Starting phenix.real_space_refine on Thu Jul 2 12:22:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzf_47328/07_2026/9dzf_47328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzf_47328/07_2026/9dzf_47328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dzf_47328/07_2026/9dzf_47328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzf_47328/07_2026/9dzf_47328.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dzf_47328/07_2026/9dzf_47328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzf_47328/07_2026/9dzf_47328.map" } resolution = 2.7 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= 0.192 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 35 5.16 5 Cl 2 4.86 5 C 5360 2.51 5 N 1430 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8452 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3168 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 13, 'ARG:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 134 Chain: "B" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3137 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 15, 'ARG:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 157 Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 156 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 777 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 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: 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: "F" 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: "G" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "L" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 1.47, per 1000 atoms: 0.17 Number of scatterers: 8452 At special positions: 0 Unit cell: (76.893, 102.885, 115.881, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 35 16.00 O 1625 8.00 N 1430 7.00 C 5360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 86 " distance=2.04 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 23 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG D 1 " - " ASN A 13 " " NAG E 1 " - " ASN A 395 " " NAG F 1 " - " ASN B 13 " " NAG G 1 " - " ASN B 395 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 304.6 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 34.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 19 through 35 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.512A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.539A pdb=" N PHE A 114 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 3.745A pdb=" N GLY A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 215 through 230 Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.739A pdb=" N GLN A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.688A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 315 through 338 removed outlier: 3.505A pdb=" N ALA A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 326 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'B' and resid 19 through 35 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.556A pdb=" N LEU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.646A pdb=" N VAL B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.771A pdb=" N GLY B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 179 Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.814A pdb=" N GLN B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.707A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 315 through 338 removed outlier: 3.633A pdb=" N ALA B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.582A pdb=" N ARG B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.534A pdb=" N GLY C 16 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.586A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.702A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 52 removed outlier: 9.104A pdb=" N VAL A 80 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 4 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU A 82 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 6 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 81 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 104 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 189 removed outlier: 5.287A pdb=" N VAL A 209 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 238 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 280 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N HIS A 240 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N TYR A 282 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE A 376 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 393 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 378 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.198A pdb=" N LEU B 3 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL B 49 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY B 51 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL B 7 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N VAL B 80 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR B 4 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 82 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 6 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE B 81 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 104 " --> pdb=" O THR B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 189 removed outlier: 6.595A pdb=" N ALA B 150 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LEU B 186 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET B 152 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE B 188 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 154 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 209 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 238 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE B 280 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS B 240 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N TYR B 282 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ALA B 277 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N MET B 381 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE B 376 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B 393 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 378 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.690A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.778A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.335A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.335A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1014 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: 0.89 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2652 1.35 - 1.47: 2344 1.47 - 1.60: 3489 1.60 - 1.72: 0 1.72 - 1.85: 54 Bond restraints: 8539 Sorted by residual: bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.14e+00 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.83e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 ... (remaining 8534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 11106 1.27 - 2.54: 442 2.54 - 3.81: 95 3.81 - 5.07: 23 5.07 - 6.34: 6 Bond angle restraints: 11672 Sorted by residual: angle pdb=" C CYS B 164 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " ideal model delta sigma weight residual 120.54 116.80 3.74 1.35e+00 5.49e-01 7.66e+00 angle pdb=" C CYS A 164 " pdb=" N PHE A 165 " pdb=" CA PHE A 165 " ideal model delta sigma weight residual 120.54 116.91 3.63 1.35e+00 5.49e-01 7.24e+00 angle pdb=" CB ARG L 93 " pdb=" CG ARG L 93 " pdb=" CD ARG L 93 " ideal model delta sigma weight residual 111.30 116.99 -5.69 2.30e+00 1.89e-01 6.12e+00 angle pdb=" C TRP A 379 " pdb=" N ASP A 380 " pdb=" CA ASP A 380 " ideal model delta sigma weight residual 122.59 126.26 -3.67 1.57e+00 4.06e-01 5.47e+00 angle pdb=" C3 BMA E 3 " pdb=" C2 BMA E 3 " pdb=" O2 BMA E 3 " ideal model delta sigma weight residual 112.95 106.61 6.34 3.00e+00 1.11e-01 4.47e+00 ... (remaining 11667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 4638 21.72 - 43.44: 334 43.44 - 65.16: 52 65.16 - 86.88: 25 86.88 - 108.60: 10 Dihedral angle restraints: 5059 sinusoidal: 1913 harmonic: 3146 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CA ARG L 93 " pdb=" C ARG L 93 " pdb=" N LYS L 94 " pdb=" CA LYS L 94 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual 180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 5056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1144 0.055 - 0.110: 146 0.110 - 0.165: 39 0.165 - 0.220: 2 0.220 - 0.274: 2 Chirality restraints: 1333 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+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 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA CYS B 164 " pdb=" N CYS B 164 " pdb=" C CYS B 164 " pdb=" CB CYS B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1330 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 317 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO B 318 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 411 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 412 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 258 " 0.153 9.50e-02 1.11e+02 6.86e-02 3.06e+00 pdb=" NE ARG A 258 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 258 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 258 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 258 " 0.003 2.00e-02 2.50e+03 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 80 2.56 - 3.14: 6291 3.14 - 3.73: 12426 3.73 - 4.31: 19747 4.31 - 4.90: 32910 Nonbonded interactions: 71454 Sorted by model distance: nonbonded pdb=" O HOH H 311 " pdb=" O HOH H 317 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP B 375 " pdb=" O HOH B1201 " model vdw 1.992 3.040 nonbonded pdb=" O HOH A1226 " pdb=" O HOH A1233 " model vdw 2.004 3.040 nonbonded pdb=" O HOH B1236 " pdb=" O HOH B1248 " model vdw 2.007 3.040 nonbonded pdb=" O HOH B1202 " pdb=" O HOH B1236 " model vdw 2.020 3.040 ... (remaining 71449 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 'A' and (resid 1 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 70 or (resid 71 and (nam \ e N or name CA or name C or name O or name CB )) or resid 72 through 118 or (res \ id 119 and (name N or name CA or name C or name O or name CB )) or resid 120 thr \ ough 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) \ or resid 185 through 191 or (resid 192 through 194 and (name N or name CA or nam \ e C or name O or name CB )) or resid 195 through 197 or (resid 198 and (name N o \ r name CA or name C or name O or name CB )) or resid 199 through 201 or (resid 2 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 203 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or r \ esid 233 through 260 or (resid 261 and (name N or name CA or name C or name O or \ name CB )) or resid 262 through 271 or (resid 272 through 273 and (name N or na \ me CA or name C or name O or name CB )) or resid 274 through 294 or (resid 295 a \ nd (name N or name CA or name C or name O or name CB )) or resid 296 through 345 \ or (resid 346 and (name N or name CA or name C or name O or name CB )) or resid \ 347 through 349 or (resid 350 and (name N or name CA or name C or name O or nam \ e CB )) or resid 351 through 409 or (resid 410 and (name N or name CA or name C \ or name O or name CB )) or resid 411 through 1101)) selection = (chain 'B' and (resid 1 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 146 or (resid 147 through 148 and ( \ name N or name CA or name C or name O or name CB )) or resid 149 through 234 or \ (resid 235 and (name N or name CA or name C or name O or name CB )) or resid 236 \ through 303 or (resid 304 and (name N or name CA or name C or name O or name CB \ )) or resid 305 through 384 or (resid 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 401 or (resid 402 through 403 and (name \ N or name CA or name C or name O or name CB )) or resid 404 through 422 or (res \ id 423 and (name N or name CA or name C or name O or name CB )) or resid 424 thr \ ough 1101)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:5.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.004 0.045 8556 Z= 0.176 Angle : 0.643 6.646 11716 Z= 0.322 Chirality : 0.044 0.274 1333 Planarity : 0.005 0.069 1483 Dihedral : 16.698 108.602 3038 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.52 % Allowed : 13.03 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1094 helix: 0.22 (0.29), residues: 330 sheet: -0.35 (0.28), residues: 305 loop : -1.09 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 258 TYR 0.014 0.001 TYR A 154 PHE 0.012 0.001 PHE B 172 TRP 0.009 0.001 TRP H 33 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 8539) covalent geometry : angle 0.62382 / 0.32 (11672) SS BOND : bond 0.00940 / 0.55 ( 7) SS BOND : angle 2.91010 / 1.86 ( 14) hydrogen bonds : bond 0.14091 / 9.35 ( 359) hydrogen bonds : angle 6.88790 / 4.99 ( 1014) link_BETA1-4 : bond 0.00499 / 0.33 ( 6) link_BETA1-4 : angle 2.66084 / 1.49 ( 18) link_NAG-ASN : bond 0.00520 / 0.32 ( 4) link_NAG-ASN : angle 2.08396 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.259 Fit side-chains REVERT: B 309 MET cc_start: 0.7414 (mtp) cc_final: 0.7164 (mtp) outliers start: 4 outliers final: 4 residues processed: 107 average time/residue: 0.4705 time to fit residues: 53.5994 Evaluate side-chains 102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain L residue 93 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 195 HIS A 249 GLN B 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125047 restraints weight = 7818.856| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.94 r_work: 0.3175 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8556 Z= 0.160 Angle : 0.643 6.139 11716 Z= 0.323 Chirality : 0.044 0.150 1333 Planarity : 0.005 0.052 1483 Dihedral : 9.725 70.986 1416 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.23 % Allowed : 12.00 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.25), residues: 1094 helix: 1.16 (0.29), residues: 330 sheet: -0.29 (0.28), residues: 305 loop : -1.02 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 258 TYR 0.011 0.001 TYR A 154 PHE 0.012 0.002 PHE B 172 TRP 0.010 0.001 TRP L 92 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 8539) covalent geometry : angle 0.62889 / 0.32 (11672) SS BOND : bond 0.00832 / 0.46 ( 7) SS BOND : angle 1.88539 / 1.37 ( 14) hydrogen bonds : bond 0.05022 / 3.36 ( 359) hydrogen bonds : angle 5.03125 / 3.64 ( 1014) link_BETA1-4 : bond 0.00651 / 0.43 ( 6) link_BETA1-4 : angle 2.52781 / 1.81 ( 18) link_NAG-ASN : bond 0.00303 / 0.19 ( 4) link_NAG-ASN : angle 2.16099 / 1.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.339 Fit side-chains REVERT: A 249 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.8026 (mp10) outliers start: 25 outliers final: 11 residues processed: 114 average time/residue: 0.5030 time to fit residues: 61.1474 Evaluate side-chains 107 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 93 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.143916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130570 restraints weight = 7739.420| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 0.82 r_work: 0.3234 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8556 Z= 0.112 Angle : 0.555 6.925 11716 Z= 0.281 Chirality : 0.042 0.141 1333 Planarity : 0.004 0.050 1483 Dihedral : 7.633 59.531 1414 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.45 % Allowed : 13.81 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.25), residues: 1094 helix: 1.52 (0.29), residues: 332 sheet: -0.16 (0.28), residues: 308 loop : -1.01 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.014 0.001 TYR A 154 PHE 0.010 0.001 PHE B 172 TRP 0.008 0.001 TRP B 18 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8539) covalent geometry : angle 0.54260 / 0.28 (11672) SS BOND : bond 0.00535 / 0.31 ( 7) SS BOND : angle 1.42878 / 0.95 ( 14) hydrogen bonds : bond 0.03870 / 2.59 ( 359) hydrogen bonds : angle 4.72303 / 3.41 ( 1014) link_BETA1-4 : bond 0.00656 / 0.43 ( 6) link_BETA1-4 : angle 2.32898 / 1.63 ( 18) link_NAG-ASN : bond 0.00378 / 0.24 ( 4) link_NAG-ASN : angle 1.87368 / 1.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.307 Fit side-chains REVERT: A 271 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8059 (tpt90) REVERT: B 149 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: B 309 MET cc_start: 0.7866 (mtp) cc_final: 0.7614 (mtm) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 0.4152 time to fit residues: 50.3467 Evaluate side-chains 103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.140340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124560 restraints weight = 7942.748| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 0.96 r_work: 0.3178 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8556 Z= 0.180 Angle : 0.656 7.130 11716 Z= 0.327 Chirality : 0.045 0.158 1333 Planarity : 0.005 0.049 1483 Dihedral : 7.132 57.667 1410 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.74 % Allowed : 13.81 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.25), residues: 1094 helix: 1.35 (0.29), residues: 332 sheet: -0.15 (0.28), residues: 308 loop : -1.07 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.010 0.002 TYR L 86 PHE 0.013 0.002 PHE B 172 TRP 0.012 0.002 TRP L 92 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 ( 8539) covalent geometry : angle 0.64102 / 0.32 (11672) SS BOND : bond 0.01007 / 0.56 ( 7) SS BOND : angle 2.34323 / 1.64 ( 14) hydrogen bonds : bond 0.05083 / 3.42 ( 359) hydrogen bonds : angle 4.79609 / 3.47 ( 1014) link_BETA1-4 : bond 0.00559 / 0.39 ( 6) link_BETA1-4 : angle 2.49307 / 1.67 ( 18) link_NAG-ASN : bond 0.00343 / 0.22 ( 4) link_NAG-ASN : angle 2.14467 / 1.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.338 Fit side-chains REVERT: A 187 GLU cc_start: 0.8787 (tt0) cc_final: 0.8561 (tt0) REVERT: A 271 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8127 (tpt90) REVERT: A 373 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7729 (mm-30) outliers start: 29 outliers final: 13 residues processed: 111 average time/residue: 0.4394 time to fit residues: 52.1362 Evaluate side-chains 111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.141926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126419 restraints weight = 7844.107| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.97 r_work: 0.3246 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8556 Z= 0.136 Angle : 0.585 7.340 11716 Z= 0.295 Chirality : 0.043 0.162 1333 Planarity : 0.005 0.048 1483 Dihedral : 6.498 56.436 1410 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.10 % Allowed : 14.71 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.25), residues: 1094 helix: 1.49 (0.29), residues: 332 sheet: -0.10 (0.28), residues: 308 loop : -1.07 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.012 0.001 TYR A 154 PHE 0.012 0.001 PHE B 172 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8539) covalent geometry : angle 0.57122 / 0.29 (11672) SS BOND : bond 0.00719 / 0.40 ( 7) SS BOND : angle 2.08234 / 1.41 ( 14) hydrogen bonds : bond 0.04261 / 2.88 ( 359) hydrogen bonds : angle 4.67298 / 3.39 ( 1014) link_BETA1-4 : bond 0.00574 / 0.39 ( 6) link_BETA1-4 : angle 2.22585 / 1.49 ( 18) link_NAG-ASN : bond 0.00406 / 0.26 ( 4) link_NAG-ASN : angle 2.01766 / 1.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.333 Fit side-chains REVERT: A 373 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: B 309 MET cc_start: 0.7761 (mtp) cc_final: 0.7440 (mtm) REVERT: H 57 TYR cc_start: 0.8825 (m-10) cc_final: 0.8600 (m-80) REVERT: L 55 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7773 (mm-40) outliers start: 24 outliers final: 13 residues processed: 113 average time/residue: 0.4472 time to fit residues: 54.0780 Evaluate side-chains 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 55 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.141790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126084 restraints weight = 7769.628| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.98 r_work: 0.3239 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8556 Z= 0.137 Angle : 0.585 7.028 11716 Z= 0.293 Chirality : 0.043 0.136 1333 Planarity : 0.004 0.048 1483 Dihedral : 6.194 56.116 1410 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.23 % Allowed : 14.84 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.02 (0.25), residues: 1094 helix: 1.55 (0.29), residues: 332 sheet: -0.06 (0.28), residues: 308 loop : -1.06 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.012 0.001 TYR A 154 PHE 0.012 0.001 PHE B 172 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8539) covalent geometry : angle 0.57242 / 0.29 (11672) SS BOND : bond 0.00753 / 0.42 ( 7) SS BOND : angle 1.86285 / 1.33 ( 14) hydrogen bonds : bond 0.04318 / 2.91 ( 359) hydrogen bonds : angle 4.61180 / 3.34 ( 1014) link_BETA1-4 : bond 0.00546 / 0.38 ( 6) link_BETA1-4 : angle 2.11713 / 1.39 ( 18) link_NAG-ASN : bond 0.00369 / 0.23 ( 4) link_NAG-ASN : angle 2.02807 / 1.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.230 Fit side-chains REVERT: A 373 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: B 309 MET cc_start: 0.7831 (mtp) cc_final: 0.7474 (mtp) REVERT: H 87 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7620 (ptt180) REVERT: L 11 LEU cc_start: 0.8402 (tp) cc_final: 0.7982 (tt) REVERT: L 55 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7773 (mm-40) outliers start: 25 outliers final: 13 residues processed: 115 average time/residue: 0.4338 time to fit residues: 53.2846 Evaluate side-chains 115 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 55 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 0.0040 chunk 50 optimal weight: 3.9990 chunk 68 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.154567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133716 restraints weight = 8358.544| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.32 r_work: 0.3473 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8556 Z= 0.126 Angle : 0.568 7.023 11716 Z= 0.287 Chirality : 0.042 0.177 1333 Planarity : 0.004 0.047 1483 Dihedral : 5.939 55.575 1409 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.71 % Allowed : 15.87 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.25), residues: 1094 helix: 1.61 (0.29), residues: 332 sheet: -0.00 (0.28), residues: 308 loop : -1.06 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.012 0.001 TYR A 154 PHE 0.011 0.001 PHE A 165 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8539) covalent geometry : angle 0.55437 / 0.28 (11672) SS BOND : bond 0.00624 / 0.34 ( 7) SS BOND : angle 2.37603 / 1.55 ( 14) hydrogen bonds : bond 0.04056 / 2.73 ( 359) hydrogen bonds : angle 4.60355 / 3.34 ( 1014) link_BETA1-4 : bond 0.00538 / 0.37 ( 6) link_BETA1-4 : angle 2.00447 / 1.31 ( 18) link_NAG-ASN : bond 0.00355 / 0.23 ( 4) link_NAG-ASN : angle 1.98571 / 1.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.317 Fit side-chains REVERT: A 162 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: A 373 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: B 309 MET cc_start: 0.7869 (mtp) cc_final: 0.7521 (mtp) REVERT: H 87 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7468 (ptt180) REVERT: L 55 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7786 (mm-40) outliers start: 21 outliers final: 12 residues processed: 114 average time/residue: 0.4418 time to fit residues: 53.9066 Evaluate side-chains 115 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.154642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133364 restraints weight = 8226.461| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.36 r_work: 0.3480 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8556 Z= 0.123 Angle : 0.565 6.792 11716 Z= 0.286 Chirality : 0.042 0.190 1333 Planarity : 0.004 0.047 1483 Dihedral : 5.808 55.343 1409 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.71 % Allowed : 16.26 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.25), residues: 1094 helix: 1.66 (0.29), residues: 332 sheet: 0.04 (0.29), residues: 308 loop : -1.04 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 355 TYR 0.015 0.001 TYR A 154 PHE 0.011 0.001 PHE B 172 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 8539) covalent geometry : angle 0.54992 / 0.28 (11672) SS BOND : bond 0.00662 / 0.37 ( 7) SS BOND : angle 2.62992 / 1.69 ( 14) hydrogen bonds : bond 0.03980 / 2.68 ( 359) hydrogen bonds : angle 4.53740 / 3.30 ( 1014) link_BETA1-4 : bond 0.00522 / 0.36 ( 6) link_BETA1-4 : angle 1.94103 / 1.26 ( 18) link_NAG-ASN : bond 0.00328 / 0.21 ( 4) link_NAG-ASN : angle 1.96249 / 1.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.279 Fit side-chains REVERT: A 373 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: B 309 MET cc_start: 0.7866 (mtp) cc_final: 0.7558 (mtp) REVERT: H 57 TYR cc_start: 0.8884 (m-80) cc_final: 0.8651 (m-80) REVERT: H 87 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7415 (ptt180) REVERT: L 11 LEU cc_start: 0.8279 (tp) cc_final: 0.7801 (tt) REVERT: L 55 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7714 (mm-40) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 0.4384 time to fit residues: 53.5028 Evaluate side-chains 116 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.139991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124307 restraints weight = 7820.153| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 0.95 r_work: 0.3224 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8556 Z= 0.203 Angle : 0.686 11.722 11716 Z= 0.345 Chirality : 0.047 0.335 1333 Planarity : 0.005 0.048 1483 Dihedral : 6.285 57.979 1409 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.71 % Allowed : 16.52 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.07 (0.25), residues: 1094 helix: 1.38 (0.29), residues: 332 sheet: -0.03 (0.28), residues: 308 loop : -1.11 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 355 TYR 0.010 0.002 TYR B 328 PHE 0.021 0.002 PHE A 165 TRP 0.014 0.002 TRP L 92 HIS 0.007 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.20 ( 8539) covalent geometry : angle 0.66459 / 0.34 (11672) SS BOND : bond 0.00992 / 0.55 ( 7) SS BOND : angle 3.97957 / 2.58 ( 14) hydrogen bonds : bond 0.05202 / 3.49 ( 359) hydrogen bonds : angle 4.83657 / 3.54 ( 1014) link_BETA1-4 : bond 0.00516 / 0.37 ( 6) link_BETA1-4 : angle 2.17267 / 1.37 ( 18) link_NAG-ASN : bond 0.00314 / 0.20 ( 4) link_NAG-ASN : angle 2.19209 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.295 Fit side-chains REVERT: A 187 GLU cc_start: 0.8645 (tt0) cc_final: 0.8392 (tt0) REVERT: A 373 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7578 (mm-30) REVERT: B 309 MET cc_start: 0.7916 (mtp) cc_final: 0.7496 (mtp) REVERT: L 11 LEU cc_start: 0.8344 (tp) cc_final: 0.7904 (tt) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 0.4548 time to fit residues: 53.9869 Evaluate side-chains 107 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 103 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.155171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133977 restraints weight = 8261.866| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.35 r_work: 0.3485 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 8556 Z= 0.129 Angle : 0.589 10.166 11716 Z= 0.300 Chirality : 0.042 0.276 1333 Planarity : 0.004 0.046 1483 Dihedral : 5.967 55.981 1409 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.94 % Allowed : 17.81 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.11 (0.25), residues: 1094 helix: 1.61 (0.29), residues: 332 sheet: 0.06 (0.28), residues: 308 loop : -1.05 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.013 0.001 TYR A 154 PHE 0.014 0.001 PHE A 165 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 8539) covalent geometry : angle 0.56881 / 0.29 (11672) SS BOND : bond 0.00514 / 0.27 ( 7) SS BOND : angle 3.56140 / 2.15 ( 14) hydrogen bonds : bond 0.03996 / 2.64 ( 359) hydrogen bonds : angle 4.73403 / 3.48 ( 1014) link_BETA1-4 : bond 0.00526 / 0.36 ( 6) link_BETA1-4 : angle 1.92214 / 1.24 ( 18) link_NAG-ASN : bond 0.00365 / 0.24 ( 4) link_NAG-ASN : angle 2.02136 / 1.59 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.208 Fit side-chains REVERT: A 373 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: B 309 MET cc_start: 0.7897 (mtp) cc_final: 0.7579 (mtp) REVERT: L 11 LEU cc_start: 0.8223 (tp) cc_final: 0.7763 (tt) REVERT: L 55 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7779 (mm-40) outliers start: 15 outliers final: 11 residues processed: 112 average time/residue: 0.4629 time to fit residues: 55.5494 Evaluate side-chains 115 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.155701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134453 restraints weight = 8257.979| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.36 r_work: 0.3488 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 8556 Z= 0.129 Angle : 0.583 10.324 11716 Z= 0.297 Chirality : 0.042 0.250 1333 Planarity : 0.004 0.047 1483 Dihedral : 5.814 55.253 1409 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.94 % Allowed : 17.94 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.19 (0.25), residues: 1094 helix: 1.71 (0.29), residues: 332 sheet: 0.11 (0.29), residues: 308 loop : -1.03 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.012 0.001 TYR H 57 PHE 0.013 0.001 PHE A 165 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 8539) covalent geometry : angle 0.56538 / 0.29 (11672) SS BOND : bond 0.00574 / 0.32 ( 7) SS BOND : angle 3.28474 / 1.98 ( 14) hydrogen bonds : bond 0.03974 / 2.61 ( 359) hydrogen bonds : angle 4.67719 / 3.44 ( 1014) link_BETA1-4 : bond 0.00523 / 0.36 ( 6) link_BETA1-4 : angle 1.85497 / 1.19 ( 18) link_NAG-ASN : bond 0.00306 / 0.20 ( 4) link_NAG-ASN : angle 1.92421 / 1.50 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.67 seconds wall clock time: 40 minutes 5.82 seconds (2405.82 seconds total)