Starting phenix.real_space_refine on Sun Sep 13 07:36:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9roe_54116/09_2026/9roe_54116_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9roe_54116/09_2026/9roe_54116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9roe_54116/09_2026/9roe_54116_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9roe_54116/09_2026/9roe_54116_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9roe_54116/09_2026/9roe_54116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9roe_54116/09_2026/9roe_54116.map" } resolution = 2.94 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: 7 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 6682 2.51 5 N 1721 2.21 5 O 1962 1.98 5 H 10290 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 20718 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 15432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 15432 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 953} 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: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4620 Classifications: {'peptide': 285} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Chain: "C" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 511 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.47, per 1000 atoms: 0.17 Number of scatterers: 20718 At special positions: 0 Unit cell: (88.1962, 85.7118, 176.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 61 16.00 P 1 15.00 Mg 1 11.99 O 1962 8.00 N 1721 7.00 C 6682 6.00 H 10290 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=2.04 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 E 1 " - " NAG E 2 " NAG-ASN " NAG B1102 " - " ASN B 193 " " NAG D 1 " - " ASN B 265 " " NAG E 1 " - " ASN B 158 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 532.4 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 50.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 88 removed outlier: 3.943A pdb=" N GLN A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 87 " --> pdb=" O CYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 109 removed outlier: 4.165A pdb=" N LEU A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 118 through 151 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 254 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 272 through 304 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 324 through 343 removed outlier: 4.101A pdb=" N ALA A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.649A pdb=" N VAL A 354 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.645A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 456 through 464 removed outlier: 4.067A pdb=" N MET A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 538 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 removed outlier: 3.557A pdb=" N ALA A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 663 removed outlier: 3.508A 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 removed outlier: 3.775A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) 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: 4.021A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 3.525A 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 removed outlier: 3.520A pdb=" N ILE A 784 " --> pdb=" O PHE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'A' and resid 805 through 812 removed outlier: 3.775A pdb=" N ALA A 809 " --> pdb=" O ASP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 836 through 846 removed outlier: 3.597A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) 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 881 Processing helix chain 'A' and resid 897 through 928 removed outlier: 3.832A 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 969 Processing helix chain 'A' and resid 974 through 979 removed outlier: 3.933A pdb=" N TRP A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 979 " --> pdb=" O PRO A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 979' Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1010 Processing helix chain 'B' and resid 30 through 59 removed outlier: 4.303A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.756A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.040A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.210A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.567A pdb=" N GLY B 157 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.244A 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 166 through 171 removed outlier: 11.617A pdb=" N GLN A 158 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS A 184 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 171 removed outlier: 11.617A pdb=" N GLN A 158 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS A 184 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.944A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 389 removed outlier: 5.153A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N LEU A 573 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N TYR A 549 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 480 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU A 469 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 482 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 389 removed outlier: 5.153A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS A 508 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A 575 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR A 510 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY A 577 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N LEU A 512 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N MET A 579 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.573A pdb=" N VAL A 422 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 438 " --> pdb=" O VAL A 422 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 656 Processing sheet with id=AA8, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.660A pdb=" N ASN B 226 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 536 hydrogen bonds defined for protein. 1548 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: 5.58 Time building geometry restraints manager: 2.80 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: 10264 1.03 - 1.23: 60 1.23 - 1.43: 4281 1.43 - 1.62: 6238 1.62 - 1.82: 91 Bond restraints: 20934 Sorted by residual: bond pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 1.816 1.774 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" CB PRO B 206 " pdb=" CG PRO B 206 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.22e+00 bond pdb=" C PHD A 366 " pdb=" O PHD A 366 " ideal model delta sigma weight residual 1.231 1.266 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" CA PHD A 366 " pdb=" C PHD A 366 " ideal model delta sigma weight residual 1.525 1.556 -0.031 2.10e-02 2.27e+03 2.24e+00 ... (remaining 20929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.06: 37867 7.06 - 14.12: 5 14.12 - 21.19: 0 21.19 - 28.25: 0 28.25 - 35.31: 12 Bond angle restraints: 37884 Sorted by residual: angle pdb=" C GLU B 300 " pdb=" CA GLU B 300 " pdb=" HA GLU B 300 " ideal model delta sigma weight residual 109.00 73.69 35.31 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C SER B 303 " pdb=" CA SER B 303 " pdb=" HA SER B 303 " ideal model delta sigma weight residual 109.00 73.69 35.31 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N SER B 303 " pdb=" CA SER B 303 " pdb=" HA SER B 303 " ideal model delta sigma weight residual 110.00 74.87 35.13 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N LYS B 302 " pdb=" CA LYS B 302 " pdb=" HA LYS B 302 " ideal model delta sigma weight residual 110.00 75.15 34.85 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C LYS B 302 " pdb=" CA LYS B 302 " pdb=" HA LYS B 302 " ideal model delta sigma weight residual 109.00 74.46 34.54 3.00e+00 1.11e-01 1.33e+02 ... (remaining 37879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 9245 21.93 - 43.85: 591 43.85 - 65.78: 186 65.78 - 87.70: 29 87.70 - 109.63: 5 Dihedral angle restraints: 10056 sinusoidal: 5666 harmonic: 4390 Sorted by residual: dihedral pdb=" CA PRO B 206 " pdb=" C PRO B 206 " pdb=" N ASN B 207 " pdb=" CA ASN B 207 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 52.68 40.32 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" C LYS B 302 " pdb=" N LYS B 302 " pdb=" CA LYS B 302 " pdb=" CB LYS B 302 " ideal model delta harmonic sigma weight residual -122.60 -134.43 11.83 0 2.50e+00 1.60e-01 2.24e+01 ... (remaining 10053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1605 0.104 - 0.207: 45 0.207 - 0.311: 1 0.311 - 0.414: 1 0.414 - 0.518: 3 Chirality restraints: 1655 Sorted by residual: chirality pdb=" CA LYS B 302 " pdb=" N LYS B 302 " pdb=" C LYS B 302 " pdb=" CB LYS B 302 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CA SER B 303 " pdb=" N SER B 303 " pdb=" C SER B 303 " pdb=" CB SER B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ARG B 27 " pdb=" N ARG B 27 " pdb=" C ARG B 27 " pdb=" CB ARG B 27 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 1652 not shown) Planarity restraints: 3088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1002 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A1003 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1003 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1003 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 235 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 584 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 585 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 585 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 585 " 0.021 5.00e-02 4.00e+02 ... (remaining 3085 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 387 2.03 - 2.68: 31994 2.68 - 3.32: 62552 3.32 - 3.96: 79947 3.96 - 4.60: 123780 Nonbonded interactions: 298660 Sorted by model distance: nonbonded pdb=" O PRO A 115 " pdb=" H ASP A 118 " model vdw 1.393 2.450 nonbonded pdb=" HH TYR A 960 " pdb=" O LEU A 973 " model vdw 1.526 2.450 nonbonded pdb=" OE1 GLU A 666 " pdb=" H GLU A 666 " model vdw 1.533 2.450 nonbonded pdb="HE21 GLN A 696 " pdb=" OD1 ASP A 719 " model vdw 1.539 2.450 nonbonded pdb=" O GLY A1005 " pdb=" H GLU A1008 " model vdw 1.543 2.450 ... (remaining 298655 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 10652 Z= 0.150 Angle : 0.517 10.371 14461 Z= 0.257 Chirality : 0.045 0.518 1655 Planarity : 0.003 0.051 1839 Dihedral : 16.300 109.626 4193 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.68 % Favored : 94.17 % Rotamer: Outliers : 1.87 % Allowed : 17.58 % Favored : 80.55 % Cbeta Deviations : 0.17 % 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: 0.75 (0.24), residues: 1303 helix: 1.70 (0.23), residues: 588 sheet: 0.19 (0.48), residues: 119 loop : -0.64 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.010 0.001 TYR A 859 PHE 0.011 0.001 PHE B 38 TRP 0.009 0.001 TRP A 921 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10644) covalent geometry : angle 0.51046 / 0.26 (14440) SS BOND : bond 0.00292 / 0.14 ( 3) SS BOND : angle 0.62233 / 0.33 ( 6) hydrogen bonds : bond 0.12560 / 8.73 ( 515) hydrogen bonds : angle 6.35226 / 4.51 ( 1548) link_BETA1-4 : bond 0.00436 / 0.23 ( 2) link_BETA1-4 : angle 2.59703 / 1.31 ( 6) link_NAG-ASN : bond 0.00244 / 0.12 ( 3) link_NAG-ASN : angle 2.44626 / 1.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.605 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: symmetry clash outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 1.0054 time to fit residues: 109.1472 Evaluate side-chains 88 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.068018 restraints weight = 64062.506| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.96 r_work: 0.2838 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10652 Z= 0.227 Angle : 0.596 11.316 14461 Z= 0.305 Chirality : 0.047 0.478 1655 Planarity : 0.004 0.050 1839 Dihedral : 8.697 76.286 1740 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 2.31 % Allowed : 17.67 % Favored : 80.02 % Cbeta Deviations : 0.17 % 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: 0.70 (0.24), residues: 1303 helix: 1.75 (0.22), residues: 584 sheet: -0.08 (0.47), residues: 122 loop : -0.70 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 901 TYR 0.015 0.001 TYR A 859 PHE 0.016 0.001 PHE A 759 TRP 0.008 0.001 TRP A 79 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (10644) covalent geometry : angle 0.59127 / 0.30 (14440) SS BOND : bond 0.00258 / 0.13 ( 3) SS BOND : angle 0.54833 / 0.28 ( 6) hydrogen bonds : bond 0.04279 / 2.90 ( 515) hydrogen bonds : angle 5.03404 / 3.59 ( 1548) link_BETA1-4 : bond 0.00342 / 0.17 ( 2) link_BETA1-4 : angle 1.78191 / 1.07 ( 6) link_NAG-ASN : bond 0.00561 / 0.27 ( 3) link_NAG-ASN : angle 2.67052 / 2.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.583 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 232 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8880 (mm) outliers start: 26 outliers final: 19 residues processed: 99 average time/residue: 1.0650 time to fit residues: 116.0580 Evaluate side-chains 93 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 32 TRP Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070277 restraints weight = 63641.531| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.86 r_work: 0.2863 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10652 Z= 0.139 Angle : 0.559 12.315 14461 Z= 0.279 Chirality : 0.045 0.467 1655 Planarity : 0.004 0.051 1839 Dihedral : 6.857 58.858 1730 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 2.66 % Allowed : 16.70 % Favored : 80.64 % Cbeta Deviations : 0.08 % 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: 0.79 (0.24), residues: 1303 helix: 1.86 (0.22), residues: 584 sheet: -0.05 (0.47), residues: 121 loop : -0.70 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 27 TYR 0.013 0.001 TYR A 859 PHE 0.014 0.001 PHE B 90 TRP 0.007 0.001 TRP A 79 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10644) covalent geometry : angle 0.55336 / 0.28 (14440) SS BOND : bond 0.00222 / 0.11 ( 3) SS BOND : angle 0.54234 / 0.28 ( 6) hydrogen bonds : bond 0.03734 / 2.53 ( 515) hydrogen bonds : angle 4.72473 / 3.37 ( 1548) link_BETA1-4 : bond 0.00393 / 0.20 ( 2) link_BETA1-4 : angle 1.45828 / 0.82 ( 6) link_NAG-ASN : bond 0.00662 / 0.32 ( 3) link_NAG-ASN : angle 3.07834 / 2.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.602 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 232 ILE cc_start: 0.9176 (mt) cc_final: 0.8909 (mm) REVERT: A 497 MET cc_start: 0.6926 (tpt) cc_final: 0.6524 (tpt) outliers start: 30 outliers final: 19 residues processed: 103 average time/residue: 1.0074 time to fit residues: 115.3308 Evaluate side-chains 93 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 114 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.068448 restraints weight = 64171.952| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.92 r_work: 0.2846 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10652 Z= 0.185 Angle : 0.566 13.165 14461 Z= 0.285 Chirality : 0.045 0.486 1655 Planarity : 0.004 0.056 1839 Dihedral : 6.364 59.970 1730 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 2.49 % Allowed : 17.32 % Favored : 80.20 % Cbeta Deviations : 0.08 % 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: 1303 helix: 1.84 (0.22), residues: 590 sheet: -0.03 (0.47), residues: 120 loop : -0.76 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 27 TYR 0.017 0.001 TYR A1013 PHE 0.014 0.001 PHE B 90 TRP 0.008 0.001 TRP A 79 HIS 0.003 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (10644) covalent geometry : angle 0.55895 / 0.28 (14440) SS BOND : bond 0.00234 / 0.12 ( 3) SS BOND : angle 0.51515 / 0.27 ( 6) hydrogen bonds : bond 0.03628 / 2.45 ( 515) hydrogen bonds : angle 4.63885 / 3.31 ( 1548) link_BETA1-4 : bond 0.00307 / 0.16 ( 2) link_BETA1-4 : angle 1.37577 / 0.81 ( 6) link_NAG-ASN : bond 0.00769 / 0.37 ( 3) link_NAG-ASN : angle 3.41398 / 2.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.693 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 232 ILE cc_start: 0.9197 (mt) cc_final: 0.8938 (mm) REVERT: A 724 MET cc_start: 0.9272 (mmm) cc_final: 0.9064 (mmm) outliers start: 28 outliers final: 19 residues processed: 101 average time/residue: 1.0115 time to fit residues: 113.3250 Evaluate side-chains 92 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.096469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.068209 restraints weight = 63778.974| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.95 r_work: 0.2830 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10652 Z= 0.203 Angle : 0.574 13.335 14461 Z= 0.290 Chirality : 0.045 0.498 1655 Planarity : 0.004 0.056 1839 Dihedral : 6.266 59.374 1729 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 2.40 % Allowed : 17.67 % Favored : 79.93 % Cbeta Deviations : 0.08 % 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: 0.70 (0.24), residues: 1303 helix: 1.76 (0.22), residues: 596 sheet: -0.04 (0.46), residues: 120 loop : -0.77 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 27 TYR 0.019 0.001 TYR A 859 PHE 0.013 0.001 PHE B 90 TRP 0.007 0.001 TRP A 79 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (10644) covalent geometry : angle 0.56735 / 0.29 (14440) SS BOND : bond 0.00245 / 0.13 ( 3) SS BOND : angle 0.51058 / 0.26 ( 6) hydrogen bonds : bond 0.03624 / 2.44 ( 515) hydrogen bonds : angle 4.55932 / 3.24 ( 1548) link_BETA1-4 : bond 0.00290 / 0.15 ( 2) link_BETA1-4 : angle 1.27713 / 0.75 ( 6) link_NAG-ASN : bond 0.00648 / 0.31 ( 3) link_NAG-ASN : angle 3.48408 / 2.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.617 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: symmetry clash REVERT: A 232 ILE cc_start: 0.9214 (mt) cc_final: 0.8957 (mm) REVERT: A 497 MET cc_start: 0.7043 (tpt) cc_final: 0.6798 (tpt) REVERT: A 644 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: A 724 MET cc_start: 0.9278 (mmm) cc_final: 0.9025 (mmm) outliers start: 27 outliers final: 21 residues processed: 100 average time/residue: 1.0891 time to fit residues: 120.2652 Evaluate side-chains 95 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 129 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.097653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.069235 restraints weight = 63533.942| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.95 r_work: 0.2858 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 0.059 10652 Z= 0.124 Angle : 0.551 13.384 14461 Z= 0.273 Chirality : 0.045 0.501 1655 Planarity : 0.004 0.055 1839 Dihedral : 6.122 57.554 1729 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.17 % Rotamer: Outliers : 2.22 % Allowed : 17.67 % Favored : 80.11 % Cbeta Deviations : 0.08 % 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: 0.83 (0.24), residues: 1303 helix: 1.90 (0.22), residues: 596 sheet: -0.06 (0.46), residues: 119 loop : -0.73 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 27 TYR 0.020 0.001 TYR A1013 PHE 0.013 0.001 PHE B 90 TRP 0.005 0.001 TRP A 79 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10644) covalent geometry : angle 0.54391 / 0.27 (14440) SS BOND : bond 0.00214 / 0.11 ( 3) SS BOND : angle 0.46777 / 0.24 ( 6) hydrogen bonds : bond 0.03375 / 2.27 ( 515) hydrogen bonds : angle 4.40125 / 3.12 ( 1548) link_BETA1-4 : bond 0.00392 / 0.20 ( 2) link_BETA1-4 : angle 1.19173 / 0.69 ( 6) link_NAG-ASN : bond 0.00578 / 0.28 ( 3) link_NAG-ASN : angle 3.46580 / 2.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.592 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: symmetry clash REVERT: A 232 ILE cc_start: 0.9215 (mt) cc_final: 0.8972 (mm) REVERT: A 497 MET cc_start: 0.7055 (tpt) cc_final: 0.6543 (tpt) REVERT: A 644 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6936 (pm20) outliers start: 25 outliers final: 17 residues processed: 99 average time/residue: 1.0554 time to fit residues: 115.3440 Evaluate side-chains 89 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 830 ARG Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.097802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.069525 restraints weight = 63101.421| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.93 r_work: 0.2865 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10652 Z= 0.126 Angle : 0.550 13.498 14461 Z= 0.273 Chirality : 0.045 0.500 1655 Planarity : 0.005 0.138 1839 Dihedral : 7.237 163.315 1728 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 2.04 % Allowed : 17.94 % Favored : 80.02 % Cbeta Deviations : 0.08 % 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: 0.91 (0.24), residues: 1303 helix: 1.92 (0.22), residues: 602 sheet: 0.26 (0.48), residues: 111 loop : -0.73 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 830 TYR 0.017 0.001 TYR A 859 PHE 0.013 0.001 PHE B 90 TRP 0.005 0.001 TRP A 79 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10644) covalent geometry : angle 0.54356 / 0.27 (14440) SS BOND : bond 0.00232 / 0.12 ( 3) SS BOND : angle 0.49904 / 0.26 ( 6) hydrogen bonds : bond 0.03329 / 2.24 ( 515) hydrogen bonds : angle 4.36441 / 3.10 ( 1548) link_BETA1-4 : bond 0.00284 / 0.15 ( 2) link_BETA1-4 : angle 1.14423 / 0.67 ( 6) link_NAG-ASN : bond 0.00560 / 0.27 ( 3) link_NAG-ASN : angle 3.43098 / 2.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.756 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 232 ILE cc_start: 0.9224 (mt) cc_final: 0.8997 (mm) REVERT: A 497 MET cc_start: 0.7065 (tpt) cc_final: 0.6533 (tpt) REVERT: A 644 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6922 (pm20) outliers start: 23 outliers final: 17 residues processed: 94 average time/residue: 1.1182 time to fit residues: 115.9587 Evaluate side-chains 88 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.097172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068790 restraints weight = 63295.684| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.95 r_work: 0.2849 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10652 Z= 0.183 Angle : 0.573 13.429 14461 Z= 0.286 Chirality : 0.045 0.489 1655 Planarity : 0.004 0.089 1839 Dihedral : 7.224 169.837 1724 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 2.31 % Allowed : 17.76 % Favored : 79.93 % Cbeta Deviations : 0.08 % 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: 0.87 (0.24), residues: 1303 helix: 1.88 (0.22), residues: 602 sheet: 0.21 (0.48), residues: 112 loop : -0.73 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 830 TYR 0.021 0.001 TYR A1013 PHE 0.012 0.001 PHE A 913 TRP 0.006 0.001 TRP A 79 HIS 0.003 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (10644) covalent geometry : angle 0.56658 / 0.28 (14440) SS BOND : bond 0.00252 / 0.13 ( 3) SS BOND : angle 0.48253 / 0.25 ( 6) hydrogen bonds : bond 0.03433 / 2.31 ( 515) hydrogen bonds : angle 4.40436 / 3.13 ( 1548) link_BETA1-4 : bond 0.00450 / 0.24 ( 2) link_BETA1-4 : angle 1.17591 / 0.71 ( 6) link_NAG-ASN : bond 0.00557 / 0.27 ( 3) link_NAG-ASN : angle 3.41945 / 2.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.596 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 232 ILE cc_start: 0.9206 (mt) cc_final: 0.8964 (mm) REVERT: A 497 MET cc_start: 0.7074 (tpt) cc_final: 0.6686 (tpt) REVERT: A 644 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6930 (pm20) outliers start: 26 outliers final: 18 residues processed: 93 average time/residue: 1.0100 time to fit residues: 104.3712 Evaluate side-chains 88 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 119 optimal weight: 0.0870 chunk 123 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.097830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.069542 restraints weight = 63530.964| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.96 r_work: 0.2865 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10652 Z= 0.128 Angle : 0.562 12.938 14461 Z= 0.277 Chirality : 0.045 0.473 1655 Planarity : 0.004 0.069 1839 Dihedral : 7.218 172.145 1724 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 2.22 % Allowed : 17.94 % Favored : 79.84 % Cbeta Deviations : 0.08 % 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: 0.98 (0.24), residues: 1303 helix: 1.97 (0.22), residues: 602 sheet: 0.23 (0.48), residues: 111 loop : -0.66 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 830 TYR 0.018 0.001 TYR A1013 PHE 0.011 0.001 PHE A 913 TRP 0.004 0.001 TRP A 880 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10644) covalent geometry : angle 0.55563 / 0.28 (14440) SS BOND : bond 0.00229 / 0.12 ( 3) SS BOND : angle 0.46175 / 0.23 ( 6) hydrogen bonds : bond 0.03310 / 2.22 ( 515) hydrogen bonds : angle 4.30541 / 3.06 ( 1548) link_BETA1-4 : bond 0.00344 / 0.18 ( 2) link_BETA1-4 : angle 1.07750 / 0.63 ( 6) link_NAG-ASN : bond 0.00518 / 0.25 ( 3) link_NAG-ASN : angle 3.38586 / 2.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.537 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: symmetry clash REVERT: A 232 ILE cc_start: 0.9223 (mt) cc_final: 0.9002 (mm) REVERT: A 497 MET cc_start: 0.7047 (tpt) cc_final: 0.6594 (tpt) REVERT: A 644 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6915 (pm20) outliers start: 25 outliers final: 18 residues processed: 94 average time/residue: 1.0596 time to fit residues: 109.9233 Evaluate side-chains 91 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069180 restraints weight = 63256.135| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.98 r_work: 0.2857 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10652 Z= 0.143 Angle : 0.565 13.521 14461 Z= 0.279 Chirality : 0.045 0.501 1655 Planarity : 0.004 0.070 1839 Dihedral : 7.191 171.997 1724 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.22 % Allowed : 17.85 % Favored : 79.93 % Cbeta Deviations : 0.08 % 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: 1.00 (0.24), residues: 1303 helix: 1.99 (0.22), residues: 602 sheet: 0.25 (0.48), residues: 111 loop : -0.65 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 830 TYR 0.019 0.001 TYR A1013 PHE 0.010 0.001 PHE A 913 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (10644) covalent geometry : angle 0.55910 / 0.28 (14440) SS BOND : bond 0.00222 / 0.11 ( 3) SS BOND : angle 0.44609 / 0.23 ( 6) hydrogen bonds : bond 0.03300 / 2.22 ( 515) hydrogen bonds : angle 4.28745 / 3.04 ( 1548) link_BETA1-4 : bond 0.00322 / 0.17 ( 2) link_BETA1-4 : angle 1.07619 / 0.63 ( 6) link_NAG-ASN : bond 0.00510 / 0.25 ( 3) link_NAG-ASN : angle 3.33392 / 2.82 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.677 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 232 ILE cc_start: 0.9205 (mt) cc_final: 0.8959 (mm) REVERT: A 497 MET cc_start: 0.7048 (tpt) cc_final: 0.6650 (tpt) REVERT: A 606 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8987 (t) REVERT: A 644 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: A 724 MET cc_start: 0.9350 (mmm) cc_final: 0.9031 (mmm) outliers start: 25 outliers final: 20 residues processed: 94 average time/residue: 0.9986 time to fit residues: 104.3677 Evaluate side-chains 92 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 977 TRP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 82 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 110 optimal weight: 0.0670 chunk 104 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.069396 restraints weight = 63328.273| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.95 r_work: 0.2865 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10652 Z= 0.143 Angle : 0.843 59.195 14461 Z= 0.463 Chirality : 0.045 0.501 1655 Planarity : 0.004 0.069 1839 Dihedral : 7.178 172.169 1724 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.13 % Allowed : 18.03 % Favored : 79.84 % Cbeta Deviations : 0.08 % 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: 1.01 (0.24), residues: 1303 helix: 2.00 (0.22), residues: 602 sheet: 0.25 (0.48), residues: 111 loop : -0.65 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 830 TYR 0.017 0.001 TYR A1013 PHE 0.010 0.001 PHE A 913 TRP 0.005 0.001 TRP A 79 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10644) covalent geometry : angle 0.83965 / 0.46 (14440) SS BOND : bond 0.00223 / 0.11 ( 3) SS BOND : angle 0.44748 / 0.23 ( 6) hydrogen bonds : bond 0.03291 / 2.21 ( 515) hydrogen bonds : angle 4.28101 / 3.04 ( 1548) link_BETA1-4 : bond 0.00299 / 0.16 ( 2) link_BETA1-4 : angle 1.10063 / 0.65 ( 6) link_NAG-ASN : bond 0.00501 / 0.24 ( 3) link_NAG-ASN : angle 3.33053 / 2.81 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6273.87 seconds wall clock time: 107 minutes 10.47 seconds (6430.47 seconds total)