Starting phenix.real_space_refine on Fri Feb 6 17:46:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mq1_48510/02_2026/9mq1_48510_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mq1_48510/02_2026/9mq1_48510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mq1_48510/02_2026/9mq1_48510_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mq1_48510/02_2026/9mq1_48510_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mq1_48510/02_2026/9mq1_48510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mq1_48510/02_2026/9mq1_48510.map" } resolution = 3.37 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= 0.016 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 73 5.16 5 C 8529 2.51 5 N 2283 2.21 5 O 2621 1.98 5 H 12860 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26366 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1837 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1712 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 102} Chain: "B" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4967 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "b" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2582 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "A" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4967 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "a" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2583 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "C" Number of atoms: 4968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4968 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "c" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2582 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.61, per 1000 atoms: 0.17 Number of scatterers: 26366 At special positions: 0 Unit cell: (104.4, 97.15, 165.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 O 2621 8.00 N 2283 7.00 C 8529 6.00 H 12860 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS b 144 " - pdb=" SG CYS b 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 141 " distance=2.02 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.02 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 148 " 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 NAG-ASN " NAG A 401 " - " ASN A 169 " " NAG A 402 " - " ASN A 21 " " NAG A 403 " - " ASN A 33 " " NAG A 404 " - " ASN A 289 " " NAG B 401 " - " ASN B 169 " " NAG B 402 " - " ASN B 289 " " NAG B 403 " - " ASN B 21 " " NAG B 404 " - " ASN B 33 " " NAG C 401 " - " ASN C 171 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 21 " " NAG C 404 " - " ASN C 291 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 847.6 milliseconds 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 43 sheets defined 21.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.583A pdb=" N TRP B 127 " --> pdb=" O LYS B 125A" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.647A pdb=" N GLN B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 59 Processing helix chain 'b' and resid 74 through 125 removed outlier: 3.508A pdb=" N LYS b 83 " --> pdb=" O ASN b 79 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU b 99 " --> pdb=" O ASN b 95 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP b 112 " --> pdb=" O LEU b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 155 removed outlier: 3.572A pdb=" N MET b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.518A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.904A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU A 78 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 removed outlier: 3.611A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'a' and resid 37 through 59 Processing helix chain 'a' and resid 74 through 125 Processing helix chain 'a' and resid 145 through 155 removed outlier: 3.732A pdb=" N MET a 149 " --> pdb=" O ASP a 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.718A pdb=" N TRP C 129 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'c' and resid 37 through 59 Processing helix chain 'c' and resid 60 through 62 No H-bonds generated for 'chain 'c' and resid 60 through 62' Processing helix chain 'c' and resid 71 through 73 No H-bonds generated for 'chain 'c' and resid 71 through 73' Processing helix chain 'c' and resid 74 through 127 removed outlier: 3.825A pdb=" N ASP c 86 " --> pdb=" O LYS c 82 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN c 104 " --> pdb=" O VAL c 100 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU c 105 " --> pdb=" O LEU c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 130 No H-bonds generated for 'chain 'c' and resid 128 through 130' Processing helix chain 'c' and resid 145 through 155 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 46 through 51 removed outlier: 6.761A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU H 96 " --> pdb=" O MET H 100H" (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET H 100H" --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.773A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.811A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 33 through 36 Processing sheet with id=AA6, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA7, first strand: chain 'L' and resid 62 through 65 Processing sheet with id=AA8, first strand: chain 'B' and resid 14 through 17 removed outlier: 3.711A pdb=" N GLY B 16 " --> pdb=" O GLY b 23 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY b 23 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB1, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.552A pdb=" N LEU B 316 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB3, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.532A pdb=" N LEU B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 53 " --> pdb=" O CYS B 277 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 279 " --> pdb=" O ASP B 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.915A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.605A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 261 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HIS B 117 " --> pdb=" O VAL B 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.605A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 130 through 131 removed outlier: 3.902A pdb=" N ILE B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.502A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.707A pdb=" N LEU B 209 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AC2, first strand: chain 'b' and resid 130 through 133 removed outlier: 3.817A pdb=" N CYS b 137 " --> pdb=" O LEU b 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AC4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.716A pdb=" N GLN A 40 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.501A pdb=" N LEU A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.808A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 115 through 121 removed outlier: 6.440A pdb=" N ILE A 115 " --> pdb=" O LYS A 262A" (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS A 262A" --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N HIS A 117 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 261 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 115 through 121 removed outlier: 6.440A pdb=" N ILE A 115 " --> pdb=" O LYS A 262A" (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS A 262A" --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N HIS A 117 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 261 " --> pdb=" O HIS A 117 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AD3, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.267A pdb=" N ALA A 138 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N ALA A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 166 through 169 Processing sheet with id=AD5, first strand: chain 'A' and resid 281 through 282 removed outlier: 4.020A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 130 through 133 removed outlier: 3.621A pdb=" N CYS a 137 " --> pdb=" O LEU a 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AD8, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AD9, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.681A pdb=" N GLN C 40 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.354A pdb=" N LEU C 51 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N CYS C 279 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 121 removed outlier: 7.801A pdb=" N LEU C 181 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE4, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AE5, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AE6, first strand: chain 'C' and resid 283 through 284 removed outlier: 3.992A pdb=" N CYS C 283 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 290 " --> pdb=" O CYS C 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 296 through 297 458 hydrogen bonds defined for protein. 1239 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: 5.29 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 12833 1.03 - 1.23: 1073 1.23 - 1.44: 5043 1.44 - 1.64: 7630 1.64 - 1.84: 106 Bond restraints: 26685 Sorted by residual: bond pdb=" N GLU C 119 " pdb=" H GLU C 119 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N HIS C 117 " pdb=" H HIS C 117 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" N PHE C 118 " pdb=" H PHE C 118 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" NE2 HIS C 117 " pdb=" HE2 HIS C 117 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" CZ PHE C 118 " pdb=" HZ PHE C 118 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.78e+01 ... (remaining 26680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 44712 1.71 - 3.41: 2894 3.41 - 5.12: 344 5.12 - 6.82: 65 6.82 - 8.53: 14 Bond angle restraints: 48029 Sorted by residual: angle pdb=" N LEU L 46 " pdb=" CA LEU L 46 " pdb=" C LEU L 46 " ideal model delta sigma weight residual 111.28 115.29 -4.01 1.09e+00 8.42e-01 1.35e+01 angle pdb=" C GLU c 165 " pdb=" N ALA c 166 " pdb=" CA ALA c 166 " ideal model delta sigma weight residual 121.70 128.20 -6.50 1.80e+00 3.09e-01 1.30e+01 angle pdb=" CA GLU H 6 " pdb=" CB GLU H 6 " pdb=" CG GLU H 6 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 120.11 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C GLU H 6 " pdb=" CA GLU H 6 " pdb=" CB GLU H 6 " ideal model delta sigma weight residual 109.84 104.68 5.16 1.63e+00 3.76e-01 1.00e+01 ... (remaining 48024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 11879 17.74 - 35.48: 711 35.48 - 53.22: 192 53.22 - 70.96: 57 70.96 - 88.70: 10 Dihedral angle restraints: 12849 sinusoidal: 7025 harmonic: 5824 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -0.34 -85.66 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS c 144 " pdb=" SG CYS c 144 " pdb=" SG CYS c 148 " pdb=" CB CYS c 148 " ideal model delta sinusoidal sigma weight residual 93.00 165.71 -72.71 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.00 -69.00 1 1.00e+01 1.00e-02 6.16e+01 ... (remaining 12846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1357 0.046 - 0.093: 496 0.093 - 0.139: 164 0.139 - 0.186: 30 0.186 - 0.232: 4 Chirality restraints: 2051 Sorted by residual: chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 289 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 297 " pdb=" CA ILE A 297 " pdb=" CG1 ILE A 297 " pdb=" CG2 ILE A 297 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 291 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2048 not shown) Planarity restraints: 4027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 38 " -0.024 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" N GLN H 39 " 0.079 2.00e-02 2.50e+03 pdb=" CA GLN H 39 " -0.020 2.00e-02 2.50e+03 pdb=" H GLN H 39 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL b 100 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C VAL b 100 " 0.066 2.00e-02 2.50e+03 pdb=" O VAL b 100 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU b 101 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " -0.027 2.00e-02 2.50e+03 2.82e-02 9.92e+00 pdb=" C7 NAG A 401 " -0.025 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.011 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " 0.048 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " 0.015 2.00e-02 2.50e+03 ... (remaining 4024 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 3170 2.26 - 2.85: 58883 2.85 - 3.43: 66577 3.43 - 4.02: 94694 4.02 - 4.60: 144247 Nonbonded interactions: 367571 Sorted by model distance: nonbonded pdb=" O GLU a 103 " pdb=" HG1 THR a 107 " model vdw 1.676 2.450 nonbonded pdb=" O ILE C 80 " pdb=" HZ3 LYS C 120 " model vdw 1.691 2.450 nonbonded pdb=" H GLY B 72 " pdb=" OD1 ASN B 150 " model vdw 1.696 2.450 nonbonded pdb=" H ALA A 317 " pdb=" OD1 ASN a 104 " model vdw 1.697 2.450 nonbonded pdb=" HH TYR H 100E" pdb=" OD2 ASP L 34 " model vdw 1.708 2.450 ... (remaining 367566 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' selection = chain 'B' selection = (chain 'C' and (resid 13 through 296 or (resid 297 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 298 through 404)) } ncs_group { reference = (chain 'a' and (resid 2 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 112 through 166)) selection = chain 'b' selection = chain 'c' } 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: 7.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.870 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 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 : 0.006 0.067 13854 Z= 0.250 Angle : 0.981 9.072 18822 Z= 0.516 Chirality : 0.053 0.232 2051 Planarity : 0.007 0.066 2418 Dihedral : 12.362 88.701 5252 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -2.47 (0.18), residues: 1661 helix: -1.12 (0.24), residues: 326 sheet: -1.42 (0.31), residues: 275 loop : -1.94 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 212 TYR 0.030 0.002 TYR C 310 PHE 0.030 0.003 PHE c 9 TRP 0.037 0.002 TRP H 34 HIS 0.013 0.002 HIS L 27D Details of bonding type rmsd covalent geometry : bond 0.00579 (13825) covalent geometry : angle 0.96748 (18752) SS BOND : bond 0.00595 ( 17) SS BOND : angle 2.63847 ( 34) hydrogen bonds : bond 0.18092 ( 436) hydrogen bonds : angle 8.41080 ( 1239) link_NAG-ASN : bond 0.00696 ( 12) link_NAG-ASN : angle 3.00787 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.616 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: 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: 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: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.6887 (mmm) cc_final: 0.6622 (mmm) REVERT: b 39 GLU cc_start: 0.7471 (pt0) cc_final: 0.7139 (mp0) REVERT: a 6 ILE cc_start: 0.6547 (mp) cc_final: 0.6075 (pt) REVERT: a 38 LYS cc_start: 0.6133 (tttp) cc_final: 0.5820 (mmtt) REVERT: a 147 GLU cc_start: 0.7009 (tp30) cc_final: 0.6370 (mm-30) REVERT: C 278 HIS cc_start: 0.7294 (m-70) cc_final: 0.7065 (m-70) REVERT: c 93 THR cc_start: 0.7900 (m) cc_final: 0.7684 (m) outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.2966 time to fit residues: 200.2491 Evaluate side-chains 335 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 114 ASN C 48 ASN C 110 HIS c 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138258 restraints weight = 66623.323| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.25 r_work: 0.3631 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13854 Z= 0.154 Angle : 0.611 6.918 18822 Z= 0.320 Chirality : 0.043 0.196 2051 Planarity : 0.005 0.058 2418 Dihedral : 5.772 52.751 2066 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.36 % Allowed : 10.47 % Favored : 88.17 % 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: -2.05 (0.18), residues: 1661 helix: -0.41 (0.26), residues: 343 sheet: -1.27 (0.30), residues: 283 loop : -1.78 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 114 TYR 0.017 0.002 TYR H 52 PHE 0.017 0.002 PHE a 9 TRP 0.008 0.001 TRP C 155 HIS 0.006 0.001 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.00335 (13825) covalent geometry : angle 0.60063 (18752) SS BOND : bond 0.00447 ( 17) SS BOND : angle 1.65522 ( 34) hydrogen bonds : bond 0.05649 ( 436) hydrogen bonds : angle 6.30230 ( 1239) link_NAG-ASN : bond 0.00404 ( 12) link_NAG-ASN : angle 2.11651 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 334 time to evaluate : 0.784 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: 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: 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: B 159 ASP cc_start: 0.8059 (t70) cc_final: 0.7842 (t70) REVERT: b 39 GLU cc_start: 0.7860 (pt0) cc_final: 0.6967 (mp0) REVERT: b 42 GLN cc_start: 0.8281 (tp40) cc_final: 0.7940 (tp40) REVERT: b 105 GLU cc_start: 0.8013 (tt0) cc_final: 0.7800 (tt0) REVERT: b 161 GLN cc_start: 0.7266 (tm-30) cc_final: 0.7048 (tm-30) REVERT: a 6 ILE cc_start: 0.6250 (mp) cc_final: 0.5402 (pt) REVERT: a 102 MET cc_start: 0.8362 (mtm) cc_final: 0.7548 (mmm) REVERT: a 128 ASP cc_start: 0.7809 (t0) cc_final: 0.7577 (t0) REVERT: a 153 ARG cc_start: 0.8247 (mtm110) cc_final: 0.7940 (mtm-85) REVERT: c 39 GLU cc_start: 0.7225 (mp0) cc_final: 0.6892 (pt0) outliers start: 20 outliers final: 17 residues processed: 348 average time/residue: 0.2932 time to fit residues: 140.5245 Evaluate side-chains 318 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 301 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 279 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 98 optimal weight: 0.0970 chunk 113 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 125 optimal weight: 0.0070 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN ** b 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 114 ASN C 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.147707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133101 restraints weight = 66614.911| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.36 r_work: 0.3560 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13854 Z= 0.167 Angle : 0.582 6.995 18822 Z= 0.306 Chirality : 0.042 0.202 2051 Planarity : 0.005 0.058 2418 Dihedral : 5.495 49.324 2066 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.90 % Allowed : 11.83 % Favored : 86.27 % 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: -1.95 (0.18), residues: 1661 helix: -0.11 (0.26), residues: 337 sheet: -1.18 (0.31), residues: 254 loop : -1.81 (0.16), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 114 TYR 0.016 0.001 TYR a 22 PHE 0.025 0.002 PHE A 118 TRP 0.008 0.001 TRP C 155 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00365 (13825) covalent geometry : angle 0.57218 (18752) SS BOND : bond 0.00435 ( 17) SS BOND : angle 1.34872 ( 34) hydrogen bonds : bond 0.05340 ( 436) hydrogen bonds : angle 5.84974 ( 1239) link_NAG-ASN : bond 0.00406 ( 12) link_NAG-ASN : angle 2.15426 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 0.707 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: 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: symmetry clash REVERT: H 92 CYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6516 (p) REVERT: b 39 GLU cc_start: 0.7922 (pt0) cc_final: 0.6988 (mp0) REVERT: A 17 TYR cc_start: 0.7279 (p90) cc_final: 0.6993 (p90) REVERT: A 159 ASP cc_start: 0.8188 (t0) cc_final: 0.7916 (t0) REVERT: a 6 ILE cc_start: 0.6404 (mp) cc_final: 0.5597 (pt) REVERT: a 102 MET cc_start: 0.8337 (mtm) cc_final: 0.7632 (mmm) REVERT: a 128 ASP cc_start: 0.7937 (t0) cc_final: 0.7668 (t0) REVERT: a 132 GLU cc_start: 0.7895 (tt0) cc_final: 0.7599 (tt0) REVERT: a 153 ARG cc_start: 0.8328 (mtm110) cc_final: 0.8028 (mtm-85) REVERT: C 111 LEU cc_start: 0.7996 (mt) cc_final: 0.7777 (mt) REVERT: C 144 GLN cc_start: 0.7237 (mt0) cc_final: 0.6683 (mm-40) outliers start: 28 outliers final: 22 residues processed: 333 average time/residue: 0.2978 time to fit residues: 137.1328 Evaluate side-chains 312 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 289 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 GLN c 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.128415 restraints weight = 67025.657| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.34 r_work: 0.3495 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13854 Z= 0.208 Angle : 0.603 7.025 18822 Z= 0.319 Chirality : 0.043 0.228 2051 Planarity : 0.004 0.046 2418 Dihedral : 5.575 42.195 2066 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.99 % Allowed : 13.12 % Favored : 83.89 % 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: -1.91 (0.18), residues: 1661 helix: -0.09 (0.26), residues: 337 sheet: -0.78 (0.35), residues: 218 loop : -1.87 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 114 TYR 0.018 0.002 TYR B 105 PHE 0.026 0.002 PHE C 79 TRP 0.010 0.001 TRP b 14 HIS 0.006 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00457 (13825) covalent geometry : angle 0.59282 (18752) SS BOND : bond 0.00489 ( 17) SS BOND : angle 1.57338 ( 34) hydrogen bonds : bond 0.05311 ( 436) hydrogen bonds : angle 5.81061 ( 1239) link_NAG-ASN : bond 0.00399 ( 12) link_NAG-ASN : angle 2.14417 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 0.762 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: 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: H 92 CYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6768 (p) REVERT: b 39 GLU cc_start: 0.7860 (pt0) cc_final: 0.7017 (mp0) REVERT: b 109 ASP cc_start: 0.7121 (m-30) cc_final: 0.6766 (m-30) REVERT: A 17 TYR cc_start: 0.7618 (p90) cc_final: 0.7315 (p90) REVERT: A 159 ASP cc_start: 0.8252 (t0) cc_final: 0.7997 (t0) REVERT: a 42 GLN cc_start: 0.7932 (tp40) cc_final: 0.7635 (tp-100) REVERT: a 102 MET cc_start: 0.8295 (mtm) cc_final: 0.7591 (mmm) REVERT: a 128 ASP cc_start: 0.7964 (t0) cc_final: 0.7683 (t0) REVERT: a 153 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8133 (mtm-85) REVERT: C 144 GLN cc_start: 0.7326 (mt0) cc_final: 0.6801 (mm-40) REVERT: C 294 MET cc_start: 0.8124 (mmm) cc_final: 0.7913 (mmm) outliers start: 44 outliers final: 35 residues processed: 324 average time/residue: 0.2878 time to fit residues: 130.1538 Evaluate side-chains 305 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain b residue 10 ILE Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 128 ASP Chi-restraints excluded: chain b residue 148 CYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 150 GLU Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.5980 chunk 132 optimal weight: 0.3980 chunk 142 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 0.0170 chunk 81 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132219 restraints weight = 66862.568| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.35 r_work: 0.3547 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13854 Z= 0.112 Angle : 0.545 6.883 18822 Z= 0.284 Chirality : 0.042 0.166 2051 Planarity : 0.004 0.074 2418 Dihedral : 5.142 40.016 2066 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.11 % Allowed : 14.48 % Favored : 83.41 % 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: -1.80 (0.19), residues: 1661 helix: 0.13 (0.27), residues: 345 sheet: -1.11 (0.31), residues: 272 loop : -1.76 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 149 TYR 0.025 0.001 TYR C 203 PHE 0.019 0.001 PHE C 79 TRP 0.007 0.001 TRP b 14 HIS 0.004 0.001 HIS a 142 Details of bonding type rmsd covalent geometry : bond 0.00247 (13825) covalent geometry : angle 0.53755 (18752) SS BOND : bond 0.00227 ( 17) SS BOND : angle 1.10235 ( 34) hydrogen bonds : bond 0.04853 ( 436) hydrogen bonds : angle 5.51675 ( 1239) link_NAG-ASN : bond 0.00457 ( 12) link_NAG-ASN : angle 1.92055 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 0.709 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: 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: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (mt) REVERT: b 39 GLU cc_start: 0.7865 (pt0) cc_final: 0.6942 (mp0) REVERT: b 41 THR cc_start: 0.8842 (m) cc_final: 0.8585 (p) REVERT: b 109 ASP cc_start: 0.7166 (m-30) cc_final: 0.6810 (m-30) REVERT: A 17 TYR cc_start: 0.7505 (p90) cc_final: 0.7158 (p90) REVERT: A 159 ASP cc_start: 0.8227 (t0) cc_final: 0.7949 (t0) REVERT: a 6 ILE cc_start: 0.6467 (mp) cc_final: 0.5628 (pt) REVERT: a 42 GLN cc_start: 0.7953 (tp40) cc_final: 0.7728 (tp-100) REVERT: a 102 MET cc_start: 0.8298 (mtm) cc_final: 0.7558 (mmm) REVERT: a 128 ASP cc_start: 0.7960 (t0) cc_final: 0.7686 (t0) REVERT: a 132 GLU cc_start: 0.8051 (tt0) cc_final: 0.7717 (tt0) REVERT: a 147 GLU cc_start: 0.7871 (tp30) cc_final: 0.6683 (mm-30) REVERT: a 153 ARG cc_start: 0.8377 (mtm110) cc_final: 0.8096 (mtm-85) REVERT: C 18 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6086 (p-80) REVERT: C 30 MET cc_start: 0.8803 (mtp) cc_final: 0.8510 (tpp) REVERT: C 144 GLN cc_start: 0.7235 (mt0) cc_final: 0.6744 (mm-40) REVERT: c 83 LYS cc_start: 0.9108 (mmtm) cc_final: 0.8812 (mmtt) outliers start: 31 outliers final: 24 residues processed: 320 average time/residue: 0.2939 time to fit residues: 131.8515 Evaluate side-chains 302 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain b residue 10 ILE Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 89 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 150 GLU Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** b 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** 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 = 0.3726 r_free = 0.3726 target = 0.139796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125524 restraints weight = 67781.328| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.26 r_work: 0.3460 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13854 Z= 0.262 Angle : 0.624 7.245 18822 Z= 0.332 Chirality : 0.043 0.266 2051 Planarity : 0.005 0.050 2418 Dihedral : 5.616 42.271 2066 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.72 % Allowed : 15.77 % Favored : 81.51 % 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: -1.95 (0.19), residues: 1661 helix: 0.15 (0.27), residues: 337 sheet: -0.94 (0.34), residues: 218 loop : -1.96 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 114 TYR 0.024 0.002 TYR C 203 PHE 0.019 0.002 PHE B 118 TRP 0.012 0.002 TRP b 14 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00585 (13825) covalent geometry : angle 0.61575 (18752) SS BOND : bond 0.00458 ( 17) SS BOND : angle 1.23104 ( 34) hydrogen bonds : bond 0.05264 ( 436) hydrogen bonds : angle 5.79195 ( 1239) link_NAG-ASN : bond 0.00424 ( 12) link_NAG-ASN : angle 2.21751 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.691 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: 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: H 37 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8331 (mt) REVERT: b 109 ASP cc_start: 0.7125 (m-30) cc_final: 0.6782 (m-30) REVERT: b 164 GLU cc_start: 0.7099 (tp30) cc_final: 0.6841 (tp30) REVERT: A 17 TYR cc_start: 0.7789 (p90) cc_final: 0.7459 (p90) REVERT: A 159 ASP cc_start: 0.8350 (t0) cc_final: 0.8089 (t0) REVERT: a 42 GLN cc_start: 0.7916 (tp40) cc_final: 0.7710 (tp-100) REVERT: a 102 MET cc_start: 0.8280 (mtm) cc_final: 0.7556 (mmm) REVERT: a 128 ASP cc_start: 0.7905 (t0) cc_final: 0.7591 (t0) REVERT: a 147 GLU cc_start: 0.7965 (tp30) cc_final: 0.6770 (mm-30) REVERT: C 18 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.6285 (p-80) REVERT: C 144 GLN cc_start: 0.7376 (mt0) cc_final: 0.6860 (mm-40) REVERT: c 83 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8770 (mmtt) outliers start: 40 outliers final: 33 residues processed: 299 average time/residue: 0.2944 time to fit residues: 123.2522 Evaluate side-chains 290 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain b residue 10 ILE Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 128 ASP Chi-restraints excluded: chain b residue 148 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 150 GLU Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 290 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 GLN c 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128731 restraints weight = 66841.714| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.30 r_work: 0.3507 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13854 Z= 0.177 Angle : 0.582 7.107 18822 Z= 0.306 Chirality : 0.043 0.222 2051 Planarity : 0.004 0.076 2418 Dihedral : 5.453 39.582 2066 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.65 % Allowed : 16.86 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.90 (0.19), residues: 1661 helix: 0.22 (0.28), residues: 337 sheet: -0.85 (0.35), residues: 215 loop : -1.95 (0.16), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 149 TYR 0.020 0.002 TYR H 52 PHE 0.014 0.002 PHE B 118 TRP 0.010 0.001 TRP b 14 HIS 0.007 0.001 HIS b 142 Details of bonding type rmsd covalent geometry : bond 0.00387 (13825) covalent geometry : angle 0.57272 (18752) SS BOND : bond 0.00286 ( 17) SS BOND : angle 1.55560 ( 34) hydrogen bonds : bond 0.05019 ( 436) hydrogen bonds : angle 5.67251 ( 1239) link_NAG-ASN : bond 0.00411 ( 12) link_NAG-ASN : angle 2.03686 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 272 time to evaluate : 0.719 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: 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: H 37 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8377 (mt) REVERT: b 41 THR cc_start: 0.8924 (m) cc_final: 0.8656 (p) REVERT: b 109 ASP cc_start: 0.7143 (m-30) cc_final: 0.6785 (m-30) REVERT: A 159 ASP cc_start: 0.8367 (t0) cc_final: 0.8147 (t0) REVERT: A 304 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: a 39 GLU cc_start: 0.7473 (pt0) cc_final: 0.7226 (pp20) REVERT: a 42 GLN cc_start: 0.7911 (tp40) cc_final: 0.7664 (tp-100) REVERT: a 102 MET cc_start: 0.8314 (mtm) cc_final: 0.7533 (mmm) REVERT: a 128 ASP cc_start: 0.7892 (t0) cc_final: 0.7554 (t0) REVERT: a 147 GLU cc_start: 0.7938 (tp30) cc_final: 0.6797 (mm-30) REVERT: C 18 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6111 (p-80) REVERT: c 83 LYS cc_start: 0.9086 (mmtm) cc_final: 0.8793 (mmtt) REVERT: c 132 GLU cc_start: 0.7735 (tt0) cc_final: 0.7488 (tt0) outliers start: 39 outliers final: 32 residues processed: 304 average time/residue: 0.3031 time to fit residues: 129.1594 Evaluate side-chains 299 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain b residue 10 ILE Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 148 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 150 GLU Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 46 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131582 restraints weight = 67003.464| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.32 r_work: 0.3545 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13854 Z= 0.117 Angle : 0.554 7.612 18822 Z= 0.288 Chirality : 0.042 0.186 2051 Planarity : 0.005 0.077 2418 Dihedral : 5.153 36.451 2066 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.11 % Allowed : 17.61 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.71 (0.19), residues: 1661 helix: 0.25 (0.27), residues: 345 sheet: -0.63 (0.35), residues: 219 loop : -1.81 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 149 TYR 0.025 0.001 TYR C 203 PHE 0.013 0.001 PHE B 118 TRP 0.008 0.001 TRP b 14 HIS 0.006 0.001 HIS b 142 Details of bonding type rmsd covalent geometry : bond 0.00260 (13825) covalent geometry : angle 0.54422 (18752) SS BOND : bond 0.00273 ( 17) SS BOND : angle 1.59009 ( 34) hydrogen bonds : bond 0.04750 ( 436) hydrogen bonds : angle 5.50074 ( 1239) link_NAG-ASN : bond 0.00448 ( 12) link_NAG-ASN : angle 1.88690 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.655 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: 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: H 100 TYR cc_start: 0.8488 (m-80) cc_final: 0.7925 (m-80) REVERT: L 60 ASP cc_start: 0.8463 (p0) cc_final: 0.8227 (t0) REVERT: b 39 GLU cc_start: 0.7690 (pt0) cc_final: 0.6755 (mp0) REVERT: b 41 THR cc_start: 0.8935 (m) cc_final: 0.8672 (p) REVERT: b 109 ASP cc_start: 0.7131 (m-30) cc_final: 0.6817 (m-30) REVERT: A 17 TYR cc_start: 0.7677 (p90) cc_final: 0.7363 (p90) REVERT: A 159 ASP cc_start: 0.8343 (t0) cc_final: 0.8116 (t0) REVERT: A 304 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: a 102 MET cc_start: 0.8277 (mtm) cc_final: 0.7496 (mmm) REVERT: a 128 ASP cc_start: 0.7903 (t0) cc_final: 0.7609 (t0) REVERT: a 147 GLU cc_start: 0.7858 (tp30) cc_final: 0.6745 (mm-30) REVERT: C 18 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6162 (p-80) REVERT: c 83 LYS cc_start: 0.9054 (mmtm) cc_final: 0.8741 (mmtt) REVERT: c 132 GLU cc_start: 0.7720 (tt0) cc_final: 0.7467 (tt0) outliers start: 31 outliers final: 24 residues processed: 301 average time/residue: 0.2962 time to fit residues: 124.8038 Evaluate side-chains 290 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 264 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain b residue 10 ILE Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 148 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 150 GLU Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 154 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 GLN a 114 ASN c 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.139897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125434 restraints weight = 67990.771| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.32 r_work: 0.3465 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13854 Z= 0.190 Angle : 0.592 9.178 18822 Z= 0.311 Chirality : 0.043 0.230 2051 Planarity : 0.004 0.057 2418 Dihedral : 5.369 40.106 2066 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.24 % Allowed : 17.61 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.85 (0.19), residues: 1661 helix: 0.35 (0.28), residues: 337 sheet: -0.83 (0.35), residues: 221 loop : -1.95 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 153 TYR 0.021 0.002 TYR A 195 PHE 0.021 0.002 PHE B 118 TRP 0.010 0.001 TRP b 14 HIS 0.005 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00423 (13825) covalent geometry : angle 0.58047 (18752) SS BOND : bond 0.00320 ( 17) SS BOND : angle 1.91947 ( 34) hydrogen bonds : bond 0.04925 ( 436) hydrogen bonds : angle 5.60654 ( 1239) link_NAG-ASN : bond 0.00371 ( 12) link_NAG-ASN : angle 2.03362 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.737 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: 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: symmetry clash REVERT: H 100 TYR cc_start: 0.8618 (m-80) cc_final: 0.7763 (m-80) REVERT: L 30 TYR cc_start: 0.8033 (m-10) cc_final: 0.7719 (m-80) REVERT: L 60 ASP cc_start: 0.8684 (p0) cc_final: 0.8216 (t0) REVERT: b 39 GLU cc_start: 0.7602 (pt0) cc_final: 0.6662 (mp0) REVERT: b 41 THR cc_start: 0.8693 (m) cc_final: 0.8377 (p) REVERT: b 109 ASP cc_start: 0.7300 (m-30) cc_final: 0.6996 (m-30) REVERT: A 159 ASP cc_start: 0.8443 (t0) cc_final: 0.8218 (t0) REVERT: A 304 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: a 102 MET cc_start: 0.8280 (mtm) cc_final: 0.7341 (mmm) REVERT: a 128 ASP cc_start: 0.7868 (t0) cc_final: 0.7458 (t0) REVERT: a 147 GLU cc_start: 0.7963 (tp30) cc_final: 0.6878 (mm-30) REVERT: C 18 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.5923 (p-80) REVERT: c 83 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8692 (mmtt) REVERT: c 132 GLU cc_start: 0.7948 (tt0) cc_final: 0.7747 (tt0) outliers start: 33 outliers final: 30 residues processed: 298 average time/residue: 0.3024 time to fit residues: 126.1409 Evaluate side-chains 295 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain b residue 10 ILE Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 148 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 150 GLU Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 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 = 0.3734 r_free = 0.3734 target = 0.139752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125719 restraints weight = 67703.701| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.19 r_work: 0.3483 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13854 Z= 0.177 Angle : 0.586 8.357 18822 Z= 0.308 Chirality : 0.043 0.214 2051 Planarity : 0.005 0.087 2418 Dihedral : 5.368 39.874 2066 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.24 % Allowed : 17.61 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.91 (0.19), residues: 1661 helix: 0.30 (0.28), residues: 337 sheet: -1.08 (0.34), residues: 226 loop : -1.93 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 149 TYR 0.021 0.002 TYR A 195 PHE 0.019 0.002 PHE B 118 TRP 0.010 0.001 TRP b 14 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00389 (13825) covalent geometry : angle 0.57648 (18752) SS BOND : bond 0.00293 ( 17) SS BOND : angle 1.67944 ( 34) hydrogen bonds : bond 0.04883 ( 436) hydrogen bonds : angle 5.60849 ( 1239) link_NAG-ASN : bond 0.00386 ( 12) link_NAG-ASN : angle 1.98178 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 0.765 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: 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: H 100 TYR cc_start: 0.8577 (m-80) cc_final: 0.7770 (m-80) REVERT: L 30 TYR cc_start: 0.7986 (m-10) cc_final: 0.7654 (m-80) REVERT: b 39 GLU cc_start: 0.7606 (pt0) cc_final: 0.6633 (mp0) REVERT: b 41 THR cc_start: 0.8756 (m) cc_final: 0.8456 (p) REVERT: b 109 ASP cc_start: 0.7227 (m-30) cc_final: 0.6888 (m-30) REVERT: A 304 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: a 102 MET cc_start: 0.8306 (mtm) cc_final: 0.7393 (mmm) REVERT: a 128 ASP cc_start: 0.7861 (t0) cc_final: 0.7557 (t0) REVERT: a 147 GLU cc_start: 0.7929 (tp30) cc_final: 0.6848 (mm-30) REVERT: a 161 GLN cc_start: 0.6247 (tp-100) cc_final: 0.5812 (tp-100) REVERT: C 18 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6005 (p-80) REVERT: c 83 LYS cc_start: 0.9039 (mmtm) cc_final: 0.8707 (mmtt) REVERT: c 132 GLU cc_start: 0.7878 (tt0) cc_final: 0.7659 (tt0) outliers start: 33 outliers final: 29 residues processed: 298 average time/residue: 0.3012 time to fit residues: 125.9702 Evaluate side-chains 292 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain b residue 10 ILE Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 148 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 150 GLU Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127122 restraints weight = 67079.305| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.30 r_work: 0.3489 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13854 Z= 0.131 Angle : 0.567 7.437 18822 Z= 0.295 Chirality : 0.042 0.186 2051 Planarity : 0.004 0.074 2418 Dihedral : 5.162 37.445 2066 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.24 % Allowed : 17.61 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.75 (0.19), residues: 1661 helix: 0.45 (0.28), residues: 337 sheet: -0.87 (0.35), residues: 225 loop : -1.86 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 114 TYR 0.019 0.001 TYR A 195 PHE 0.016 0.001 PHE B 118 TRP 0.008 0.001 TRP b 14 HIS 0.004 0.001 HIS b 142 Details of bonding type rmsd covalent geometry : bond 0.00290 (13825) covalent geometry : angle 0.55782 (18752) SS BOND : bond 0.00220 ( 17) SS BOND : angle 1.54409 ( 34) hydrogen bonds : bond 0.04722 ( 436) hydrogen bonds : angle 5.47916 ( 1239) link_NAG-ASN : bond 0.00407 ( 12) link_NAG-ASN : angle 1.89166 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6770.50 seconds wall clock time: 115 minutes 55.01 seconds (6955.01 seconds total)