ( 524) hydrogen bonds : angle 4.16088 / 3.02 ( 1515) link_BETA1-4 : bond 0.00543 / 0.27 ( 4) link_BETA1-4 : angle 2.77993 / 1.28 ( 12) link_NAG-ASN : bond 0.00575 / 0.29 ( 3) link_NAG-ASN : angle 3.71607 / 1.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7996 (pmm) cc_final: 0.7696 (pmm) REVERT: A 472 PHE cc_start: 0.8647 (t80) cc_final: 0.8345 (t80) REVERT: A 799 CYS cc_start: 0.9283 (m) cc_final: 0.9030 (m) REVERT: A 842 MET cc_start: 0.8893 (tpt) cc_final: 0.8681 (tpp) REVERT: B 184 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8735 (tt) REVERT: B 268 MET cc_start: 0.9204 (mmm) cc_final: 0.8427 (mmm) REVERT: B 285 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8233 (m-80) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.2406 time to fit residues: 38.3944 Evaluate side-chains 106 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 92 optimal weight: 0.0770 chunk 123 optimal weight: 0.0170 chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.098775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.070624 restraints weight = 63617.720| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.01 r_work: 0.2934 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10429 Z= 0.121 Angle : 0.526 8.101 14170 Z= 0.251 Chirality : 0.041 0.322 1627 Planarity : 0.004 0.057 1790 Dihedral : 7.326 71.953 1729 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.64 % Allowed : 14.25 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1.54 (0.25), residues: 1262 helix: 2.33 (0.22), residues: 576 sheet: -0.71 (0.43), residues: 142 loop : 0.14 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.015 0.001 TYR A 859 PHE 0.010 0.001 PHE B 108 TRP 0.006 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10419) covalent geometry : angle 0.51155 / 0.25 (14143) SS BOND : bond 0.00117 / 0.06 ( 3) SS BOND : angle 0.25389 / 0.13 ( 6) hydrogen bonds : bond 0.03229 / 2.19 ( 524) hydrogen bonds : angle 4.13170 / 2.99 ( 1515) link_BETA1-4 : bond 0.00563 / 0.28 ( 4) link_BETA1-4 : angle 2.75988 / 1.28 ( 12) link_NAG-ASN : bond 0.00556 / 0.28 ( 3) link_NAG-ASN : angle 3.67039 / 1.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8004 (pmm) cc_final: 0.7699 (pmm) REVERT: A 799 CYS cc_start: 0.9242 (m) cc_final: 0.8993 (m) REVERT: A 842 MET cc_start: 0.8901 (tpt) cc_final: 0.8675 (tpp) REVERT: B 184 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 285 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8235 (m-80) outliers start: 18 outliers final: 14 residues processed: 108 average time/residue: 0.2163 time to fit residues: 34.2883 Evaluate side-chains 107 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.098637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070361 restraints weight = 64435.493| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.04 r_work: 0.2929 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10429 Z= 0.138 Angle : 0.530 7.991 14170 Z= 0.254 Chirality : 0.041 0.324 1627 Planarity : 0.004 0.055 1790 Dihedral : 7.130 71.744 1729 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.55 % Allowed : 14.43 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.25), residues: 1262 helix: 2.34 (0.22), residues: 576 sheet: -0.71 (0.43), residues: 142 loop : 0.12 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.022 0.001 TYR A 859 PHE 0.009 0.001 PHE B 108 TRP 0.006 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10419) covalent geometry : angle 0.51664 / 0.25 (14143) SS BOND : bond 0.00141 / 0.07 ( 3) SS BOND : angle 0.24815 / 0.13 ( 6) hydrogen bonds : bond 0.03236 / 2.18 ( 524) hydrogen bonds : angle 4.13936 / 3.00 ( 1515) link_BETA1-4 : bond 0.00588 / 0.30 ( 4) link_BETA1-4 : angle 2.72945 / 1.28 ( 12) link_NAG-ASN : bond 0.00558 / 0.28 ( 3) link_NAG-ASN : angle 3.66716 / 1.97 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8022 (pmm) cc_final: 0.7720 (pmm) REVERT: A 799 CYS cc_start: 0.9262 (m) cc_final: 0.9003 (m) REVERT: A 842 MET cc_start: 0.8908 (tpt) cc_final: 0.8682 (tpp) REVERT: B 184 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8740 (tt) REVERT: B 285 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8240 (m-80) outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 0.2293 time to fit residues: 35.5576 Evaluate side-chains 108 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.099050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.070778 restraints weight = 63990.813| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.07 r_work: 0.2937 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10429 Z= 0.113 Angle : 0.521 7.807 14170 Z= 0.248 Chirality : 0.041 0.317 1627 Planarity : 0.004 0.071 1790 Dihedral : 6.928 71.298 1729 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.46 % Allowed : 14.52 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.25), residues: 1262 helix: 2.38 (0.22), residues: 576 sheet: -0.69 (0.43), residues: 142 loop : 0.15 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 830 TYR 0.020 0.001 TYR A 859 PHE 0.010 0.001 PHE B 108 TRP 0.007 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10419) covalent geometry : angle 0.50755 / 0.25 (14143) SS BOND : bond 0.00109 / 0.06 ( 3) SS BOND : angle 0.25194 / 0.13 ( 6) hydrogen bonds : bond 0.03173 / 2.15 ( 524) hydrogen bonds : angle 4.07778 / 2.95 ( 1515) link_BETA1-4 : bond 0.00649 / 0.33 ( 4) link_BETA1-4 : angle 2.75420 / 1.29 ( 12) link_NAG-ASN : bond 0.00528 / 0.26 ( 3) link_NAG-ASN : angle 3.63165 / 1.95 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5003.99 seconds wall clock time: 85 minutes 54.56 seconds (5154.56 seconds total)