Starting phenix.real_space_refine on Sun Aug 24 12:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nqa_0480/08_2025/6nqa_0480.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nqa_0480/08_2025/6nqa_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_0480/08_2025/6nqa_0480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nqa_0480/08_2025/6nqa_0480.map" model { file = "/net/cci-nas-00/data/ceres_data/6nqa_0480/08_2025/6nqa_0480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nqa_0480/08_2025/6nqa_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.37, per 1000 atoms: 0.22 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: 1.15 Conformation dependent library (CDL) restraints added in 318.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.61 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: 2.41 Time building geometry restraints manager: 1.54 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 1.422 1.500 -0.078 3.00e-02 1.11e+03 6.74e+00 bond pdb=" C2 SAM K 500 " pdb=" N3 SAM K 500 " ideal model delta sigma weight residual 1.322 1.372 -0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" C8 SAM K 500 " pdb=" N7 SAM K 500 " ideal model delta sigma weight residual 1.298 1.348 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C2 SAM K 500 " pdb=" N1 SAM K 500 " ideal model delta sigma weight residual 1.329 1.377 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" C3' DG J 136 " pdb=" O3' DG J 136 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.09e+00 ... (remaining 16203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 21782 1.71 - 3.41: 1226 3.41 - 5.12: 109 5.12 - 6.83: 24 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 120.20 126.26 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" N ALA C 47 " pdb=" CA ALA C 47 " pdb=" C ALA C 47 " ideal model delta sigma weight residual 109.81 117.39 -7.58 2.21e+00 2.05e-01 1.18e+01 angle pdb=" C3' DG J 136 " pdb=" O3' DG J 136 " pdb=" P DG J 137 " ideal model delta sigma weight residual 120.20 125.31 -5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N LEU A 65 " pdb=" CA LEU A 65 " pdb=" C LEU A 65 " ideal model delta sigma weight residual 109.81 117.15 -7.34 2.21e+00 2.05e-01 1.10e+01 angle pdb=" C ASN K 57 " pdb=" N TYR K 58 " pdb=" CA TYR K 58 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 ... (remaining 23154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 7527 33.91 - 67.82: 1475 67.82 - 101.73: 21 101.73 - 135.64: 1 135.64 - 169.55: 3 Dihedral angle restraints: 9027 sinusoidal: 5631 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 9024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2194 0.063 - 0.127: 369 0.127 - 0.190: 49 0.190 - 0.253: 9 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.007 0.078 16208 Z= 0.300 Angle : 0.873 8.533 23159 Z= 0.504 Chirality : 0.050 0.317 2622 Planarity : 0.007 0.075 1924 Dihedral : 25.521 169.552 6831 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 aren 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 covalent geometry : bond 0.00678 (16208) covalent geometry : angle 0.87293 (23159) hydrogen bonds : bond 0.14078 ( 768) hydrogen bonds : angle 5.06222 ( 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 : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 74 GLU cc_start: 0.7162 (tt0) cc_final: 0.6696 (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: 0.8052 (t0) REVERT: G 110 ASN cc_start: 0.7994 (t0) cc_final: 0.7445 (p0) REVERT: H 71 GLU cc_start: 0.7633 (tp30) cc_final: 0.7291 (tt0) REVERT: K 30 HIS cc_start: 0.2938 (p90) cc_final: 0.2635 (m170) REVERT: K 35 HIS cc_start: 0.7108 (m-70) cc_final: 0.6708 (m90) REVERT: K 96 MET cc_start: 0.3458 (ppp) cc_final: 0.1293 (mtp) REVERT: K 147 MET cc_start: 0.7385 (tpp) cc_final: 0.7017 (tmm) REVERT: K 208 TRP cc_start: 0.8677 (t60) cc_final: 0.8271 (t60) REVERT: K 311 SER cc_start: 0.8179 (p) cc_final: 0.7686 (m) REVERT: L 27 LYS cc_start: 0.7287 (mttt) cc_final: 0.6863 (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: 0.7127 (mtp85) REVERT: A 123 ASP cc_start: 0.8648 (m-30) cc_final: 0.8433 (m-30) REVERT: D 43 LYS cc_start: 0.8581 (mttt) cc_final: 0.8223 (ttmm) REVERT: D 59 MET cc_start: 0.8414 (tpp) cc_final: 0.7720 (tpt) REVERT: D 68 ASP cc_start: 0.7757 (t70) cc_final: 0.7557 (t0) REVERT: D 71 GLU cc_start: 0.7539 (tp30) cc_final: 0.7000 (tt0) REVERT: C 36 LYS cc_start: 0.8534 (mttt) cc_final: 0.8281 (pptt) REVERT: C 61 GLU cc_start: 0.8282 (tp30) cc_final: 0.7916 (tp30) REVERT: C 68 ASN cc_start: 0.8125 (t0) cc_final: 0.7736 (m-40) REVERT: C 73 ASN cc_start: 0.8356 (t0) cc_final: 0.7818 (t0) REVERT: B 35 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7994 (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: 0.1975 time to fit residues: 82.4561 Evaluate side-chains 194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN G 112 GLN K 35 HIS K 181 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103016 restraints weight = 21494.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105558 restraints weight = 17137.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105916 restraints weight = 11155.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105974 restraints weight = 11105.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106398 restraints weight = 9752.425| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16208 Z= 0.169 Angle : 0.581 5.888 23159 Z= 0.336 Chirality : 0.036 0.155 2622 Planarity : 0.005 0.047 1924 Dihedral : 28.093 167.476 4524 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.73 % Allowed : 15.86 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.23), residues: 1126 helix: -0.64 (0.19), residues: 628 sheet: -1.31 (0.58), residues: 63 loop : -2.02 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 71 TYR 0.011 0.001 TYR B 51 PHE 0.020 0.002 PHE K 68 TRP 0.011 0.002 TRP K 228 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00381 (16208) covalent geometry : angle 0.58096 (23159) hydrogen bonds : bond 0.04073 ( 768) hydrogen bonds : angle 2.86351 ( 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 238 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8898 (t0) cc_final: 0.8348 (t0) REVERT: F 77 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7961 (mmtm) REVERT: G 73 ASN cc_start: 0.8299 (t0) cc_final: 0.7548 (t0) REVERT: H 99 ARG cc_start: 0.8321 (mtp180) cc_final: 0.8050 (mtm180) REVERT: K 96 MET cc_start: 0.3210 (ppp) cc_final: 0.1551 (mmm) REVERT: K 147 MET cc_start: 0.7470 (tpp) cc_final: 0.7203 (tmm) REVERT: K 208 TRP cc_start: 0.8269 (t60) cc_final: 0.7949 (t60) REVERT: L 27 LYS cc_start: 0.7557 (mttt) cc_final: 0.7197 (mttm) REVERT: L 72 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7127 (ptp90) REVERT: E 41 TYR cc_start: 0.8862 (m-80) cc_final: 0.8624 (m-80) REVERT: E 56 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7664 (mttt) REVERT: E 123 ASP cc_start: 0.8310 (m-30) cc_final: 0.7486 (m-30) REVERT: E 125 GLN cc_start: 0.8839 (mt0) cc_final: 0.8521 (mt0) REVERT: A 42 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7350 (mtp85) REVERT: A 68 GLN cc_start: 0.8275 (tt0) cc_final: 0.8028 (tt0) REVERT: A 74 ILE cc_start: 0.9024 (tt) cc_final: 0.8780 (tt) REVERT: D 40 TYR cc_start: 0.8437 (m-80) cc_final: 0.8235 (m-80) REVERT: D 43 LYS cc_start: 0.8657 (mttt) cc_final: 0.8452 (ttmm) REVERT: D 59 MET cc_start: 0.8562 (tpp) cc_final: 0.7982 (tpt) REVERT: D 71 GLU cc_start: 0.7694 (tp30) cc_final: 0.7354 (tt0) REVERT: D 116 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8372 (pttp) REVERT: C 61 GLU cc_start: 0.8262 (tp30) cc_final: 0.7876 (tp30) REVERT: C 68 ASN cc_start: 0.8486 (t0) cc_final: 0.8067 (m-40) REVERT: C 73 ASN cc_start: 0.8369 (t0) cc_final: 0.7858 (t0) REVERT: B 35 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: B 64 ASN cc_start: 0.8324 (t0) cc_final: 0.8060 (m-40) outliers start: 27 outliers final: 19 residues processed: 230 average time/residue: 0.1561 time to fit residues: 48.9337 Evaluate side-chains 202 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 112 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 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 88 THR 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 107 VAL 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: 2.9990 chunk 5 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 HIS E 93 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.149269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099148 restraints weight = 21794.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100476 restraints weight = 17488.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100362 restraints weight = 13850.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100967 restraints weight = 13404.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100949 restraints weight = 12227.682| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16208 Z= 0.195 Angle : 0.591 7.052 23159 Z= 0.338 Chirality : 0.037 0.157 2622 Planarity : 0.005 0.074 1924 Dihedral : 28.451 167.577 4523 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.04 % Allowed : 16.36 % Favored : 79.60 % 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 aren not related in a simple way. whole: -1.14 (0.25), residues: 1126 helix: -0.06 (0.20), residues: 641 sheet: -0.63 (0.63), residues: 64 loop : -1.77 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 35 TYR 0.013 0.002 TYR G 57 PHE 0.019 0.002 PHE E 84 TRP 0.013 0.002 TRP K 228 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00453 (16208) covalent geometry : angle 0.59079 (23159) hydrogen bonds : bond 0.04598 ( 768) hydrogen bonds : angle 2.83595 ( 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 235 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.447 Fit side-chains REVERT: F 77 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8037 (mmtm) REVERT: G 73 ASN cc_start: 0.8383 (t0) cc_final: 0.8071 (t0) REVERT: K 20 TYR cc_start: 0.7278 (m-80) cc_final: 0.7006 (m-10) REVERT: K 43 TRP cc_start: 0.8636 (m100) cc_final: 0.8210 (m100) REVERT: K 96 MET cc_start: 0.2931 (ppp) cc_final: 0.1439 (mmm) REVERT: K 147 MET cc_start: 0.7574 (tpp) cc_final: 0.7097 (ttp) REVERT: K 208 TRP cc_start: 0.8243 (t60) cc_final: 0.7751 (t60) REVERT: L 27 LYS cc_start: 0.7842 (mttt) cc_final: 0.7299 (mmtp) REVERT: E 56 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7764 (mttt) REVERT: E 97 GLU cc_start: 0.7654 (tt0) cc_final: 0.7360 (tt0) REVERT: E 123 ASP cc_start: 0.8349 (m-30) cc_final: 0.7991 (m-30) REVERT: A 42 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7407 (mtp85) REVERT: A 68 GLN cc_start: 0.8397 (tt0) cc_final: 0.8175 (tt0) REVERT: D 40 TYR cc_start: 0.8473 (m-80) cc_final: 0.8211 (m-80) REVERT: D 43 LYS cc_start: 0.8911 (mttt) cc_final: 0.8573 (ttmm) REVERT: D 59 MET cc_start: 0.8461 (tpp) cc_final: 0.7919 (tpt) REVERT: D 86 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7483 (mtt90) REVERT: C 61 GLU cc_start: 0.8265 (tp30) cc_final: 0.7814 (tp30) REVERT: C 73 ASN cc_start: 0.8451 (t0) cc_final: 0.8040 (t0) REVERT: C 84 GLN cc_start: 0.8899 (tp40) cc_final: 0.8073 (tt0) REVERT: B 35 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7902 (ttm-80) REVERT: B 64 ASN cc_start: 0.8468 (t0) cc_final: 0.8180 (m-40) outliers start: 40 outliers final: 29 residues processed: 226 average time/residue: 0.1585 time to fit residues: 48.6997 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 : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR 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 155 ASP Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 45 THR 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 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.0870 chunk 104 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 overall best weight: 0.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN L 68 HIS E 125 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106584 restraints weight = 21925.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107043 restraints weight = 19039.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107237 restraints weight = 17022.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107728 restraints weight = 17975.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107681 restraints weight = 16531.206| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16208 Z= 0.142 Angle : 0.533 7.616 23159 Z= 0.310 Chirality : 0.034 0.144 2622 Planarity : 0.004 0.036 1924 Dihedral : 28.184 164.973 4523 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.13 % Allowed : 19.09 % Favored : 77.78 % 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 aren not related in a simple way. whole: -0.42 (0.25), residues: 1126 helix: 0.56 (0.21), residues: 637 sheet: -0.30 (0.66), residues: 64 loop : -1.52 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.011 0.001 TYR K 63 PHE 0.020 0.001 PHE K 68 TRP 0.013 0.001 TRP K 22 HIS 0.006 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00317 (16208) covalent geometry : angle 0.53283 (23159) hydrogen bonds : bond 0.03504 ( 768) hydrogen bonds : angle 2.62914 ( 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 217 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.440 Fit side-chains REVERT: F 77 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8113 (mmtm) REVERT: K 43 TRP cc_start: 0.8615 (m100) cc_final: 0.8197 (m100) REVERT: K 96 MET cc_start: 0.2792 (ppp) cc_final: 0.1548 (mmm) REVERT: K 147 MET cc_start: 0.7573 (tpp) cc_final: 0.7082 (ttp) REVERT: K 208 TRP cc_start: 0.8099 (t60) cc_final: 0.7654 (t60) REVERT: L 27 LYS cc_start: 0.7782 (mttt) cc_final: 0.7277 (mttm) REVERT: E 97 GLU cc_start: 0.7434 (tt0) cc_final: 0.7168 (tt0) REVERT: E 123 ASP cc_start: 0.8260 (m-30) cc_final: 0.7512 (m-30) REVERT: A 42 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7430 (mtp85) REVERT: D 40 TYR cc_start: 0.8421 (m-80) cc_final: 0.8146 (m-80) REVERT: D 43 LYS cc_start: 0.8889 (mttt) cc_final: 0.8627 (ttmm) REVERT: D 54 ILE cc_start: 0.8725 (pt) cc_final: 0.8376 (tt) REVERT: D 59 MET cc_start: 0.8350 (tpp) cc_final: 0.7862 (tpt) REVERT: D 99 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8317 (ttp-170) REVERT: C 61 GLU cc_start: 0.8254 (tp30) cc_final: 0.7888 (tp30) REVERT: C 68 ASN cc_start: 0.8517 (t0) cc_final: 0.8276 (m-40) REVERT: C 73 ASN cc_start: 0.8369 (t0) cc_final: 0.8044 (t0) REVERT: C 84 GLN cc_start: 0.8879 (tp40) cc_final: 0.8271 (tt0) REVERT: B 35 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7904 (ttm-80) REVERT: B 64 ASN cc_start: 0.8459 (t0) cc_final: 0.8114 (m-40) REVERT: B 93 GLN cc_start: 0.8323 (mt0) cc_final: 0.8108 (mt0) outliers start: 31 outliers final: 24 residues processed: 214 average time/residue: 0.1436 time to fit residues: 42.0981 Evaluate side-chains 198 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER 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 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 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 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN L 68 HIS D 49 HIS B 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105864 restraints weight = 22075.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106377 restraints weight = 19346.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106465 restraints weight = 17967.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106967 restraints weight = 16256.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107004 restraints weight = 15436.280| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16208 Z= 0.164 Angle : 0.545 6.771 23159 Z= 0.315 Chirality : 0.035 0.152 2622 Planarity : 0.004 0.034 1924 Dihedral : 28.259 164.976 4523 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.74 % Allowed : 19.09 % 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 aren not related in a simple way. whole: -0.10 (0.26), residues: 1126 helix: 0.79 (0.21), residues: 637 sheet: -0.37 (0.67), residues: 64 loop : -1.29 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.019 0.001 TYR K 78 PHE 0.012 0.001 PHE G 25 TRP 0.012 0.001 TRP K 22 HIS 0.004 0.001 HIS K 315 Details of bonding type rmsd covalent geometry : bond 0.00376 (16208) covalent geometry : angle 0.54499 (23159) hydrogen bonds : bond 0.03862 ( 768) hydrogen bonds : angle 2.66090 ( 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 217 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.314 Fit side-chains REVERT: F 77 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8135 (mmtm) REVERT: K 20 TYR cc_start: 0.7006 (m-10) cc_final: 0.6618 (m-10) REVERT: K 43 TRP cc_start: 0.8598 (m100) cc_final: 0.8185 (m100) REVERT: K 96 MET cc_start: 0.2687 (ppp) cc_final: 0.1542 (mmm) REVERT: K 147 MET cc_start: 0.7633 (tpp) cc_final: 0.7181 (ttp) REVERT: K 208 TRP cc_start: 0.8056 (t60) cc_final: 0.7643 (t60) REVERT: K 226 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7142 (mm-30) REVERT: K 311 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7666 (m) REVERT: L 27 LYS cc_start: 0.7864 (mttt) cc_final: 0.7321 (mttm) REVERT: E 56 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7579 (mttt) REVERT: E 97 GLU cc_start: 0.7434 (tt0) cc_final: 0.7163 (tt0) REVERT: E 123 ASP cc_start: 0.8337 (m-30) cc_final: 0.7411 (m-30) REVERT: A 42 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7484 (mtp85) REVERT: D 40 TYR cc_start: 0.8431 (m-80) cc_final: 0.8167 (m-80) REVERT: D 43 LYS cc_start: 0.8892 (mttt) cc_final: 0.8661 (ttmm) REVERT: D 47 GLN cc_start: 0.7899 (mt0) cc_final: 0.7660 (tt0) REVERT: D 54 ILE cc_start: 0.8789 (pt) cc_final: 0.8449 (tt) REVERT: D 59 MET cc_start: 0.8409 (tpp) cc_final: 0.7939 (tpt) REVERT: D 86 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7409 (mtt90) REVERT: D 99 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8350 (ttp-170) REVERT: C 61 GLU cc_start: 0.8182 (tp30) cc_final: 0.7810 (tp30) REVERT: C 73 ASN cc_start: 0.8299 (t0) cc_final: 0.8068 (t0) REVERT: C 84 GLN cc_start: 0.8902 (tp40) cc_final: 0.8333 (tt0) REVERT: B 35 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7927 (ttm-80) REVERT: B 64 ASN cc_start: 0.8458 (t0) cc_final: 0.8078 (m-40) outliers start: 37 outliers final: 32 residues processed: 210 average time/residue: 0.1264 time to fit residues: 37.1516 Evaluate side-chains 204 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 279 ILE 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 311 SER Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 44 ILE 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 45 THR 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 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR 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: 2.9990 chunk 87 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 53 optimal weight: 0.0070 chunk 102 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 HIS B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108343 restraints weight = 21886.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108619 restraints weight = 19024.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108835 restraints weight = 17738.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109151 restraints weight = 18494.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109209 restraints weight = 16710.234| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16208 Z= 0.132 Angle : 0.518 5.385 23159 Z= 0.302 Chirality : 0.034 0.141 2622 Planarity : 0.004 0.037 1924 Dihedral : 28.079 162.899 4523 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.73 % Allowed : 20.61 % Favored : 76.67 % 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 aren not related in a simple way. whole: 0.22 (0.26), residues: 1126 helix: 1.06 (0.21), residues: 644 sheet: -0.32 (0.67), residues: 64 loop : -1.20 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 23 TYR 0.016 0.001 TYR K 78 PHE 0.023 0.001 PHE K 68 TRP 0.009 0.001 TRP K 22 HIS 0.003 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00291 (16208) covalent geometry : angle 0.51839 (23159) hydrogen bonds : bond 0.03269 ( 768) hydrogen bonds : angle 2.55622 ( 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 200 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.310 Fit side-chains REVERT: F 74 GLU cc_start: 0.6963 (tt0) cc_final: 0.6601 (tt0) REVERT: F 77 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8134 (mmtm) REVERT: K 20 TYR cc_start: 0.7021 (m-10) cc_final: 0.6645 (m-80) REVERT: K 43 TRP cc_start: 0.8578 (m100) cc_final: 0.8176 (m100) REVERT: K 96 MET cc_start: 0.2913 (ppp) cc_final: 0.1854 (mmm) REVERT: K 112 GLN cc_start: 0.8193 (tp40) cc_final: 0.7916 (tp40) REVERT: K 147 MET cc_start: 0.7625 (tpp) cc_final: 0.7136 (ttp) REVERT: K 208 TRP cc_start: 0.7976 (t60) cc_final: 0.7548 (t60) REVERT: K 226 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7133 (mm-30) REVERT: K 311 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7560 (m) REVERT: L 27 LYS cc_start: 0.7891 (mttt) cc_final: 0.7334 (mttm) REVERT: E 56 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7613 (mttt) REVERT: E 97 GLU cc_start: 0.7465 (tt0) cc_final: 0.7202 (tt0) REVERT: E 123 ASP cc_start: 0.8295 (m-30) cc_final: 0.7442 (m-30) REVERT: A 42 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7484 (mtp85) REVERT: D 40 TYR cc_start: 0.8423 (m-80) cc_final: 0.8153 (m-80) REVERT: D 43 LYS cc_start: 0.8876 (mttt) cc_final: 0.8594 (ttmm) REVERT: D 47 GLN cc_start: 0.7784 (mt0) cc_final: 0.7575 (tt0) REVERT: D 54 ILE cc_start: 0.8731 (pt) cc_final: 0.8385 (tt) REVERT: D 59 MET cc_start: 0.8221 (tpp) cc_final: 0.7769 (tpt) REVERT: D 86 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7328 (mtt90) REVERT: D 99 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8297 (ttp-170) REVERT: C 61 GLU cc_start: 0.8137 (tp30) cc_final: 0.7837 (tp30) REVERT: C 73 ASN cc_start: 0.8350 (t0) cc_final: 0.8108 (t0) REVERT: C 91 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 35 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7919 (ttt-90) REVERT: B 64 ASN cc_start: 0.8382 (t0) cc_final: 0.8170 (m-40) REVERT: B 77 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8280 (mtpp) outliers start: 27 outliers final: 18 residues processed: 196 average time/residue: 0.1348 time to fit residues: 36.7534 Evaluate side-chains 187 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE 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 76 THR 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: 0.9980 chunk 94 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104272 restraints weight = 21854.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104916 restraints weight = 19707.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104915 restraints weight = 18786.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105440 restraints weight = 16578.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105523 restraints weight = 15277.603| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16208 Z= 0.193 Angle : 0.568 5.529 23159 Z= 0.325 Chirality : 0.036 0.151 2622 Planarity : 0.004 0.038 1924 Dihedral : 28.416 164.145 4523 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.64 % Allowed : 20.61 % Favored : 75.76 % 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 aren not related in a simple way. whole: 0.21 (0.26), residues: 1126 helix: 0.95 (0.21), residues: 646 sheet: -0.41 (0.67), residues: 63 loop : -0.99 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.013 0.001 TYR K 78 PHE 0.015 0.002 PHE G 25 TRP 0.011 0.002 TRP K 22 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd covalent geometry : bond 0.00451 (16208) covalent geometry : angle 0.56759 (23159) hydrogen bonds : bond 0.04259 ( 768) hydrogen bonds : angle 2.69758 ( 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 212 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.334 Fit side-chains REVERT: F 77 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8187 (mmtm) REVERT: H 34 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8091 (mmtt) REVERT: K 20 TYR cc_start: 0.7254 (m-10) cc_final: 0.6721 (m-80) REVERT: K 43 TRP cc_start: 0.8652 (m100) cc_final: 0.8248 (m100) REVERT: K 96 MET cc_start: 0.3191 (ppp) cc_final: 0.2017 (mmm) REVERT: K 147 MET cc_start: 0.7750 (tpp) cc_final: 0.7424 (ttp) REVERT: K 208 TRP cc_start: 0.8054 (t60) cc_final: 0.7687 (t60) REVERT: K 226 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7243 (mm-30) REVERT: L 27 LYS cc_start: 0.7709 (mttt) cc_final: 0.7353 (mttm) REVERT: E 56 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7665 (mttt) REVERT: E 97 GLU cc_start: 0.7486 (tt0) cc_final: 0.7195 (tt0) REVERT: E 123 ASP cc_start: 0.8348 (m-30) cc_final: 0.8036 (m-30) REVERT: A 42 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7478 (mtp85) REVERT: D 40 TYR cc_start: 0.8421 (m-80) cc_final: 0.8152 (m-80) REVERT: D 43 LYS cc_start: 0.8909 (mttt) cc_final: 0.8624 (ttmm) REVERT: D 54 ILE cc_start: 0.8782 (pt) cc_final: 0.8510 (tt) REVERT: D 59 MET cc_start: 0.8510 (tpp) cc_final: 0.8111 (tpt) REVERT: D 86 ARG cc_start: 0.7665 (mtt90) cc_final: 0.7399 (mtt90) REVERT: C 61 GLU cc_start: 0.8159 (tp30) cc_final: 0.7798 (tp30) REVERT: C 91 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 35 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: B 64 ASN cc_start: 0.8418 (t0) cc_final: 0.8210 (m-40) outliers start: 36 outliers final: 29 residues processed: 206 average time/residue: 0.1282 time to fit residues: 36.6756 Evaluate side-chains 197 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU 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 H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER 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 5 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 44 ILE 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 E residue 117 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER 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 62 ILE Chi-restraints excluded: chain C residue 76 THR 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: 0.4980 chunk 91 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 HIS B 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.153002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108321 restraints weight = 22100.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108491 restraints weight = 19265.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108708 restraints weight = 17287.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109036 restraints weight = 18025.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109093 restraints weight = 16408.031| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16208 Z= 0.133 Angle : 0.521 5.460 23159 Z= 0.303 Chirality : 0.034 0.145 2622 Planarity : 0.004 0.041 1924 Dihedral : 28.142 162.370 4523 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.12 % Allowed : 22.83 % Favored : 75.05 % 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 aren not related in a simple way. whole: 0.59 (0.26), residues: 1126 helix: 1.26 (0.21), residues: 644 sheet: -0.55 (0.66), residues: 73 loop : -0.76 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.012 0.001 TYR K 78 PHE 0.022 0.001 PHE K 68 TRP 0.008 0.001 TRP K 305 HIS 0.003 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00294 (16208) covalent geometry : angle 0.52120 (23159) hydrogen bonds : bond 0.03265 ( 768) hydrogen bonds : angle 2.51233 ( 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 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.455 Fit side-chains REVERT: F 74 GLU cc_start: 0.6935 (tt0) cc_final: 0.6531 (tt0) REVERT: F 77 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8178 (mmtm) REVERT: H 34 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8067 (mmtt) REVERT: K 20 TYR cc_start: 0.7126 (m-10) cc_final: 0.6750 (m-80) REVERT: K 43 TRP cc_start: 0.8559 (m100) cc_final: 0.8142 (m100) REVERT: K 96 MET cc_start: 0.2989 (ppp) cc_final: 0.2005 (mmm) REVERT: K 147 MET cc_start: 0.7722 (tpp) cc_final: 0.7404 (ttp) REVERT: K 208 TRP cc_start: 0.7980 (t60) cc_final: 0.7578 (t60) REVERT: L 27 LYS cc_start: 0.7702 (mttt) cc_final: 0.7349 (mttm) REVERT: L 72 ARG cc_start: 0.7459 (ptp90) cc_final: 0.7024 (ptp90) REVERT: E 56 LYS cc_start: 0.8025 (ttpp) cc_final: 0.7701 (mttt) REVERT: E 97 GLU cc_start: 0.7524 (tt0) cc_final: 0.7271 (tt0) REVERT: E 123 ASP cc_start: 0.8244 (m-30) cc_final: 0.7397 (m-30) REVERT: E 133 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 42 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7426 (mtp85) REVERT: D 40 TYR cc_start: 0.8404 (m-80) cc_final: 0.8157 (m-80) REVERT: D 43 LYS cc_start: 0.8902 (mttt) cc_final: 0.8599 (ttmm) REVERT: D 54 ILE cc_start: 0.8695 (pt) cc_final: 0.8358 (tt) REVERT: D 59 MET cc_start: 0.8227 (tpp) cc_final: 0.7779 (tpt) REVERT: D 86 ARG cc_start: 0.7667 (mtt90) cc_final: 0.7366 (mtt90) REVERT: C 61 GLU cc_start: 0.8140 (tp30) cc_final: 0.7829 (tp30) REVERT: C 91 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 35 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7898 (ttt-90) REVERT: B 64 ASN cc_start: 0.8442 (t0) cc_final: 0.8190 (m-40) outliers start: 21 outliers final: 19 residues processed: 199 average time/residue: 0.1570 time to fit residues: 42.5763 Evaluate side-chains 191 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL 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 H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain C residue 76 THR 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: 2.9990 chunk 28 optimal weight: 0.0270 chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 117 optimal weight: 0.0980 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN K 112 GLN L 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.153090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108413 restraints weight = 21940.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108560 restraints weight = 18981.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108782 restraints weight = 17585.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109052 restraints weight = 18167.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109134 restraints weight = 16575.963| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16208 Z= 0.136 Angle : 0.531 6.034 23159 Z= 0.306 Chirality : 0.034 0.143 2622 Planarity : 0.004 0.040 1924 Dihedral : 28.172 162.204 4523 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.12 % Allowed : 23.03 % Favored : 74.85 % 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 aren not related in a simple way. whole: 0.62 (0.26), residues: 1126 helix: 1.28 (0.21), residues: 654 sheet: -0.44 (0.68), residues: 73 loop : -0.82 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.013 0.001 TYR K 78 PHE 0.009 0.001 PHE G 25 TRP 0.008 0.001 TRP K 305 HIS 0.003 0.001 HIS K 315 Details of bonding type rmsd covalent geometry : bond 0.00304 (16208) covalent geometry : angle 0.53076 (23159) hydrogen bonds : bond 0.03338 ( 768) hydrogen bonds : angle 2.54213 ( 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 193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.362 Fit side-chains REVERT: F 74 GLU cc_start: 0.6973 (tt0) cc_final: 0.6575 (tt0) REVERT: F 77 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8215 (mmtm) REVERT: H 34 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8055 (mmtt) REVERT: K 20 TYR cc_start: 0.7238 (m-10) cc_final: 0.6895 (m-80) REVERT: K 43 TRP cc_start: 0.8550 (m100) cc_final: 0.8134 (m100) REVERT: K 96 MET cc_start: 0.3028 (ppp) cc_final: 0.1991 (mmm) REVERT: K 147 MET cc_start: 0.7686 (tpp) cc_final: 0.7357 (tmm) REVERT: K 208 TRP cc_start: 0.7993 (t60) cc_final: 0.7591 (t60) REVERT: L 27 LYS cc_start: 0.7679 (mttt) cc_final: 0.7327 (mttm) REVERT: E 56 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7707 (mttt) REVERT: E 97 GLU cc_start: 0.7524 (tt0) cc_final: 0.7279 (tt0) REVERT: E 123 ASP cc_start: 0.8172 (m-30) cc_final: 0.7309 (m-30) REVERT: E 133 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 42 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7368 (mtp85) REVERT: D 40 TYR cc_start: 0.8381 (m-80) cc_final: 0.8143 (m-80) REVERT: D 43 LYS cc_start: 0.8925 (mttt) cc_final: 0.8638 (ttmm) REVERT: D 54 ILE cc_start: 0.8713 (pt) cc_final: 0.8341 (tt) REVERT: D 59 MET cc_start: 0.8238 (tpp) cc_final: 0.7794 (tpt) REVERT: D 86 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7366 (mtt90) REVERT: D 99 ARG cc_start: 0.8602 (ttm-80) cc_final: 0.8093 (ttp-170) REVERT: C 61 GLU cc_start: 0.8139 (tp30) cc_final: 0.7854 (tp30) REVERT: B 35 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7918 (ttt-90) REVERT: B 64 ASN cc_start: 0.8409 (t0) cc_final: 0.8162 (m-40) outliers start: 21 outliers final: 20 residues processed: 190 average time/residue: 0.1444 time to fit residues: 37.6783 Evaluate side-chains 187 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain C residue 76 THR 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: 2.9990 chunk 87 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 chunk 98 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN L 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108809 restraints weight = 21997.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109056 restraints weight = 19171.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109249 restraints weight = 17626.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109592 restraints weight = 18187.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109658 restraints weight = 16717.189| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16208 Z= 0.135 Angle : 0.528 6.467 23159 Z= 0.306 Chirality : 0.034 0.142 2622 Planarity : 0.004 0.041 1924 Dihedral : 28.143 161.868 4523 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.92 % Allowed : 23.43 % Favored : 74.65 % 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 aren not related in a simple way. whole: 0.70 (0.26), residues: 1126 helix: 1.34 (0.21), residues: 654 sheet: -0.44 (0.68), residues: 73 loop : -0.78 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 23 TYR 0.012 0.001 TYR K 78 PHE 0.025 0.001 PHE K 68 TRP 0.008 0.001 TRP K 305 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00300 (16208) covalent geometry : angle 0.52814 (23159) hydrogen bonds : bond 0.03291 ( 768) hydrogen bonds : angle 2.52868 ( 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 194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.448 Fit side-chains REVERT: F 74 GLU cc_start: 0.6956 (tt0) cc_final: 0.6573 (tt0) REVERT: F 77 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8231 (mmtm) REVERT: H 34 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8044 (mmtt) REVERT: K 20 TYR cc_start: 0.7200 (m-10) cc_final: 0.6855 (m-80) REVERT: K 43 TRP cc_start: 0.8534 (m100) cc_final: 0.7996 (m100) REVERT: K 96 MET cc_start: 0.2987 (ppp) cc_final: 0.2038 (mmm) REVERT: K 147 MET cc_start: 0.7640 (tpp) cc_final: 0.7250 (ttp) REVERT: K 208 TRP cc_start: 0.7996 (t60) cc_final: 0.7607 (t60) REVERT: L 27 LYS cc_start: 0.7676 (mttt) cc_final: 0.7314 (mttm) REVERT: E 56 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7719 (mttt) REVERT: E 123 ASP cc_start: 0.8139 (m-30) cc_final: 0.7831 (m-30) REVERT: A 42 ARG cc_start: 0.7566 (mtp180) cc_final: 0.7343 (mtp85) REVERT: D 43 LYS cc_start: 0.8929 (mttt) cc_final: 0.8633 (ttmm) REVERT: D 54 ILE cc_start: 0.8673 (pt) cc_final: 0.8326 (tt) REVERT: D 59 MET cc_start: 0.8219 (tpp) cc_final: 0.7790 (tpt) REVERT: D 86 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7357 (mtt90) REVERT: D 99 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8090 (ttp-170) REVERT: C 61 GLU cc_start: 0.8149 (tp30) cc_final: 0.7852 (tp30) REVERT: B 35 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7907 (ttt-90) REVERT: B 64 ASN cc_start: 0.8390 (t0) cc_final: 0.8177 (m-40) outliers start: 19 outliers final: 19 residues processed: 191 average time/residue: 0.1618 time to fit residues: 42.0895 Evaluate side-chains 190 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain C residue 76 THR 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: 0.9980 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN L 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.153443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108781 restraints weight = 21920.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108950 restraints weight = 19159.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109205 restraints weight = 17354.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109506 restraints weight = 17824.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109585 restraints weight = 16424.428| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16208 Z= 0.138 Angle : 0.531 7.077 23159 Z= 0.306 Chirality : 0.034 0.142 2622 Planarity : 0.004 0.040 1924 Dihedral : 28.156 161.924 4523 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.42 % Allowed : 22.93 % Favored : 74.65 % 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 aren not related in a simple way. whole: 0.74 (0.26), residues: 1126 helix: 1.37 (0.21), residues: 654 sheet: -0.40 (0.68), residues: 73 loop : -0.76 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.012 0.001 TYR K 78 PHE 0.009 0.001 PHE G 25 TRP 0.007 0.001 TRP K 305 HIS 0.003 0.001 HIS K 315 Details of bonding type rmsd covalent geometry : bond 0.00309 (16208) covalent geometry : angle 0.53092 (23159) hydrogen bonds : bond 0.03353 ( 768) hydrogen bonds : angle 2.53333 ( 1924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.40 seconds wall clock time: 36 minutes 15.17 seconds (2175.17 seconds total)