Starting phenix.real_space_refine on Sun Sep 13 01:50:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nqa_0480/09_2026/6nqa_0480.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nqa_0480/09_2026/6nqa_0480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nqa_0480/09_2026/6nqa_0480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nqa_0480/09_2026/6nqa_0480.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nqa_0480/09_2026/6nqa_0480.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nqa_0480/09_2026/6nqa_0480.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nqa_0480/09_2026/6nqa_0480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nqa_0480/09_2026/6nqa_0480.cif" } resolution = 3.54 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 24 5.16 5 C 8747 2.51 5 N 2825 2.21 5 O 3434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15322 Number of models: 1 Model: "" Number of chains: 13 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2673 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 17, 'TRANS': 310} Chain: "L" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "C" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 Time building chain proxies: 3.22, per 1000 atoms: 0.21 Number of scatterers: 15322 At special positions: 0 Unit cell: (125.552, 126.616, 119.168, 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 24 16.00 P 292 15.00 O 3434 8.00 N 2825 7.00 C 8747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 469.8 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 58.1% alpha, 3.5% beta 135 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.910A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.707A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 75 removed outlier: 4.300A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.527A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.618A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.502A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.216A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.631A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 47 removed outlier: 3.566A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 81 removed outlier: 3.790A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 removed outlier: 3.770A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 4.128A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 48 removed outlier: 3.552A pdb=" N GLU K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 removed outlier: 3.716A pdb=" N LYS K 52 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 90 removed outlier: 4.038A pdb=" N MET K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 119 removed outlier: 4.074A pdb=" N VAL K 119 " --> pdb=" O TYR K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 removed outlier: 3.553A pdb=" N LEU K 125 " --> pdb=" O PRO K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.851A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE K 151 " --> pdb=" O MET K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 177 removed outlier: 3.752A pdb=" N LEU K 171 " --> pdb=" O GLY K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 209 removed outlier: 3.698A pdb=" N ALA K 192 " --> pdb=" O ALA K 188 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR K 194 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 227 No H-bonds generated for 'chain 'K' and resid 225 through 227' Processing helix chain 'K' and resid 228 through 233 Processing helix chain 'K' and resid 247 through 257 removed outlier: 3.941A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 289 removed outlier: 3.940A pdb=" N THR K 289 " --> pdb=" O ASP K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 286 through 289' Processing helix chain 'K' and resid 319 through 328 removed outlier: 3.963A pdb=" N GLU K 323 " --> pdb=" O ARG K 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.507A pdb=" N ASN L 60 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 4.575A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.619A pdb=" N ALA E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 98 removed outlier: 3.559A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 removed outlier: 4.023A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.698A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 removed outlier: 4.484A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.561A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.576A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.626A pdb=" N ILE A 124 " --> pdb=" O NLE A 120 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.609A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.612A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.646A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 removed outlier: 4.208A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 4.176A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.606A pdb=" N LYS C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.953A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.642A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.741A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.985A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.526A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.268A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'K' and resid 217 through 218 removed outlier: 3.778A pdb=" N THR K 217 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY K 184 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL K 160 " --> pdb=" O PHE K 239 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 291 through 294 Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.541A pdb=" N ARG L 42 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.716A pdb=" N ILE D 89 " --> pdb=" O ARG C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 418 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3019 1.33 - 1.45: 4917 1.45 - 1.57: 7648 1.57 - 1.69: 582 1.69 - 1.81: 42 Bond restraints: 16208 Sorted by residual: bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.500 -0.065 1.30e-02 5.92e+03 2.49e+01 bond pdb=" C3' DG J 136 " pdb=" O3' DG J 136 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.34e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C5' DA I 131 " pdb=" C4' DA I 131 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.16e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (remaining 16203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 21174 1.71 - 3.41: 1817 3.41 - 5.12: 124 5.12 - 6.83: 26 6.83 - 8.53: 18 Bond angle restraints: 23159 Sorted by residual: angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 119.70 126.26 -6.56 1.20e+00 6.94e-01 2.99e+01 angle pdb=" O4' DA J 14 " pdb=" C4' DA J 14 " pdb=" C3' DA J 14 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.75e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.82 -2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" O5' DG I 121 " pdb=" C5' DG I 121 " pdb=" C4' DG I 121 " ideal model delta sigma weight residual 109.40 113.28 -3.88 8.00e-01 1.56e+00 2.35e+01 angle pdb=" O5' DA I 131 " pdb=" C5' DA I 131 " pdb=" C4' DA I 131 " ideal model delta sigma weight residual 109.40 113.19 -3.79 8.00e-01 1.56e+00 2.25e+01 ... (remaining 23154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 7506 33.91 - 67.82: 1464 67.82 - 101.73: 21 101.73 - 135.64: 1 135.64 - 169.55: 3 Dihedral angle restraints: 8995 sinusoidal: 5599 harmonic: 3396 Sorted by residual: dihedral pdb=" CA ASP K 62 " pdb=" C ASP K 62 " pdb=" N TYR K 63 " pdb=" CA TYR K 63 " ideal model delta harmonic sigma weight residual 180.00 -148.04 -31.96 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA TYR K 312 " pdb=" C TYR K 312 " pdb=" N TYR K 313 " pdb=" CA TYR K 313 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLN E 85 " pdb=" C GLN E 85 " pdb=" N SER E 86 " pdb=" CA SER E 86 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2021 0.063 - 0.127: 527 0.127 - 0.190: 61 0.190 - 0.253: 12 0.253 - 0.317: 1 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CB ILE H 89 " pdb=" CA ILE H 89 " pdb=" CG1 ILE H 89 " pdb=" CG2 ILE H 89 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE K 279 " pdb=" CA ILE K 279 " pdb=" CG1 ILE K 279 " pdb=" CG2 ILE K 279 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TYR K 312 " pdb=" N TYR K 312 " pdb=" C TYR K 312 " pdb=" CB TYR K 312 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2619 not shown) Planarity restraints: 1924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO A 66 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 190 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO K 191 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO K 191 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 191 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 132 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO K 133 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO K 133 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 133 " -0.034 5.00e-02 4.00e+02 ... (remaining 1921 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3631 2.81 - 3.33: 12598 3.33 - 3.85: 28011 3.85 - 4.38: 30323 4.38 - 4.90: 44412 Nonbonded interactions: 118975 Sorted by model distance: nonbonded pdb=" O SER D 91 " pdb=" OG SER D 91 " model vdw 2.283 3.040 nonbonded pdb=" O SER H 91 " pdb=" OG SER H 91 " model vdw 2.291 3.040 nonbonded pdb=" OP1 DG I 122 " pdb=" OH TYR H 40 " model vdw 2.299 3.040 nonbonded pdb=" O SER D 123 " pdb=" OG SER D 123 " model vdw 2.317 3.040 nonbonded pdb=" OD1 ASP K 199 " pdb=" OH TYR K 216 " model vdw 2.342 3.040 ... (remaining 118970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 124) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.008 0.076 16208 Z= 0.605 Angle : 0.981 8.533 23159 Z= 0.753 Chirality : 0.056 0.317 2622 Planarity : 0.007 0.075 1924 Dihedral : 25.498 169.552 6799 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.40 % Allowed : 10.10 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.04 (0.19), residues: 1126 helix: -2.61 (0.15), residues: 599 sheet: -2.24 (0.55), residues: 70 loop : -2.66 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 72 TYR 0.025 0.002 TYR K 312 PHE 0.021 0.003 PHE K 223 TRP 0.017 0.002 TRP K 305 HIS 0.010 0.002 HIS K 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.60 (16208) covalent geometry : angle 0.98076 / 0.75 (23159) hydrogen bonds : bond 0.14078 / 14.97 ( 768) hydrogen bonds : angle 5.06222 / 6.77 ( 1924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 322 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: F 74 GLU cc_start: 0.7162 (tt0) cc_final: 0.6701 (tt0) REVERT: F 91 LYS cc_start: 0.8355 (tttt) cc_final: 0.8047 (ttpp) REVERT: G 15 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7266 (tttt) REVERT: G 73 ASN cc_start: 0.8440 (t0) cc_final: 0.8056 (t0) REVERT: G 110 ASN cc_start: 0.7994 (t0) cc_final: 0.7448 (p0) REVERT: H 71 GLU cc_start: 0.7633 (tp30) cc_final: 0.7293 (tt0) REVERT: K 30 HIS cc_start: 0.2938 (p90) cc_final: 0.2637 (m170) REVERT: K 35 HIS cc_start: 0.7107 (m-70) cc_final: 0.6708 (m90) REVERT: K 96 MET cc_start: 0.3457 (ppp) cc_final: 0.1290 (mtp) REVERT: K 147 MET cc_start: 0.7385 (tpp) cc_final: 0.7020 (tmm) REVERT: K 208 TRP cc_start: 0.8677 (t60) cc_final: 0.8269 (t60) REVERT: K 311 SER cc_start: 0.8179 (p) cc_final: 0.7691 (m) REVERT: L 27 LYS cc_start: 0.7287 (mttt) cc_final: 0.6861 (mttm) REVERT: E 41 TYR cc_start: 0.8533 (m-80) cc_final: 0.8187 (m-80) REVERT: E 123 ASP cc_start: 0.7818 (m-30) cc_final: 0.7241 (m-30) REVERT: A 42 ARG cc_start: 0.7564 (mtp180) cc_final: 0.7290 (mtp85) REVERT: A 123 ASP cc_start: 0.8648 (m-30) cc_final: 0.8436 (m-30) REVERT: D 43 LYS cc_start: 0.8581 (mttt) cc_final: 0.8220 (ttmm) REVERT: D 59 MET cc_start: 0.8414 (tpp) cc_final: 0.7721 (tpt) REVERT: D 71 GLU cc_start: 0.7539 (tp30) cc_final: 0.7002 (tt0) REVERT: C 36 LYS cc_start: 0.8534 (mttt) cc_final: 0.8268 (pptt) REVERT: C 61 GLU cc_start: 0.8282 (tp30) cc_final: 0.7915 (tp30) REVERT: C 68 ASN cc_start: 0.8125 (t0) cc_final: 0.7733 (m-40) REVERT: C 73 ASN cc_start: 0.8356 (t0) cc_final: 0.7811 (t0) REVERT: B 35 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7821 (ttm-80) REVERT: B 64 ASN cc_start: 0.8235 (t0) cc_final: 0.7908 (m-40) outliers start: 4 outliers final: 1 residues processed: 324 average time/residue: 0.1904 time to fit residues: 80.7176 Evaluate side-chains 195 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN G 38 ASN G 112 GLN K 35 HIS K 181 HIS E 93 GLN A 68 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN C 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105606 restraints weight = 21696.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106755 restraints weight = 17337.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106704 restraints weight = 14360.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107295 restraints weight = 13534.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107332 restraints weight = 12455.087| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16208 Z= 0.181 Angle : 0.667 6.630 23159 Z= 0.392 Chirality : 0.046 0.316 2622 Planarity : 0.005 0.046 1924 Dihedral : 28.540 171.002 4492 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.53 % Allowed : 16.77 % Favored : 80.71 % 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: -2.31 (0.23), residues: 1126 helix: -0.85 (0.19), residues: 629 sheet: -1.86 (0.56), residues: 73 loop : -2.39 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 278 TYR 0.013 0.002 TYR G 57 PHE 0.020 0.002 PHE K 159 TRP 0.011 0.001 TRP K 22 HIS 0.009 0.001 HIS K 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (16208) covalent geometry : angle 0.66689 / 0.39 (23159) hydrogen bonds : bond 0.06096 / 6.72 ( 768) hydrogen bonds : angle 3.26676 / 4.35 ( 1924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 74 GLU cc_start: 0.7047 (tt0) cc_final: 0.6756 (tt0) REVERT: G 15 LYS cc_start: 0.7839 (ttpp) cc_final: 0.7434 (tttt) REVERT: G 73 ASN cc_start: 0.8257 (t0) cc_final: 0.7726 (t0) REVERT: H 34 LYS cc_start: 0.7756 (mmtp) cc_final: 0.7367 (mmtm) REVERT: K 96 MET cc_start: 0.3168 (ppp) cc_final: 0.1412 (mmm) REVERT: K 147 MET cc_start: 0.7546 (tpp) cc_final: 0.6963 (tmm) REVERT: K 208 TRP cc_start: 0.8346 (t60) cc_final: 0.8137 (t60) REVERT: K 248 GLU cc_start: 0.8720 (tp30) cc_final: 0.8332 (mm-30) REVERT: L 27 LYS cc_start: 0.7508 (mttt) cc_final: 0.7236 (mttm) REVERT: E 41 TYR cc_start: 0.8648 (m-80) cc_final: 0.8308 (m-80) REVERT: E 56 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7765 (mttt) REVERT: E 123 ASP cc_start: 0.8110 (m-30) cc_final: 0.7276 (m-30) REVERT: D 35 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8011 (mt-10) REVERT: D 43 LYS cc_start: 0.8621 (mttt) cc_final: 0.8402 (ttmm) REVERT: D 59 MET cc_start: 0.8545 (tpp) cc_final: 0.7884 (tpt) REVERT: D 71 GLU cc_start: 0.7588 (tp30) cc_final: 0.7271 (tt0) REVERT: C 61 GLU cc_start: 0.8326 (tp30) cc_final: 0.7949 (tp30) REVERT: C 68 ASN cc_start: 0.8452 (t0) cc_final: 0.8055 (m-40) REVERT: C 73 ASN cc_start: 0.8254 (t0) cc_final: 0.7828 (t0) REVERT: B 35 ARG cc_start: 0.8291 (ttm-80) cc_final: 0.8009 (ttm-80) REVERT: B 64 ASN cc_start: 0.8423 (t0) cc_final: 0.8081 (m-40) outliers start: 25 outliers final: 14 residues processed: 217 average time/residue: 0.1470 time to fit residues: 43.7133 Evaluate side-chains 199 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 81 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 5 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.0170 chunk 133 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN H 47 GLN K 30 HIS K 109 HIS A 125 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.155409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106087 restraints weight = 21775.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108915 restraints weight = 17303.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109023 restraints weight = 11589.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109338 restraints weight = 10440.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109512 restraints weight = 9844.349| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16208 Z= 0.135 Angle : 0.583 6.203 23159 Z= 0.348 Chirality : 0.042 0.312 2622 Planarity : 0.004 0.043 1924 Dihedral : 28.530 169.751 4491 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.22 % Allowed : 18.38 % Favored : 79.39 % 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: -1.13 (0.24), residues: 1126 helix: 0.16 (0.20), residues: 630 sheet: -1.41 (0.58), residues: 73 loop : -1.97 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 99 TYR 0.015 0.001 TYR C 57 PHE 0.013 0.001 PHE K 159 TRP 0.012 0.001 TRP K 22 HIS 0.018 0.001 HIS K 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (16208) covalent geometry : angle 0.58341 / 0.35 (23159) hydrogen bonds : bond 0.04753 / 5.18 ( 768) hydrogen bonds : angle 2.84191 / 3.75 ( 1924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 74 GLU cc_start: 0.7123 (tt0) cc_final: 0.6839 (tt0) REVERT: G 15 LYS cc_start: 0.7923 (ttpp) cc_final: 0.7370 (tttt) REVERT: G 73 ASN cc_start: 0.8262 (t0) cc_final: 0.7648 (t0) REVERT: H 34 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7524 (mmtm) REVERT: H 99 ARG cc_start: 0.8216 (mtp180) cc_final: 0.7866 (mtm180) REVERT: K 96 MET cc_start: 0.3110 (ppp) cc_final: 0.1534 (mmm) REVERT: K 147 MET cc_start: 0.7390 (tpp) cc_final: 0.6991 (tmm) REVERT: K 216 TYR cc_start: 0.8272 (p90) cc_final: 0.7957 (p90) REVERT: K 248 GLU cc_start: 0.8648 (tp30) cc_final: 0.8353 (mm-30) REVERT: L 72 ARG cc_start: 0.7364 (ttp80) cc_final: 0.6947 (ptt-90) REVERT: E 41 TYR cc_start: 0.8710 (m-80) cc_final: 0.8432 (m-80) REVERT: E 56 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7698 (mttt) REVERT: E 123 ASP cc_start: 0.8119 (m-30) cc_final: 0.7372 (m-30) REVERT: A 42 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7894 (mtp-110) REVERT: D 59 MET cc_start: 0.8414 (tpp) cc_final: 0.7768 (tpt) REVERT: D 71 GLU cc_start: 0.7649 (tp30) cc_final: 0.7183 (tt0) REVERT: D 116 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8322 (pttp) REVERT: C 61 GLU cc_start: 0.8237 (tp30) cc_final: 0.7899 (tp30) REVERT: C 68 ASN cc_start: 0.8402 (t0) cc_final: 0.8041 (m-40) REVERT: C 73 ASN cc_start: 0.8173 (t0) cc_final: 0.7756 (t0) REVERT: C 92 GLU cc_start: 0.7726 (tp30) cc_final: 0.7510 (tp30) REVERT: B 35 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7901 (ttm-80) REVERT: B 64 ASN cc_start: 0.8336 (t0) cc_final: 0.8020 (m-40) outliers start: 22 outliers final: 9 residues processed: 211 average time/residue: 0.1555 time to fit residues: 45.3896 Evaluate side-chains 191 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 120 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 40.0000 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 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 = 0.3899 r_free = 0.3899 target = 0.152722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103756 restraints weight = 21781.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105539 restraints weight = 17914.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105338 restraints weight = 13923.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105920 restraints weight = 12692.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105949 restraints weight = 11883.993| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16208 Z= 0.153 Angle : 0.590 5.983 23159 Z= 0.345 Chirality : 0.042 0.316 2622 Planarity : 0.004 0.040 1924 Dihedral : 28.604 170.423 4491 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.33 % Allowed : 17.27 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1126 helix: 0.60 (0.21), residues: 629 sheet: -0.74 (0.63), residues: 64 loop : -1.84 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.015 0.001 TYR K 63 PHE 0.017 0.002 PHE K 68 TRP 0.026 0.002 TRP K 208 HIS 0.003 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (16208) covalent geometry : angle 0.59047 / 0.34 (23159) hydrogen bonds : bond 0.04789 / 5.30 ( 768) hydrogen bonds : angle 2.81857 / 3.71 ( 1924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8741 (t0) cc_final: 0.8435 (t0) REVERT: G 73 ASN cc_start: 0.8328 (t0) cc_final: 0.7537 (t0) REVERT: G 85 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8960 (mp) REVERT: H 34 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7676 (mmtm) REVERT: H 99 ARG cc_start: 0.8316 (mtp180) cc_final: 0.8063 (mtp180) REVERT: K 35 HIS cc_start: 0.6940 (m90) cc_final: 0.6247 (m-70) REVERT: K 96 MET cc_start: 0.3108 (ppp) cc_final: 0.1588 (mmm) REVERT: K 147 MET cc_start: 0.7523 (tpp) cc_final: 0.7286 (tmm) REVERT: K 208 TRP cc_start: 0.8077 (t60) cc_final: 0.7387 (t60) REVERT: L 72 ARG cc_start: 0.7197 (ttp80) cc_final: 0.6991 (ptp90) REVERT: E 41 TYR cc_start: 0.8867 (m-80) cc_final: 0.8647 (m-80) REVERT: E 56 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7702 (mttt) REVERT: E 123 ASP cc_start: 0.8337 (m-30) cc_final: 0.7407 (m-30) REVERT: D 43 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8247 (mtpt) REVERT: D 59 MET cc_start: 0.8549 (tpp) cc_final: 0.7894 (tpt) REVERT: D 71 GLU cc_start: 0.7509 (tp30) cc_final: 0.7214 (tt0) REVERT: D 116 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8314 (pttp) REVERT: C 61 GLU cc_start: 0.8261 (tp30) cc_final: 0.7865 (tp30) REVERT: C 68 ASN cc_start: 0.8470 (t0) cc_final: 0.8068 (m-40) REVERT: C 73 ASN cc_start: 0.8244 (t0) cc_final: 0.7789 (t0) REVERT: B 35 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7915 (ttm-80) REVERT: B 64 ASN cc_start: 0.8488 (t0) cc_final: 0.8196 (m-40) outliers start: 33 outliers final: 26 residues processed: 219 average time/residue: 0.1506 time to fit residues: 46.0049 Evaluate side-chains 210 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 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 = 0.3902 r_free = 0.3902 target = 0.153134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103092 restraints weight = 21678.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105736 restraints weight = 16672.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106119 restraints weight = 10576.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106266 restraints weight = 10331.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106517 restraints weight = 9486.808| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16208 Z= 0.133 Angle : 0.556 6.064 23159 Z= 0.329 Chirality : 0.040 0.318 2622 Planarity : 0.004 0.037 1924 Dihedral : 28.562 169.704 4491 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.42 % Allowed : 19.29 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1126 helix: 0.96 (0.21), residues: 633 sheet: -0.41 (0.65), residues: 64 loop : -1.57 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.013 0.001 TYR C 57 PHE 0.009 0.001 PHE K 159 TRP 0.015 0.002 TRP K 208 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (16208) covalent geometry : angle 0.55577 / 0.33 (23159) hydrogen bonds : bond 0.04303 / 4.73 ( 768) hydrogen bonds : angle 2.70501 / 3.57 ( 1924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.435 Fit side-chains REVERT: F 25 ASN cc_start: 0.8601 (t0) cc_final: 0.8020 (t0) REVERT: G 73 ASN cc_start: 0.8320 (t0) cc_final: 0.7557 (t0) REVERT: G 85 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.9009 (mp) REVERT: H 99 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7987 (mtp180) REVERT: K 35 HIS cc_start: 0.7071 (m90) cc_final: 0.6276 (m-70) REVERT: K 55 MET cc_start: 0.7253 (tpp) cc_final: 0.6662 (tmm) REVERT: K 96 MET cc_start: 0.3064 (ppp) cc_final: 0.1694 (mmm) REVERT: K 147 MET cc_start: 0.7395 (tpp) cc_final: 0.7080 (tmm) REVERT: K 208 TRP cc_start: 0.8187 (t60) cc_final: 0.7548 (t60) REVERT: E 56 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7703 (mttt) REVERT: E 123 ASP cc_start: 0.8351 (m-30) cc_final: 0.7451 (m-30) REVERT: E 125 GLN cc_start: 0.8803 (mt0) cc_final: 0.8549 (mt0) REVERT: A 42 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7594 (mtp85) REVERT: D 40 TYR cc_start: 0.8426 (m-80) cc_final: 0.8193 (m-80) REVERT: D 59 MET cc_start: 0.8370 (tpp) cc_final: 0.7915 (tpt) REVERT: D 99 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8186 (ttp-170) REVERT: D 116 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8346 (pttp) REVERT: C 36 LYS cc_start: 0.8367 (pttp) cc_final: 0.8128 (pptt) REVERT: C 61 GLU cc_start: 0.8248 (tp30) cc_final: 0.7877 (tp30) REVERT: C 68 ASN cc_start: 0.8402 (t0) cc_final: 0.8047 (m-40) REVERT: C 73 ASN cc_start: 0.8297 (t0) cc_final: 0.7812 (t0) REVERT: C 84 GLN cc_start: 0.8656 (tp40) cc_final: 0.7928 (tt0) REVERT: B 35 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.7920 (ttm-80) REVERT: B 64 ASN cc_start: 0.8537 (t0) cc_final: 0.8202 (m-40) outliers start: 24 outliers final: 18 residues processed: 213 average time/residue: 0.1399 time to fit residues: 41.5075 Evaluate side-chains 208 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** 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 = 0.3879 r_free = 0.3879 target = 0.151209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102314 restraints weight = 21590.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102906 restraints weight = 17336.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103651 restraints weight = 13963.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103900 restraints weight = 14634.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103948 restraints weight = 12857.919| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16208 Z= 0.159 Angle : 0.588 5.931 23159 Z= 0.338 Chirality : 0.042 0.318 2622 Planarity : 0.004 0.045 1924 Dihedral : 28.683 170.373 4491 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.23 % Allowed : 19.49 % Favored : 77.27 % 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: -0.04 (0.26), residues: 1126 helix: 0.98 (0.21), residues: 638 sheet: -0.34 (0.68), residues: 64 loop : -1.53 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 86 TYR 0.013 0.001 TYR C 57 PHE 0.018 0.002 PHE K 68 TRP 0.015 0.002 TRP K 22 HIS 0.004 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (16208) covalent geometry : angle 0.58833 / 0.34 (23159) hydrogen bonds : bond 0.04670 / 5.14 ( 768) hydrogen bonds : angle 2.76287 / 3.65 ( 1924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.466 Fit side-chains REVERT: F 25 ASN cc_start: 0.8759 (t0) cc_final: 0.8257 (t0) REVERT: G 85 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8935 (mp) REVERT: K 35 HIS cc_start: 0.6922 (m90) cc_final: 0.6180 (m-70) REVERT: K 55 MET cc_start: 0.7104 (tpp) cc_final: 0.6682 (tmm) REVERT: K 96 MET cc_start: 0.3008 (ppp) cc_final: 0.1677 (mmm) REVERT: K 147 MET cc_start: 0.7619 (tpp) cc_final: 0.7332 (ttp) REVERT: K 208 TRP cc_start: 0.8056 (t60) cc_final: 0.7420 (t60) REVERT: K 311 SER cc_start: 0.8176 (p) cc_final: 0.7734 (m) REVERT: E 56 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7703 (mttt) REVERT: E 123 ASP cc_start: 0.8398 (m-30) cc_final: 0.7452 (m-30) REVERT: E 125 GLN cc_start: 0.8837 (mt0) cc_final: 0.8633 (mt0) REVERT: A 42 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7642 (mtp85) REVERT: D 40 TYR cc_start: 0.8435 (m-80) cc_final: 0.8165 (m-80) REVERT: D 59 MET cc_start: 0.8366 (tpp) cc_final: 0.7829 (tpt) REVERT: D 99 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8203 (ttp-170) REVERT: D 116 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8379 (pttp) REVERT: C 61 GLU cc_start: 0.8263 (tp30) cc_final: 0.7883 (tp30) REVERT: C 68 ASN cc_start: 0.8507 (t0) cc_final: 0.8115 (m-40) REVERT: C 73 ASN cc_start: 0.8313 (t0) cc_final: 0.7879 (t0) REVERT: C 91 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 35 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7897 (ttm-80) REVERT: B 64 ASN cc_start: 0.8569 (t0) cc_final: 0.8195 (m-40) outliers start: 32 outliers final: 27 residues processed: 212 average time/residue: 0.1563 time to fit residues: 46.3483 Evaluate side-chains 204 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** 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 = 0.3883 r_free = 0.3883 target = 0.151565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100966 restraints weight = 21376.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104473 restraints weight = 16000.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104167 restraints weight = 10982.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104460 restraints weight = 9659.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104612 restraints weight = 8942.758| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16208 Z= 0.143 Angle : 0.563 5.945 23159 Z= 0.327 Chirality : 0.041 0.320 2622 Planarity : 0.004 0.036 1924 Dihedral : 28.685 169.715 4491 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.64 % Allowed : 19.29 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1126 helix: 1.11 (0.21), residues: 639 sheet: -0.29 (0.69), residues: 64 loop : -1.43 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.012 0.001 TYR C 57 PHE 0.010 0.001 PHE E 84 TRP 0.012 0.002 TRP K 22 HIS 0.004 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (16208) covalent geometry : angle 0.56304 / 0.33 (23159) hydrogen bonds : bond 0.04335 / 4.73 ( 768) hydrogen bonds : angle 2.69970 / 3.53 ( 1924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.384 Fit side-chains REVERT: F 25 ASN cc_start: 0.8658 (t0) cc_final: 0.8061 (t0) REVERT: F 74 GLU cc_start: 0.7307 (tt0) cc_final: 0.6916 (tt0) REVERT: G 85 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8953 (mp) REVERT: K 35 HIS cc_start: 0.7071 (m90) cc_final: 0.6250 (m-70) REVERT: K 55 MET cc_start: 0.7186 (tpp) cc_final: 0.6660 (tmm) REVERT: K 96 MET cc_start: 0.3080 (ppp) cc_final: 0.1720 (mmm) REVERT: K 147 MET cc_start: 0.7584 (tpp) cc_final: 0.7296 (ttp) REVERT: K 208 TRP cc_start: 0.8160 (t60) cc_final: 0.7536 (t60) REVERT: K 311 SER cc_start: 0.8120 (p) cc_final: 0.7732 (m) REVERT: E 56 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7648 (mttt) REVERT: E 123 ASP cc_start: 0.8427 (m-30) cc_final: 0.7492 (m-30) REVERT: A 42 ARG cc_start: 0.8030 (mtp180) cc_final: 0.7581 (mtp85) REVERT: D 40 TYR cc_start: 0.8462 (m-80) cc_final: 0.8134 (m-80) REVERT: D 59 MET cc_start: 0.8417 (tpp) cc_final: 0.7900 (tpt) REVERT: D 99 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8243 (ttp-170) REVERT: D 116 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8388 (pttp) REVERT: C 61 GLU cc_start: 0.8248 (tp30) cc_final: 0.7847 (tp30) REVERT: C 68 ASN cc_start: 0.8447 (t0) cc_final: 0.8068 (m-40) REVERT: C 73 ASN cc_start: 0.8359 (t0) cc_final: 0.7914 (t0) REVERT: C 84 GLN cc_start: 0.8794 (tp40) cc_final: 0.8120 (tt0) REVERT: C 91 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 35 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7878 (ttm-80) REVERT: B 64 ASN cc_start: 0.8586 (t0) cc_final: 0.8161 (m-40) outliers start: 36 outliers final: 27 residues processed: 210 average time/residue: 0.1458 time to fit residues: 43.3336 Evaluate side-chains 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 69 optimal weight: 0.0770 chunk 91 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 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 = 0.3884 r_free = 0.3884 target = 0.151744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100655 restraints weight = 21607.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103599 restraints weight = 14557.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103762 restraints weight = 9874.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103872 restraints weight = 9158.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104029 restraints weight = 8986.926| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16208 Z= 0.138 Angle : 0.565 6.787 23159 Z= 0.327 Chirality : 0.041 0.319 2622 Planarity : 0.004 0.041 1924 Dihedral : 28.709 169.593 4491 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.23 % Allowed : 19.49 % Favored : 77.27 % 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: 0.26 (0.26), residues: 1126 helix: 1.22 (0.21), residues: 634 sheet: -0.22 (0.69), residues: 64 loop : -1.35 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 23 TYR 0.011 0.001 TYR K 63 PHE 0.022 0.001 PHE K 68 TRP 0.012 0.002 TRP K 22 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (16208) covalent geometry : angle 0.56543 / 0.33 (23159) hydrogen bonds : bond 0.04241 / 4.64 ( 768) hydrogen bonds : angle 2.68308 / 3.52 ( 1924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.535 Fit side-chains REVERT: F 25 ASN cc_start: 0.8601 (t0) cc_final: 0.8026 (t0) REVERT: G 85 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8947 (mp) REVERT: K 35 HIS cc_start: 0.7093 (m90) cc_final: 0.6304 (m-70) REVERT: K 55 MET cc_start: 0.7282 (tpp) cc_final: 0.6668 (tmm) REVERT: K 96 MET cc_start: 0.3020 (ppp) cc_final: 0.1732 (mmm) REVERT: K 147 MET cc_start: 0.7525 (tpp) cc_final: 0.7265 (ttp) REVERT: K 208 TRP cc_start: 0.8150 (t60) cc_final: 0.7564 (t60) REVERT: E 56 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7664 (mttt) REVERT: E 123 ASP cc_start: 0.8309 (m-30) cc_final: 0.7400 (m-30) REVERT: A 42 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7584 (mtp85) REVERT: D 40 TYR cc_start: 0.8462 (m-80) cc_final: 0.8145 (m-80) REVERT: D 59 MET cc_start: 0.8433 (tpp) cc_final: 0.7907 (tpt) REVERT: D 99 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8235 (ttp-170) REVERT: C 61 GLU cc_start: 0.8232 (tp30) cc_final: 0.7840 (tp30) REVERT: C 68 ASN cc_start: 0.8467 (t0) cc_final: 0.8066 (m-40) REVERT: C 73 ASN cc_start: 0.8324 (t0) cc_final: 0.7926 (t0) REVERT: C 84 GLN cc_start: 0.8820 (tp40) cc_final: 0.8123 (tt0) REVERT: C 91 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7952 (tm-30) REVERT: B 35 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7878 (ttm-80) REVERT: B 64 ASN cc_start: 0.8563 (t0) cc_final: 0.8135 (m-40) outliers start: 32 outliers final: 30 residues processed: 194 average time/residue: 0.1505 time to fit residues: 41.0895 Evaluate side-chains 195 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 136 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** 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 = 0.3876 r_free = 0.3876 target = 0.151000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101123 restraints weight = 21515.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102995 restraints weight = 17148.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102969 restraints weight = 12922.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103470 restraints weight = 12493.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103479 restraints weight = 11081.078| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16208 Z= 0.151 Angle : 0.577 5.954 23159 Z= 0.331 Chirality : 0.041 0.320 2622 Planarity : 0.004 0.037 1924 Dihedral : 28.801 169.406 4491 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.54 % Allowed : 19.19 % Favored : 77.27 % 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: 0.36 (0.26), residues: 1126 helix: 1.25 (0.21), residues: 634 sheet: -0.21 (0.69), residues: 64 loop : -1.22 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.016 0.001 TYR D 83 PHE 0.015 0.002 PHE K 68 TRP 0.013 0.002 TRP K 208 HIS 0.004 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (16208) covalent geometry : angle 0.57709 / 0.33 (23159) hydrogen bonds : bond 0.04363 / 4.76 ( 768) hydrogen bonds : angle 2.72679 / 3.57 ( 1924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.454 Fit side-chains REVERT: F 25 ASN cc_start: 0.8712 (t0) cc_final: 0.8080 (t0) REVERT: F 45 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7367 (mtm180) REVERT: F 74 GLU cc_start: 0.7071 (tt0) cc_final: 0.6557 (tt0) REVERT: K 35 HIS cc_start: 0.7082 (m90) cc_final: 0.6343 (m-70) REVERT: K 55 MET cc_start: 0.7232 (tpp) cc_final: 0.6917 (tpt) REVERT: K 96 MET cc_start: 0.2852 (ppp) cc_final: 0.1689 (mmm) REVERT: K 147 MET cc_start: 0.7598 (tpp) cc_final: 0.7388 (ttp) REVERT: E 56 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7689 (mttt) REVERT: E 123 ASP cc_start: 0.8319 (m-30) cc_final: 0.7378 (m-30) REVERT: A 42 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7649 (mtp85) REVERT: D 40 TYR cc_start: 0.8452 (m-80) cc_final: 0.8144 (m-80) REVERT: D 59 MET cc_start: 0.8376 (tpp) cc_final: 0.7829 (tpt) REVERT: D 86 ARG cc_start: 0.7691 (mtt90) cc_final: 0.7457 (mtt90) REVERT: D 99 ARG cc_start: 0.8655 (ttm-80) cc_final: 0.8235 (ttp-170) REVERT: C 61 GLU cc_start: 0.8232 (tp30) cc_final: 0.7838 (tp30) REVERT: C 68 ASN cc_start: 0.8514 (t0) cc_final: 0.8087 (m-40) REVERT: C 73 ASN cc_start: 0.8360 (t0) cc_final: 0.8027 (t0) REVERT: C 91 GLU cc_start: 0.8275 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 35 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7868 (ttm-80) REVERT: B 64 ASN cc_start: 0.8590 (t0) cc_final: 0.8231 (m-40) outliers start: 35 outliers final: 33 residues processed: 198 average time/residue: 0.1628 time to fit residues: 44.9264 Evaluate side-chains 198 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 34 optimal weight: 0.0980 chunk 87 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 129 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 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 = 0.3896 r_free = 0.3896 target = 0.152743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102641 restraints weight = 21504.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105234 restraints weight = 16809.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105375 restraints weight = 11070.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105604 restraints weight = 10755.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105987 restraints weight = 9502.923| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16208 Z= 0.124 Angle : 0.548 6.896 23159 Z= 0.319 Chirality : 0.040 0.319 2622 Planarity : 0.004 0.037 1924 Dihedral : 28.725 168.502 4491 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.93 % Allowed : 19.80 % Favored : 77.27 % 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: 0.58 (0.26), residues: 1126 helix: 1.40 (0.21), residues: 640 sheet: -0.15 (0.69), residues: 64 loop : -1.11 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 23 TYR 0.024 0.001 TYR K 78 PHE 0.022 0.001 PHE K 68 TRP 0.036 0.002 TRP K 208 HIS 0.004 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (16208) covalent geometry : angle 0.54765 / 0.32 (23159) hydrogen bonds : bond 0.03892 / 4.26 ( 768) hydrogen bonds : angle 2.62363 / 3.43 ( 1924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.445 Fit side-chains REVERT: F 25 ASN cc_start: 0.8522 (t0) cc_final: 0.7862 (t0) REVERT: K 35 HIS cc_start: 0.7037 (m90) cc_final: 0.6268 (m-70) REVERT: K 55 MET cc_start: 0.7221 (tpp) cc_final: 0.6921 (tpt) REVERT: K 96 MET cc_start: 0.2906 (ppp) cc_final: 0.1803 (mmm) REVERT: K 147 MET cc_start: 0.7511 (tpp) cc_final: 0.7132 (ttp) REVERT: E 56 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7672 (mttt) REVERT: E 123 ASP cc_start: 0.8248 (m-30) cc_final: 0.7898 (m-30) REVERT: A 42 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7583 (mtp85) REVERT: D 40 TYR cc_start: 0.8440 (m-80) cc_final: 0.8079 (m-80) REVERT: D 54 ILE cc_start: 0.8740 (pt) cc_final: 0.8078 (pt) REVERT: D 59 MET cc_start: 0.8287 (tpp) cc_final: 0.7745 (tpt) REVERT: D 86 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7410 (mtt90) REVERT: D 99 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8215 (ttp-170) REVERT: C 61 GLU cc_start: 0.8248 (tp30) cc_final: 0.7894 (tp30) REVERT: C 68 ASN cc_start: 0.8426 (t0) cc_final: 0.8057 (m-40) REVERT: C 73 ASN cc_start: 0.8331 (t0) cc_final: 0.8033 (t0) REVERT: C 91 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 35 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7839 (ttm-80) REVERT: B 64 ASN cc_start: 0.8567 (t0) cc_final: 0.8201 (m-40) outliers start: 29 outliers final: 28 residues processed: 195 average time/residue: 0.1671 time to fit residues: 45.2179 Evaluate side-chains 193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 97 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101570 restraints weight = 21426.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105267 restraints weight = 15214.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105176 restraints weight = 9571.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105377 restraints weight = 9172.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105315 restraints weight = 9256.619| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16208 Z= 0.125 Angle : 0.554 8.126 23159 Z= 0.320 Chirality : 0.040 0.317 2622 Planarity : 0.004 0.039 1924 Dihedral : 28.746 168.504 4491 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.42 % Allowed : 20.40 % Favored : 77.17 % 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: 0.65 (0.26), residues: 1126 helix: 1.46 (0.21), residues: 646 sheet: -0.19 (0.69), residues: 64 loop : -1.11 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 23 TYR 0.017 0.001 TYR K 78 PHE 0.008 0.001 PHE G 25 TRP 0.026 0.002 TRP K 208 HIS 0.004 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (16208) covalent geometry : angle 0.55384 / 0.32 (23159) hydrogen bonds : bond 0.03940 / 4.29 ( 768) hydrogen bonds : angle 2.62915 / 3.41 ( 1924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.06 seconds wall clock time: 40 minutes 40.59 seconds (2440.59 seconds total)