Starting phenix.real_space_refine on Sat Sep 12 10:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk5_27483/09_2026/8dk5_27483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk5_27483/09_2026/8dk5_27483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dk5_27483/09_2026/8dk5_27483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk5_27483/09_2026/8dk5_27483.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk5_27483/09_2026/8dk5_27483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk5_27483/09_2026/8dk5_27483.cif" } resolution = 2.71 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= 0.005 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 298 5.49 5 S 32 5.16 5 C 8911 2.51 5 N 2816 2.21 5 O 3561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15618 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1759 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "I" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3088 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3021 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Time building chain proxies: 3.59, per 1000 atoms: 0.23 Number of scatterers: 15618 At special positions: 0 Unit cell: (138.336, 124.608, 121.44, 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 32 16.00 P 298 15.00 O 3561 8.00 N 2816 7.00 C 8911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 501.2 milliseconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 21 sheets defined 46.9% alpha, 19.8% beta 123 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.591A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.804A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.645A pdb=" N LEU C 55 " --> pdb=" O MET C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.547A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.609A pdb=" N TYR D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.531A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.510A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.620A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.548A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 removed outlier: 4.114A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.828A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.674A pdb=" N ASP N 112 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 113' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.708A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 237 through 241' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.573A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.155A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.501A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.139A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.564A pdb=" N VAL K 101 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 7.998A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.501A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.501A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR K 255 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.274A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.029A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 39 through 43 Processing sheet with id=AC2, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.956A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.816A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 296 hydrogen bonds 592 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 15 1.20 - 1.36: 4547 1.36 - 1.52: 7263 1.52 - 1.67: 4647 1.67 - 1.83: 53 Bond restraints: 16525 Sorted by residual: bond pdb=" O3' DG I 92 " pdb=" P DA I 93 " ideal model delta sigma weight residual 1.607 1.382 0.225 1.20e-02 6.94e+03 3.50e+02 bond pdb=" O3' DG I 110 " pdb=" P DC I 111 " ideal model delta sigma weight residual 1.607 1.393 0.214 1.20e-02 6.94e+03 3.19e+02 bond pdb=" O3' DG I 60 " pdb=" P DA I 61 " ideal model delta sigma weight residual 1.607 1.403 0.204 1.20e-02 6.94e+03 2.88e+02 bond pdb=" C LEU B 90 " pdb=" O LEU B 90 " ideal model delta sigma weight residual 1.237 1.052 0.184 1.19e-02 7.06e+03 2.40e+02 bond pdb=" O3' DG J 34 " pdb=" P DG J 35 " ideal model delta sigma weight residual 1.607 1.425 0.182 1.20e-02 6.94e+03 2.31e+02 ... (remaining 16520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 23474 5.96 - 11.91: 115 11.91 - 17.87: 23 17.87 - 23.83: 1 23.83 - 29.78: 1 Bond angle restraints: 23614 Sorted by residual: angle pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" C SER H 33 " ideal model delta sigma weight residual 110.61 126.96 -16.35 1.25e+00 6.40e-01 1.71e+02 angle pdb=" C3' DG I 60 " pdb=" O3' DG I 60 " pdb=" P DA I 61 " ideal model delta sigma weight residual 119.70 132.96 -13.26 1.20e+00 6.94e-01 1.22e+02 angle pdb=" C3' DT J 76 " pdb=" O3' DT J 76 " pdb=" P DT J 77 " ideal model delta sigma weight residual 119.70 132.68 -12.98 1.20e+00 6.94e-01 1.17e+02 angle pdb=" C3' DT I 127 " pdb=" O3' DT I 127 " pdb=" P DC I 128 " ideal model delta sigma weight residual 119.70 132.39 -12.69 1.20e+00 6.94e-01 1.12e+02 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 82.92 29.78 3.00e+00 1.11e-01 9.85e+01 ... (remaining 23609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 7383 32.07 - 64.14: 1797 64.14 - 96.21: 54 96.21 - 128.28: 1 128.28 - 160.35: 3 Dihedral angle restraints: 9238 sinusoidal: 5726 harmonic: 3512 Sorted by residual: dihedral pdb=" C LEU E 82 " pdb=" N LEU E 82 " pdb=" CA LEU E 82 " pdb=" CB LEU E 82 " ideal model delta harmonic sigma weight residual -122.60 -108.52 -14.08 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" C SER H 33 " pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual -122.60 -134.49 11.89 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual -180.00 -156.75 -23.25 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 9235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2567 0.137 - 0.275: 69 0.275 - 0.412: 16 0.412 - 0.550: 9 0.550 - 0.687: 2 Chirality restraints: 2663 Sorted by residual: chirality pdb=" CA SER H 33 " pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CB SER H 33 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CG LEU C 93 " pdb=" CB LEU C 93 " pdb=" CD1 LEU C 93 " pdb=" CD2 LEU C 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DA I 93 " pdb=" OP1 DA I 93 " pdb=" OP2 DA I 93 " pdb=" O5' DA I 93 " both_signs ideal model delta sigma weight residual True 2.34 -1.79 0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 2660 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 36 " 0.080 2.00e-02 2.50e+03 6.68e-02 1.23e+02 pdb=" N9 DA J 36 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DA J 36 " 0.033 2.00e-02 2.50e+03 pdb=" N7 DA J 36 " 0.021 2.00e-02 2.50e+03 pdb=" C5 DA J 36 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DA J 36 " -0.084 2.00e-02 2.50e+03 pdb=" N6 DA J 36 " 0.053 2.00e-02 2.50e+03 pdb=" N1 DA J 36 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DA J 36 " 0.082 2.00e-02 2.50e+03 pdb=" N3 DA J 36 " -0.017 2.00e-02 2.50e+03 pdb=" C4 DA J 36 " -0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " -0.035 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C GLU C 92 " 0.127 2.00e-02 2.50e+03 pdb=" O GLU C 92 " -0.049 2.00e-02 2.50e+03 pdb=" N LEU C 93 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 46 " -0.038 2.00e-02 2.50e+03 4.12e-02 4.66e+01 pdb=" N9 DA I 46 " -0.009 2.00e-02 2.50e+03 pdb=" C8 DA I 46 " -0.013 2.00e-02 2.50e+03 pdb=" N7 DA I 46 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 46 " 0.113 2.00e-02 2.50e+03 pdb=" C6 DA I 46 " -0.030 2.00e-02 2.50e+03 pdb=" N6 DA I 46 " -0.041 2.00e-02 2.50e+03 pdb=" N1 DA I 46 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DA I 46 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DA I 46 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 46 " 0.034 2.00e-02 2.50e+03 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 369 2.65 - 3.21: 12316 3.21 - 3.78: 27747 3.78 - 4.34: 39127 4.34 - 4.90: 56293 Nonbonded interactions: 135852 Sorted by model distance: nonbonded pdb=" O SER H 33 " pdb=" OG SER H 33 " model vdw 2.088 3.040 nonbonded pdb=" CA MET C 51 " pdb=" SD MET C 51 " model vdw 2.308 3.064 nonbonded pdb=" O MET C 51 " pdb=" CG MET C 51 " model vdw 2.318 3.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.325 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.350 3.040 ... (remaining 135847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 118)) } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and resid 32 through 125) } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 23 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB )) or resid 189 through 264 or (resid 265 and (name N o \ r name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.440 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.011 0.225 16529 Z= 0.864 Angle : 1.196 29.781 23622 Z= 0.821 Chirality : 0.069 0.687 2663 Planarity : 0.008 0.126 1949 Dihedral : 27.411 160.347 6976 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.55 % Favored : 95.28 % Rotamer: Outliers : 0.39 % Allowed : 21.94 % Favored : 77.67 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.22), residues: 1186 helix: -0.21 (0.19), residues: 537 sheet: -0.23 (0.34), residues: 234 loop : -1.27 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 100 TYR 0.045 0.002 TYR H 41 PHE 0.029 0.003 PHE A 78 TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01141 / 0.86 (16525) covalent geometry : angle 1.19550 / 0.82 (23614) SS BOND : bond 0.00319 / 0.21 ( 4) SS BOND : angle 1.23486 / 0.67 ( 8) hydrogen bonds : bond 0.13579 / 9.31 ( 828) hydrogen bonds : angle 6.60538 / 4.85 ( 2122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 252 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7437 (tpt90) REVERT: A 133 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7320 (mt-10) REVERT: D 43 TYR cc_start: 0.7937 (t80) cc_final: 0.7608 (t80) REVERT: D 60 MET cc_start: 0.8470 (tpp) cc_final: 0.8268 (tpp) REVERT: D 84 TYR cc_start: 0.8471 (m-10) cc_final: 0.8263 (m-10) REVERT: D 87 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7551 (mtt-85) REVERT: E 115 LYS cc_start: 0.8747 (mttt) cc_final: 0.8515 (mppt) REVERT: E 133 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7889 (mt-10) REVERT: F 79 LYS cc_start: 0.8287 (mttt) cc_final: 0.7933 (mttp) REVERT: H 72 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7111 (mt-10) REVERT: H 87 ARG cc_start: 0.7953 (mmt-90) cc_final: 0.7673 (mmt180) REVERT: K 42 MET cc_start: 0.8184 (mtt) cc_final: 0.7805 (mtt) REVERT: K 109 THR cc_start: 0.6745 (m) cc_final: 0.6463 (t) REVERT: K 261 LYS cc_start: 0.8368 (mttm) cc_final: 0.7979 (mtpm) REVERT: N 95 ASP cc_start: 0.7821 (t70) cc_final: 0.7548 (t0) REVERT: N 170 HIS cc_start: 0.7954 (m90) cc_final: 0.6579 (m90) REVERT: N 173 LEU cc_start: 0.8157 (mm) cc_final: 0.7857 (tm) REVERT: N 180 THR cc_start: 0.8870 (m) cc_final: 0.8351 (p) outliers start: 4 outliers final: 3 residues processed: 255 average time/residue: 0.8358 time to fit residues: 229.8792 Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 25 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 57 GLN K 196 GLN N 196 GLN N 227 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108530 restraints weight = 18656.555| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.85 r_work: 0.3237 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16529 Z= 0.226 Angle : 0.772 10.843 23622 Z= 0.418 Chirality : 0.052 0.325 2663 Planarity : 0.005 0.080 1949 Dihedral : 30.146 157.261 4684 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.02 % Allowed : 23.11 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1186 helix: 1.20 (0.21), residues: 545 sheet: 0.01 (0.33), residues: 234 loop : -1.10 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 40 TYR 0.024 0.002 TYR H 41 PHE 0.011 0.002 PHE E 84 TRP 0.013 0.002 TRP N 58 HIS 0.006 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (16525) covalent geometry : angle 0.77206 / 0.42 (23614) SS BOND : bond 0.00684 / 0.38 ( 4) SS BOND : angle 1.31573 / 0.71 ( 8) hydrogen bonds : bond 0.05349 / 3.63 ( 828) hydrogen bonds : angle 3.93027 / 2.93 ( 2122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 120 MET cc_start: 0.7726 (mmt) cc_final: 0.7480 (mtt) REVERT: A 129 ARG cc_start: 0.7874 (ttt180) cc_final: 0.6796 (tpt90) REVERT: A 133 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6699 (mt-10) REVERT: B 35 ARG cc_start: 0.7145 (ttm170) cc_final: 0.6881 (ttm-80) REVERT: B 79 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7070 (mttp) REVERT: D 43 TYR cc_start: 0.7591 (t80) cc_final: 0.7245 (t80) REVERT: D 60 MET cc_start: 0.8308 (tpp) cc_final: 0.8082 (tpp) REVERT: D 87 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7032 (ttm170) REVERT: E 115 LYS cc_start: 0.8305 (mttt) cc_final: 0.8098 (mmtp) REVERT: E 133 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7360 (mt-10) REVERT: F 45 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6425 (mtm180) REVERT: G 73 ASN cc_start: 0.6911 (t0) cc_final: 0.6620 (t0) REVERT: G 91 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: H 36 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: H 72 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7215 (mt-10) REVERT: H 87 ARG cc_start: 0.7717 (mmt-90) cc_final: 0.7170 (mmt90) REVERT: K 25 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: K 175 GLU cc_start: 0.8375 (tt0) cc_final: 0.7217 (mt-10) REVERT: K 261 LYS cc_start: 0.8111 (mttm) cc_final: 0.7564 (mtpm) REVERT: N 23 GLU cc_start: 0.6652 (tt0) cc_final: 0.6317 (tt0) REVERT: N 25 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: N 95 ASP cc_start: 0.7588 (t70) cc_final: 0.7278 (t70) REVERT: N 137 SER cc_start: 0.7049 (OUTLIER) cc_final: 0.6731 (t) REVERT: N 170 HIS cc_start: 0.7761 (m90) cc_final: 0.7509 (m-70) REVERT: N 180 THR cc_start: 0.8604 (m) cc_final: 0.8010 (p) REVERT: N 219 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7716 (mtp180) REVERT: N 247 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7851 (tp) outliers start: 41 outliers final: 14 residues processed: 192 average time/residue: 0.8602 time to fit residues: 177.4848 Evaluate side-chains 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110828 restraints weight = 18627.016| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.75 r_work: 0.3282 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16529 Z= 0.159 Angle : 0.659 8.886 23622 Z= 0.371 Chirality : 0.046 0.324 2663 Planarity : 0.004 0.059 1949 Dihedral : 30.110 158.218 4682 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.02 % Allowed : 23.80 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1186 helix: 1.82 (0.21), residues: 549 sheet: 0.18 (0.34), residues: 234 loop : -0.97 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 23 TYR 0.018 0.001 TYR H 41 PHE 0.006 0.001 PHE H 71 TRP 0.009 0.001 TRP N 58 HIS 0.014 0.001 HIS N 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (16525) covalent geometry : angle 0.65924 / 0.37 (23614) SS BOND : bond 0.00468 / 0.28 ( 4) SS BOND : angle 0.83595 / 0.43 ( 8) hydrogen bonds : bond 0.04602 / 3.12 ( 828) hydrogen bonds : angle 3.64357 / 2.69 ( 2122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7739 (mm-30) REVERT: A 120 MET cc_start: 0.7949 (mmt) cc_final: 0.7669 (mtt) REVERT: A 129 ARG cc_start: 0.8068 (ttt180) cc_final: 0.6938 (tpt90) REVERT: A 133 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6939 (mt-10) REVERT: B 35 ARG cc_start: 0.7269 (ttm170) cc_final: 0.6986 (ttm-80) REVERT: B 91 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8144 (ttpp) REVERT: C 41 GLU cc_start: 0.8343 (tt0) cc_final: 0.8078 (tt0) REVERT: C 51 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7928 (ttp) REVERT: D 43 TYR cc_start: 0.7719 (t80) cc_final: 0.7312 (t80) REVERT: D 87 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7113 (mmt-90) REVERT: E 115 LYS cc_start: 0.8406 (mttt) cc_final: 0.7768 (mtmt) REVERT: G 73 ASN cc_start: 0.7225 (t0) cc_final: 0.7024 (t0) REVERT: G 91 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: H 36 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: H 72 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7412 (mt-10) REVERT: H 87 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.7263 (mmt90) REVERT: K 169 MET cc_start: 0.8042 (ppp) cc_final: 0.7710 (ppp) REVERT: K 175 GLU cc_start: 0.8390 (tt0) cc_final: 0.7296 (mt-10) REVERT: K 258 SER cc_start: 0.8460 (m) cc_final: 0.7858 (p) REVERT: K 261 LYS cc_start: 0.8314 (mttm) cc_final: 0.7680 (mtpm) REVERT: N 32 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6419 (mm-30) REVERT: N 95 ASP cc_start: 0.7657 (t70) cc_final: 0.7405 (t0) REVERT: N 137 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6747 (t) REVERT: N 165 SER cc_start: 0.6745 (OUTLIER) cc_final: 0.6419 (m) REVERT: N 180 THR cc_start: 0.8609 (m) cc_final: 0.8137 (p) REVERT: N 247 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8036 (tp) outliers start: 41 outliers final: 14 residues processed: 192 average time/residue: 0.8501 time to fit residues: 175.7358 Evaluate side-chains 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.169269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117267 restraints weight = 18241.324| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.64 r_work: 0.3368 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16529 Z= 0.148 Angle : 0.639 7.926 23622 Z= 0.360 Chirality : 0.045 0.333 2663 Planarity : 0.004 0.052 1949 Dihedral : 30.069 157.176 4680 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.02 % Allowed : 24.19 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1186 helix: 2.16 (0.21), residues: 547 sheet: 0.28 (0.34), residues: 234 loop : -0.92 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.025 0.001 TYR K 82 PHE 0.006 0.001 PHE N 229 TRP 0.008 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (16525) covalent geometry : angle 0.63922 / 0.36 (23614) SS BOND : bond 0.00468 / 0.27 ( 4) SS BOND : angle 0.81316 / 0.40 ( 8) hydrogen bonds : bond 0.04315 / 2.91 ( 828) hydrogen bonds : angle 3.52251 / 2.61 ( 2122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 120 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: A 129 ARG cc_start: 0.8334 (ttt180) cc_final: 0.7336 (tpt90) REVERT: A 133 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 91 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8399 (ttpp) REVERT: C 41 GLU cc_start: 0.8374 (tt0) cc_final: 0.8091 (tt0) REVERT: D 43 TYR cc_start: 0.8087 (t80) cc_final: 0.7680 (t80) REVERT: D 87 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7399 (mmt-90) REVERT: E 49 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6824 (ptp90) REVERT: E 115 LYS cc_start: 0.8664 (mttt) cc_final: 0.8056 (mtmt) REVERT: F 84 MET cc_start: 0.8448 (mmm) cc_final: 0.8126 (mmm) REVERT: G 91 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: H 36 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: H 72 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7663 (mt-10) REVERT: H 87 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7548 (mmt90) REVERT: K 103 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.5922 (tpt) REVERT: K 169 MET cc_start: 0.8038 (ppp) cc_final: 0.7807 (ppp) REVERT: K 258 SER cc_start: 0.8601 (m) cc_final: 0.8033 (p) REVERT: K 261 LYS cc_start: 0.8484 (mttm) cc_final: 0.7831 (mtpm) REVERT: N 25 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: N 59 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8438 (p) REVERT: N 95 ASP cc_start: 0.7870 (t70) cc_final: 0.7664 (t0) REVERT: N 137 SER cc_start: 0.7304 (OUTLIER) cc_final: 0.7066 (t) REVERT: N 176 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7816 (ttm-80) REVERT: N 180 THR cc_start: 0.8752 (m) cc_final: 0.8238 (p) outliers start: 41 outliers final: 14 residues processed: 179 average time/residue: 0.8292 time to fit residues: 160.2218 Evaluate side-chains 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 162 MET Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 112 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN K 196 GLN N 164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.169236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115833 restraints weight = 18255.096| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.73 r_work: 0.3340 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16529 Z= 0.210 Angle : 0.686 8.602 23622 Z= 0.378 Chirality : 0.047 0.331 2663 Planarity : 0.005 0.055 1949 Dihedral : 30.179 159.591 4680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.51 % Allowed : 24.88 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1186 helix: 2.03 (0.22), residues: 548 sheet: 0.25 (0.34), residues: 234 loop : -0.99 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.018 0.002 TYR H 41 PHE 0.011 0.002 PHE N 229 TRP 0.014 0.002 TRP N 58 HIS 0.007 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (16525) covalent geometry : angle 0.68585 / 0.38 (23614) SS BOND : bond 0.00546 / 0.30 ( 4) SS BOND : angle 0.95828 / 0.49 ( 8) hydrogen bonds : bond 0.04981 / 3.35 ( 828) hydrogen bonds : angle 3.58666 / 2.65 ( 2122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.460 Fit side-chains REVERT: A 94 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 120 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8036 (mtt) REVERT: A 129 ARG cc_start: 0.8372 (ttt180) cc_final: 0.7379 (tpt90) REVERT: A 133 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 35 ARG cc_start: 0.7499 (ttm170) cc_final: 0.7197 (ttm-80) REVERT: B 91 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8385 (ttpp) REVERT: C 41 GLU cc_start: 0.8476 (tt0) cc_final: 0.8163 (tt0) REVERT: D 39 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8658 (m) REVERT: D 43 TYR cc_start: 0.8060 (t80) cc_final: 0.7644 (t80) REVERT: D 48 GLN cc_start: 0.7648 (mt0) cc_final: 0.7437 (tt0) REVERT: D 87 ARG cc_start: 0.7555 (mtp85) cc_final: 0.7306 (mmt-90) REVERT: E 42 ARG cc_start: 0.7238 (mmp80) cc_final: 0.6867 (mtm180) REVERT: E 49 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6390 (ptp90) REVERT: E 63 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7960 (mmt-90) REVERT: E 115 LYS cc_start: 0.8664 (mttt) cc_final: 0.8034 (mtmt) REVERT: E 131 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7567 (mtp85) REVERT: F 35 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7293 (mtm-85) REVERT: F 45 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7095 (mtm180) REVERT: G 91 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: H 36 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: H 72 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7728 (mt-10) REVERT: H 87 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7737 (mmt90) REVERT: K 258 SER cc_start: 0.8635 (m) cc_final: 0.8077 (p) REVERT: K 261 LYS cc_start: 0.8396 (mttm) cc_final: 0.7839 (mtpm) REVERT: N 25 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: N 95 ASP cc_start: 0.7908 (t70) cc_final: 0.7670 (t0) REVERT: N 137 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.7150 (t) REVERT: N 165 SER cc_start: 0.7228 (OUTLIER) cc_final: 0.6895 (m) REVERT: N 176 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7782 (ttm-80) REVERT: N 180 THR cc_start: 0.8674 (m) cc_final: 0.8255 (p) REVERT: N 263 GLU cc_start: 0.8217 (pm20) cc_final: 0.8010 (pm20) outliers start: 46 outliers final: 15 residues processed: 174 average time/residue: 0.8841 time to fit residues: 165.3264 Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 125 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 17 optimal weight: 0.9990 chunk 142 optimal weight: 30.0000 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.170965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117692 restraints weight = 18166.676| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.73 r_work: 0.3361 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16529 Z= 0.134 Angle : 0.655 8.088 23622 Z= 0.364 Chirality : 0.045 0.334 2663 Planarity : 0.004 0.045 1949 Dihedral : 30.146 158.769 4680 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.53 % Allowed : 25.95 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1186 helix: 2.20 (0.22), residues: 548 sheet: 0.25 (0.34), residues: 234 loop : -0.91 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.014 0.001 TYR N 72 PHE 0.008 0.001 PHE N 229 TRP 0.010 0.001 TRP N 58 HIS 0.004 0.001 HIS N 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (16525) covalent geometry : angle 0.65469 / 0.36 (23614) SS BOND : bond 0.00591 / 0.37 ( 4) SS BOND : angle 1.10741 / 0.53 ( 8) hydrogen bonds : bond 0.04323 / 2.90 ( 828) hydrogen bonds : angle 3.54081 / 2.62 ( 2122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.491 Fit side-chains REVERT: A 94 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8001 (mm-30) REVERT: A 120 MET cc_start: 0.8204 (mmt) cc_final: 0.7940 (mtt) REVERT: A 129 ARG cc_start: 0.8355 (ttt180) cc_final: 0.7325 (tpt90) REVERT: A 133 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7377 (mt-10) REVERT: B 35 ARG cc_start: 0.7468 (ttm170) cc_final: 0.7225 (ttm-80) REVERT: B 91 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8349 (ttpp) REVERT: C 41 GLU cc_start: 0.8466 (tt0) cc_final: 0.8196 (tt0) REVERT: D 43 TYR cc_start: 0.8018 (t80) cc_final: 0.7572 (t80) REVERT: D 48 GLN cc_start: 0.7590 (mt0) cc_final: 0.7364 (tt0) REVERT: D 87 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7263 (mmt-90) REVERT: E 42 ARG cc_start: 0.7257 (mmp80) cc_final: 0.6864 (mtm180) REVERT: E 49 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6375 (ptp90) REVERT: E 63 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7908 (mmt-90) REVERT: E 115 LYS cc_start: 0.8634 (mttt) cc_final: 0.8001 (mtmt) REVERT: E 131 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7581 (mtp85) REVERT: F 45 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7031 (mtm180) REVERT: F 84 MET cc_start: 0.8409 (mmm) cc_final: 0.8184 (mmm) REVERT: G 91 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: H 36 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: H 72 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7638 (mt-10) REVERT: H 87 ARG cc_start: 0.8088 (mmt-90) cc_final: 0.7688 (mmt90) REVERT: K 103 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.5856 (tpt) REVERT: K 258 SER cc_start: 0.8623 (m) cc_final: 0.8066 (p) REVERT: K 261 LYS cc_start: 0.8419 (mttm) cc_final: 0.7813 (mtpm) REVERT: N 25 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: N 59 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8543 (p) REVERT: N 95 ASP cc_start: 0.7896 (t70) cc_final: 0.7647 (t0) REVERT: N 137 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.7150 (t) REVERT: N 165 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6840 (m) REVERT: N 180 THR cc_start: 0.8658 (m) cc_final: 0.8253 (p) REVERT: N 263 GLU cc_start: 0.8244 (pm20) cc_final: 0.7875 (pm20) outliers start: 36 outliers final: 16 residues processed: 160 average time/residue: 0.8424 time to fit residues: 145.3530 Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 162 MET Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.169081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115694 restraints weight = 18143.733| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.72 r_work: 0.3330 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16529 Z= 0.195 Angle : 0.659 7.898 23622 Z= 0.365 Chirality : 0.046 0.332 2663 Planarity : 0.004 0.048 1949 Dihedral : 30.156 158.818 4680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.21 % Allowed : 25.37 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.24), residues: 1186 helix: 2.14 (0.21), residues: 548 sheet: 0.28 (0.34), residues: 234 loop : -0.86 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.016 0.002 TYR D 41 PHE 0.010 0.002 PHE F 100 TRP 0.014 0.002 TRP N 58 HIS 0.005 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (16525) covalent geometry : angle 0.65918 / 0.36 (23614) SS BOND : bond 0.00562 / 0.33 ( 4) SS BOND : angle 0.89622 / 0.49 ( 8) hydrogen bonds : bond 0.04647 / 3.10 ( 828) hydrogen bonds : angle 3.56399 / 2.64 ( 2122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.413 Fit side-chains REVERT: A 94 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 120 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7999 (mtt) REVERT: A 129 ARG cc_start: 0.8352 (ttt180) cc_final: 0.7309 (tpt90) REVERT: A 133 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7323 (mt-10) REVERT: B 35 ARG cc_start: 0.7480 (ttm170) cc_final: 0.7164 (ttm-80) REVERT: B 91 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8350 (ttpp) REVERT: C 41 GLU cc_start: 0.8448 (tt0) cc_final: 0.8163 (tt0) REVERT: D 39 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8644 (m) REVERT: D 43 TYR cc_start: 0.7954 (t80) cc_final: 0.7498 (t80) REVERT: D 48 GLN cc_start: 0.7635 (mt0) cc_final: 0.7424 (tt0) REVERT: D 87 ARG cc_start: 0.7428 (mtp85) cc_final: 0.7147 (mmt-90) REVERT: E 42 ARG cc_start: 0.7372 (mmp80) cc_final: 0.7084 (mtm180) REVERT: E 49 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6391 (ptp90) REVERT: E 63 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7883 (mmt-90) REVERT: E 115 LYS cc_start: 0.8629 (mttt) cc_final: 0.7989 (mtmt) REVERT: E 131 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7512 (mtp85) REVERT: F 35 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7172 (mtm-85) REVERT: F 45 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.6998 (mtm180) REVERT: G 91 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: H 36 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: H 72 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7731 (mt-10) REVERT: H 87 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7711 (mmt90) REVERT: K 103 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.5910 (tpt) REVERT: K 258 SER cc_start: 0.8629 (m) cc_final: 0.8076 (p) REVERT: K 261 LYS cc_start: 0.8412 (mttm) cc_final: 0.7828 (mtpm) REVERT: N 25 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: N 95 ASP cc_start: 0.7870 (t70) cc_final: 0.7623 (t0) REVERT: N 137 SER cc_start: 0.7311 (OUTLIER) cc_final: 0.7071 (t) REVERT: N 165 SER cc_start: 0.7445 (OUTLIER) cc_final: 0.7177 (m) REVERT: N 180 THR cc_start: 0.8634 (m) cc_final: 0.8232 (p) REVERT: N 263 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7667 (pm20) outliers start: 43 outliers final: 16 residues processed: 163 average time/residue: 0.8722 time to fit residues: 152.9053 Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 130 optimal weight: 40.0000 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.166469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114378 restraints weight = 18164.217| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.61 r_work: 0.3331 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16529 Z= 0.128 Angle : 0.644 8.522 23622 Z= 0.358 Chirality : 0.045 0.335 2663 Planarity : 0.004 0.042 1949 Dihedral : 30.129 158.001 4680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.72 % Allowed : 25.66 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.25), residues: 1186 helix: 2.34 (0.22), residues: 548 sheet: 0.29 (0.34), residues: 234 loop : -0.81 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.014 0.001 TYR H 41 PHE 0.006 0.001 PHE N 229 TRP 0.009 0.001 TRP N 58 HIS 0.005 0.001 HIS K 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (16525) covalent geometry : angle 0.64343 / 0.36 (23614) SS BOND : bond 0.00564 / 0.34 ( 4) SS BOND : angle 1.05449 / 0.51 ( 8) hydrogen bonds : bond 0.04128 / 2.74 ( 828) hydrogen bonds : angle 3.51613 / 2.60 ( 2122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7995 (mm-30) REVERT: A 120 MET cc_start: 0.8199 (mmt) cc_final: 0.7973 (mtt) REVERT: A 129 ARG cc_start: 0.8402 (ttt180) cc_final: 0.7419 (tpt90) REVERT: A 133 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7410 (mt-10) REVERT: B 35 ARG cc_start: 0.7552 (ttm170) cc_final: 0.7338 (ttm-80) REVERT: B 79 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7602 (mttp) REVERT: B 91 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8421 (ttpp) REVERT: C 41 GLU cc_start: 0.8447 (tt0) cc_final: 0.8169 (tt0) REVERT: D 39 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8623 (m) REVERT: D 43 TYR cc_start: 0.8040 (t80) cc_final: 0.7591 (t80) REVERT: D 48 GLN cc_start: 0.7678 (mt0) cc_final: 0.7456 (tt0) REVERT: E 42 ARG cc_start: 0.7346 (mmp80) cc_final: 0.7091 (mtm180) REVERT: E 49 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6471 (ptp90) REVERT: E 63 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8115 (mmt-90) REVERT: E 115 LYS cc_start: 0.8667 (mttt) cc_final: 0.8050 (mtmt) REVERT: E 131 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7535 (mtp85) REVERT: F 45 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7085 (mtm180) REVERT: G 91 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: H 36 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: H 87 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7766 (mmt90) REVERT: K 103 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.6028 (tpt) REVERT: K 258 SER cc_start: 0.8645 (m) cc_final: 0.8100 (p) REVERT: K 261 LYS cc_start: 0.8486 (mttm) cc_final: 0.7919 (mtpm) REVERT: N 25 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: N 81 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8440 (ttpt) REVERT: N 95 ASP cc_start: 0.7934 (t70) cc_final: 0.7701 (t0) REVERT: N 111 GLU cc_start: 0.7853 (pp20) cc_final: 0.7598 (pp20) REVERT: N 137 SER cc_start: 0.7338 (OUTLIER) cc_final: 0.7113 (t) REVERT: N 165 SER cc_start: 0.7324 (OUTLIER) cc_final: 0.7031 (m) REVERT: N 180 THR cc_start: 0.8651 (m) cc_final: 0.8286 (p) REVERT: N 263 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7771 (pm20) outliers start: 38 outliers final: 15 residues processed: 174 average time/residue: 0.8404 time to fit residues: 157.5591 Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 128 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.169296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.115963 restraints weight = 18264.419| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.72 r_work: 0.3326 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16529 Z= 0.186 Angle : 0.657 10.305 23622 Z= 0.362 Chirality : 0.045 0.331 2663 Planarity : 0.004 0.043 1949 Dihedral : 30.116 158.344 4680 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.62 % Allowed : 25.95 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.24), residues: 1186 helix: 2.22 (0.22), residues: 548 sheet: 0.62 (0.36), residues: 214 loop : -0.95 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 87 TYR 0.015 0.002 TYR N 72 PHE 0.009 0.001 PHE F 100 TRP 0.012 0.001 TRP N 58 HIS 0.005 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (16525) covalent geometry : angle 0.65684 / 0.36 (23614) SS BOND : bond 0.00604 / 0.37 ( 4) SS BOND : angle 0.99682 / 0.57 ( 8) hydrogen bonds : bond 0.04474 / 2.98 ( 828) hydrogen bonds : angle 3.54462 / 2.62 ( 2122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7994 (mm-30) REVERT: A 120 MET cc_start: 0.8236 (mmt) cc_final: 0.7983 (mtt) REVERT: A 129 ARG cc_start: 0.8363 (ttt180) cc_final: 0.7306 (tpt90) REVERT: A 133 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 35 ARG cc_start: 0.7478 (ttm170) cc_final: 0.7224 (ttm-80) REVERT: B 91 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8327 (ttpp) REVERT: C 41 GLU cc_start: 0.8438 (tt0) cc_final: 0.8141 (tt0) REVERT: D 39 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8557 (m) REVERT: D 43 TYR cc_start: 0.7902 (t80) cc_final: 0.7408 (t80) REVERT: E 42 ARG cc_start: 0.7385 (mmp80) cc_final: 0.7130 (mtm180) REVERT: E 49 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6405 (ptp90) REVERT: E 63 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7903 (mmt-90) REVERT: E 115 LYS cc_start: 0.8591 (mttt) cc_final: 0.7941 (mtmt) REVERT: E 131 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7529 (mtp85) REVERT: F 45 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7084 (mtm180) REVERT: G 91 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: H 36 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: H 87 ARG cc_start: 0.8091 (mmt-90) cc_final: 0.7701 (mmt90) REVERT: K 103 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.5910 (tpt) REVERT: K 258 SER cc_start: 0.8617 (m) cc_final: 0.8062 (p) REVERT: K 261 LYS cc_start: 0.8505 (mttm) cc_final: 0.8019 (mtpm) REVERT: N 25 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: N 95 ASP cc_start: 0.7869 (t70) cc_final: 0.7612 (t0) REVERT: N 111 GLU cc_start: 0.7836 (pp20) cc_final: 0.7596 (pp20) REVERT: N 137 SER cc_start: 0.7303 (OUTLIER) cc_final: 0.7069 (t) REVERT: N 165 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7111 (m) REVERT: N 176 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7803 (ttm-80) REVERT: N 180 THR cc_start: 0.8568 (m) cc_final: 0.8187 (p) REVERT: N 263 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7755 (pm20) outliers start: 37 outliers final: 15 residues processed: 167 average time/residue: 0.8707 time to fit residues: 156.4555 Evaluate side-chains 169 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 76 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.165437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113300 restraints weight = 18080.187| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.59 r_work: 0.3315 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16529 Z= 0.156 Angle : 0.652 11.524 23622 Z= 0.359 Chirality : 0.045 0.333 2663 Planarity : 0.004 0.041 1949 Dihedral : 30.111 158.103 4680 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.23 % Allowed : 26.44 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1186 helix: 2.26 (0.22), residues: 548 sheet: 0.62 (0.36), residues: 214 loop : -0.94 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.014 0.001 TYR N 72 PHE 0.007 0.001 PHE N 229 TRP 0.011 0.001 TRP N 58 HIS 0.004 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (16525) covalent geometry : angle 0.65154 / 0.36 (23614) SS BOND : bond 0.00508 / 0.30 ( 4) SS BOND : angle 1.06477 / 0.68 ( 8) hydrogen bonds : bond 0.04299 / 2.86 ( 828) hydrogen bonds : angle 3.53457 / 2.61 ( 2122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8042 (mm-30) REVERT: A 120 MET cc_start: 0.8249 (mmt) cc_final: 0.8008 (mtt) REVERT: A 129 ARG cc_start: 0.8446 (ttt180) cc_final: 0.7436 (tpt90) REVERT: A 133 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7411 (mt-10) REVERT: B 35 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7341 (ttm-80) REVERT: B 79 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7597 (mttp) REVERT: B 91 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8399 (ttpp) REVERT: C 41 GLU cc_start: 0.8427 (tt0) cc_final: 0.8144 (tt0) REVERT: D 39 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8568 (m) REVERT: D 43 TYR cc_start: 0.8018 (t80) cc_final: 0.7527 (t80) REVERT: E 42 ARG cc_start: 0.7418 (mmp80) cc_final: 0.7151 (mtm180) REVERT: E 49 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6514 (ptp90) REVERT: E 63 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7997 (mmt-90) REVERT: E 115 LYS cc_start: 0.8669 (mttt) cc_final: 0.8052 (mtmt) REVERT: E 131 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7592 (mtp85) REVERT: F 45 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7154 (mtm180) REVERT: G 91 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: H 36 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: H 87 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7785 (mmt90) REVERT: K 103 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.5989 (tpt) REVERT: K 258 SER cc_start: 0.8639 (m) cc_final: 0.8096 (p) REVERT: K 261 LYS cc_start: 0.8547 (mttm) cc_final: 0.8068 (mtpm) REVERT: N 25 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: N 68 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: N 95 ASP cc_start: 0.7942 (t70) cc_final: 0.7705 (t0) REVERT: N 111 GLU cc_start: 0.7835 (pp20) cc_final: 0.7607 (pp20) REVERT: N 137 SER cc_start: 0.7390 (OUTLIER) cc_final: 0.7148 (t) REVERT: N 165 SER cc_start: 0.7343 (OUTLIER) cc_final: 0.7033 (m) REVERT: N 180 THR cc_start: 0.8618 (m) cc_final: 0.8258 (p) REVERT: N 263 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7899 (pm20) outliers start: 33 outliers final: 15 residues processed: 166 average time/residue: 0.8759 time to fit residues: 156.4864 Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.169817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116852 restraints weight = 18169.323| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.71 r_work: 0.3341 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16529 Z= 0.153 Angle : 0.647 11.545 23622 Z= 0.357 Chirality : 0.044 0.334 2663 Planarity : 0.004 0.041 1949 Dihedral : 30.102 157.988 4680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.33 % Allowed : 26.35 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1186 helix: 2.28 (0.22), residues: 548 sheet: 0.62 (0.36), residues: 214 loop : -0.93 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 87 TYR 0.021 0.001 TYR F 88 PHE 0.007 0.001 PHE N 229 TRP 0.010 0.001 TRP N 58 HIS 0.004 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (16525) covalent geometry : angle 0.64699 / 0.36 (23614) SS BOND : bond 0.00508 / 0.31 ( 4) SS BOND : angle 0.98243 / 0.57 ( 8) hydrogen bonds : bond 0.04228 / 2.80 ( 828) hydrogen bonds : angle 3.52046 / 2.60 ( 2122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6588.12 seconds wall clock time: 112 minutes 48.68 seconds (6768.68 seconds total)