Starting phenix.real_space_refine on Sat Aug 23 23:03:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk5_27483/08_2025/8dk5_27483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk5_27483/08_2025/8dk5_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dk5_27483/08_2025/8dk5_27483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk5_27483/08_2025/8dk5_27483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dk5_27483/08_2025/8dk5_27483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk5_27483/08_2025/8dk5_27483.map" } 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-2.0-5787/lib/python3.9/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: 3.17, per 1000 atoms: 0.20 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: 1.03 Conformation dependent library (CDL) restraints added in 391.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.01 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: 2.44 Time building geometry restraints manager: 1.39 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=" 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 I 92 " pdb=" P DA I 93 " ideal model delta sigma weight residual 1.607 1.382 0.225 1.50e-02 4.44e+03 2.24e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.236 1.045 0.191 1.29e-02 6.01e+03 2.20e+02 bond pdb=" C LEU C 93 " pdb=" O LEU C 93 " ideal model delta sigma weight residual 1.237 1.069 0.168 1.17e-02 7.31e+03 2.06e+02 bond pdb=" O3' DG I 110 " pdb=" P DC I 111 " ideal model delta sigma weight residual 1.607 1.393 0.214 1.50e-02 4.44e+03 2.04e+02 ... (remaining 16520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 23480 5.96 - 11.91: 110 11.91 - 17.87: 22 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=" O3' DA J 94 " pdb=" C3' DA J 94 " pdb=" C2' DA J 94 " ideal model delta sigma weight residual 111.50 126.85 -15.35 1.50e+00 4.44e-01 1.05e+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 angle pdb=" C3' DG I 60 " pdb=" O3' DG I 60 " pdb=" P DA I 61 " ideal model delta sigma weight residual 120.20 132.96 -12.76 1.50e+00 4.44e-01 7.24e+01 angle pdb=" C3' DT J 76 " pdb=" O3' DT J 76 " pdb=" P DT J 77 " ideal model delta sigma weight residual 120.20 132.68 -12.48 1.50e+00 4.44e-01 6.92e+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: 2570 0.137 - 0.275: 66 0.275 - 0.412: 16 0.412 - 0.550: 8 0.550 - 0.687: 3 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 2.35 -1.79 0.55 2.00e-01 2.50e+01 7.70e+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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.620 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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= 0.647 Angle : 1.114 29.781 23622 Z= 0.625 Chirality : 0.065 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 aren 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 covalent geometry : bond 0.01079 (16525) covalent geometry : angle 1.11356 (23614) SS BOND : bond 0.00319 ( 4) SS BOND : angle 1.23486 ( 8) hydrogen bonds : bond 0.13579 ( 828) hydrogen bonds : angle 6.60538 ( 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 : 0.475 Fit side-chains 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: 0.7319 (mt-10) REVERT: D 36 GLU cc_start: 0.7481 (pt0) cc_final: 0.7195 (pt0) REVERT: D 43 TYR cc_start: 0.7937 (t80) cc_final: 0.7572 (t80) REVERT: D 60 MET cc_start: 0.8470 (tpp) cc_final: 0.8267 (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: 0.7550 (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: 0.7670 (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: 0.7978 (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: 0.7856 (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: 0.7794 time to fit residues: 213.4412 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 : 0.464 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.167049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115051 restraints weight = 18092.990| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.64 r_work: 0.3331 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16529 Z= 0.230 Angle : 0.645 7.301 23622 Z= 0.371 Chirality : 0.039 0.166 2663 Planarity : 0.005 0.080 1949 Dihedral : 29.919 157.939 4684 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.53 % Allowed : 23.02 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.24), residues: 1186 helix: 1.27 (0.21), residues: 550 sheet: 0.08 (0.34), residues: 234 loop : -1.15 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.025 0.002 TYR H 41 PHE 0.009 0.002 PHE N 229 TRP 0.015 0.002 TRP N 58 HIS 0.006 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00529 (16525) covalent geometry : angle 0.64455 (23614) SS BOND : bond 0.00627 ( 4) SS BOND : angle 1.10126 ( 8) hydrogen bonds : bond 0.04696 ( 828) hydrogen bonds : angle 3.68118 ( 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 199 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 129 ARG cc_start: 0.8448 (ttt180) cc_final: 0.7478 (tpt90) REVERT: A 133 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7450 (mt-10) REVERT: D 43 TYR cc_start: 0.8187 (t80) cc_final: 0.7892 (t80) REVERT: D 87 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7488 (mmt-90) REVERT: E 63 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8107 (mmt-90) REVERT: G 91 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: H 36 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: H 72 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7696 (mt-10) REVERT: H 87 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7683 (mmt90) REVERT: K 42 MET cc_start: 0.8658 (mtt) cc_final: 0.8432 (mtt) REVERT: K 258 SER cc_start: 0.8688 (m) cc_final: 0.8127 (p) REVERT: K 261 LYS cc_start: 0.8574 (mttm) cc_final: 0.8129 (mtpm) REVERT: N 137 SER cc_start: 0.7473 (OUTLIER) cc_final: 0.7244 (t) REVERT: N 180 THR cc_start: 0.8816 (m) cc_final: 0.8246 (p) outliers start: 36 outliers final: 11 residues processed: 183 average time/residue: 0.7676 time to fit residues: 151.2149 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR 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 93 THR Chi-restraints excluded: chain K residue 255 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 163 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 0.0040 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.170197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118705 restraints weight = 18334.230| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.64 r_work: 0.3423 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16529 Z= 0.149 Angle : 0.563 7.706 23622 Z= 0.329 Chirality : 0.035 0.143 2663 Planarity : 0.004 0.061 1949 Dihedral : 29.559 155.160 4680 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.13 % Allowed : 24.88 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.24), residues: 1186 helix: 1.99 (0.21), residues: 552 sheet: 0.35 (0.35), residues: 234 loop : -0.86 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.018 0.001 TYR H 41 PHE 0.006 0.001 PHE N 229 TRP 0.007 0.001 TRP N 69 HIS 0.005 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00328 (16525) covalent geometry : angle 0.56242 (23614) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.88006 ( 8) hydrogen bonds : bond 0.03716 ( 828) hydrogen bonds : angle 3.37416 ( 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 197 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.485 Fit side-chains REVERT: A 94 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7945 (mm-30) REVERT: A 129 ARG cc_start: 0.8357 (ttt180) cc_final: 0.7358 (tpt90) REVERT: A 133 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7567 (mt-10) REVERT: B 27 GLN cc_start: 0.8642 (mm110) cc_final: 0.8408 (mm-40) REVERT: B 31 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7705 (tttm) REVERT: D 43 TYR cc_start: 0.7989 (t80) cc_final: 0.7626 (t80) REVERT: G 91 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: H 36 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7311 (mm-30) REVERT: H 43 TYR cc_start: 0.7871 (t80) cc_final: 0.7257 (t80) REVERT: H 72 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7530 (mt-10) REVERT: H 87 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7495 (mmt90) REVERT: K 42 MET cc_start: 0.8620 (mtt) cc_final: 0.8167 (mtt) REVERT: K 81 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8030 (ttpt) REVERT: K 84 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7633 (pm20) REVERT: K 103 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.5791 (tpt) REVERT: K 258 SER cc_start: 0.8609 (m) cc_final: 0.8038 (p) REVERT: K 261 LYS cc_start: 0.8442 (mttm) cc_final: 0.7824 (mtpm) REVERT: N 95 ASP cc_start: 0.7942 (t0) cc_final: 0.7685 (t70) REVERT: N 137 SER cc_start: 0.7296 (OUTLIER) cc_final: 0.7087 (t) REVERT: N 165 SER cc_start: 0.6714 (OUTLIER) cc_final: 0.6327 (m) REVERT: N 170 HIS cc_start: 0.8084 (m-70) cc_final: 0.7651 (m-70) REVERT: N 175 GLU cc_start: 0.8842 (pt0) cc_final: 0.8402 (pm20) REVERT: N 180 THR cc_start: 0.8693 (m) cc_final: 0.8301 (p) REVERT: N 219 ARG cc_start: 0.8268 (mtm110) cc_final: 0.8023 (mtp180) outliers start: 32 outliers final: 7 residues processed: 180 average time/residue: 0.8909 time to fit residues: 172.3073 Evaluate side-chains 147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE 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 81 LYS Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 223 SER 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: 0.9990 chunk 132 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 GLN N 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111159 restraints weight = 18193.458| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.67 r_work: 0.3278 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16529 Z= 0.254 Angle : 0.637 9.115 23622 Z= 0.365 Chirality : 0.039 0.154 2663 Planarity : 0.005 0.055 1949 Dihedral : 29.913 158.768 4679 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.51 % Allowed : 23.70 % 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 aren not related in a simple way. whole: 0.93 (0.24), residues: 1186 helix: 1.84 (0.21), residues: 548 sheet: 0.68 (0.36), residues: 214 loop : -1.06 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 95 TYR 0.017 0.002 TYR N 72 PHE 0.011 0.002 PHE N 229 TRP 0.013 0.002 TRP N 58 HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00588 (16525) covalent geometry : angle 0.63639 (23614) SS BOND : bond 0.00701 ( 4) SS BOND : angle 1.06467 ( 8) hydrogen bonds : bond 0.04649 ( 828) hydrogen bonds : angle 3.58119 ( 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 193 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 0.566 Fit side-chains REVERT: A 94 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8048 (mm-30) REVERT: A 129 ARG cc_start: 0.8421 (ttt180) cc_final: 0.7400 (tpt90) REVERT: A 133 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7434 (mt-10) REVERT: B 27 GLN cc_start: 0.8742 (mm110) cc_final: 0.8511 (mm110) REVERT: B 31 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7709 (tttm) REVERT: B 91 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8380 (ttpp) REVERT: D 34 ARG cc_start: 0.6723 (ptm160) cc_final: 0.4998 (ptt180) REVERT: D 39 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8732 (m) REVERT: D 43 TYR cc_start: 0.8047 (t80) cc_final: 0.7800 (t80) REVERT: D 102 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8239 (mp) REVERT: E 42 ARG cc_start: 0.7501 (mmp80) cc_final: 0.7300 (mtm180) REVERT: E 49 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6430 (ptp90) REVERT: E 63 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8106 (mmt-90) REVERT: E 131 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7638 (mtp85) REVERT: F 35 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7288 (mtm-85) REVERT: F 93 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: G 91 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: H 36 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: H 87 ARG cc_start: 0.8106 (mmt-90) cc_final: 0.7650 (mmt90) REVERT: K 42 MET cc_start: 0.8681 (mtt) cc_final: 0.8329 (mtt) REVERT: K 81 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8160 (ttpt) REVERT: K 103 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.6021 (tpt) REVERT: K 258 SER cc_start: 0.8732 (m) cc_final: 0.8178 (p) REVERT: K 261 LYS cc_start: 0.8425 (mttm) cc_final: 0.8026 (mtpm) REVERT: N 25 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: N 68 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: N 95 ASP cc_start: 0.7908 (t0) cc_final: 0.7653 (t70) REVERT: N 137 SER cc_start: 0.7410 (OUTLIER) cc_final: 0.7179 (t) REVERT: N 176 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7788 (ttm-80) REVERT: N 180 THR cc_start: 0.8570 (m) cc_final: 0.8082 (p) outliers start: 46 outliers final: 10 residues processed: 171 average time/residue: 0.9314 time to fit residues: 170.3805 Evaluate side-chains 155 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 102 LEU 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 109 LEU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 93 GLN 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 81 LYS Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU 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 137 SER Chi-restraints excluded: chain N residue 176 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 80 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.165273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113314 restraints weight = 18172.941| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.60 r_work: 0.3304 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16529 Z= 0.165 Angle : 0.592 7.676 23622 Z= 0.345 Chirality : 0.036 0.143 2663 Planarity : 0.004 0.048 1949 Dihedral : 29.841 157.290 4679 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.21 % Allowed : 24.49 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.24), residues: 1186 helix: 2.07 (0.22), residues: 548 sheet: 0.68 (0.36), residues: 214 loop : -0.96 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 87 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 H 50 Details of bonding type rmsd covalent geometry : bond 0.00369 (16525) covalent geometry : angle 0.59175 (23614) SS BOND : bond 0.00469 ( 4) SS BOND : angle 0.94120 ( 8) hydrogen bonds : bond 0.04090 ( 828) hydrogen bonds : angle 3.49231 ( 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 192 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.471 Fit side-chains REVERT: A 94 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 129 ARG cc_start: 0.8402 (ttt180) cc_final: 0.7437 (tpt90) REVERT: A 133 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7521 (mt-10) REVERT: B 27 GLN cc_start: 0.8749 (mm110) cc_final: 0.8530 (mm110) REVERT: B 31 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7736 (tttm) REVERT: B 91 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8415 (ttpp) REVERT: D 34 ARG cc_start: 0.6722 (ptm160) cc_final: 0.5007 (ptt180) REVERT: D 39 SER cc_start: 0.8985 (OUTLIER) cc_final: 0.8728 (m) REVERT: D 43 TYR cc_start: 0.8018 (t80) cc_final: 0.7723 (t80) REVERT: E 42 ARG cc_start: 0.7528 (mmp80) cc_final: 0.7229 (mtm180) REVERT: E 49 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6629 (ptp90) REVERT: E 63 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8106 (mmt-90) REVERT: E 125 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8418 (mp10) REVERT: F 84 MET cc_start: 0.8465 (mmm) cc_final: 0.8133 (mmm) REVERT: F 93 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: F 95 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7950 (mtp85) REVERT: G 91 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: H 36 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: H 87 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7639 (mmt90) REVERT: K 103 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.5997 (tpt) REVERT: K 258 SER cc_start: 0.8704 (m) cc_final: 0.8155 (p) REVERT: K 261 LYS cc_start: 0.8465 (mttm) cc_final: 0.7956 (mtpm) REVERT: N 25 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: N 59 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8604 (p) REVERT: N 68 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: N 95 ASP cc_start: 0.7904 (t0) cc_final: 0.7638 (t70) REVERT: N 137 SER cc_start: 0.7396 (OUTLIER) cc_final: 0.7151 (t) REVERT: N 165 SER cc_start: 0.7461 (OUTLIER) cc_final: 0.7141 (m) REVERT: N 170 HIS cc_start: 0.8122 (m-70) cc_final: 0.7715 (m-70) REVERT: N 176 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7730 (ttm-80) REVERT: N 180 THR cc_start: 0.8530 (m) cc_final: 0.8179 (p) outliers start: 43 outliers final: 14 residues processed: 173 average time/residue: 0.9148 time to fit residues: 169.6744 Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 86 LYS 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 109 LEU Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 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 K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 212 LEU 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 137 SER Chi-restraints excluded: chain N residue 159 ASP 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: 7.9990 chunk 128 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.166896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115169 restraints weight = 18111.947| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.60 r_work: 0.3336 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16529 Z= 0.156 Angle : 0.572 7.732 23622 Z= 0.333 Chirality : 0.035 0.179 2663 Planarity : 0.004 0.044 1949 Dihedral : 29.642 155.407 4679 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.21 % Allowed : 24.98 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.24), residues: 1186 helix: 2.30 (0.22), residues: 549 sheet: 0.65 (0.36), residues: 214 loop : -0.90 (0.29), residues: 423 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 0.006 0.001 PHE F 61 TRP 0.008 0.001 TRP N 58 HIS 0.004 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00348 (16525) covalent geometry : angle 0.57152 (23614) SS BOND : bond 0.00367 ( 4) SS BOND : angle 0.84203 ( 8) hydrogen bonds : bond 0.03720 ( 828) hydrogen bonds : angle 3.37622 ( 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 191 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.468 Fit side-chains REVERT: A 94 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8017 (mm-30) REVERT: A 129 ARG cc_start: 0.8408 (ttt180) cc_final: 0.7448 (tpt90) REVERT: A 133 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7561 (mt-10) REVERT: B 31 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7728 (tttm) REVERT: B 91 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8417 (ttpp) REVERT: D 34 ARG cc_start: 0.6676 (ptm160) cc_final: 0.4969 (ptt180) REVERT: D 43 TYR cc_start: 0.8005 (t80) cc_final: 0.7688 (t80) REVERT: D 48 GLN cc_start: 0.7866 (tt0) cc_final: 0.7609 (tt0) REVERT: E 42 ARG cc_start: 0.7503 (mmp80) cc_final: 0.7218 (mtm180) REVERT: E 49 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6796 (ptp90) REVERT: E 131 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7630 (mtp85) REVERT: G 91 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: H 36 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: H 87 ARG cc_start: 0.8067 (mmt-90) cc_final: 0.7620 (mmt90) REVERT: K 103 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.6006 (tpt) REVERT: K 258 SER cc_start: 0.8646 (m) cc_final: 0.8087 (p) REVERT: K 261 LYS cc_start: 0.8445 (mttm) cc_final: 0.7912 (mtpm) REVERT: N 59 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8515 (p) REVERT: N 68 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: N 95 ASP cc_start: 0.7901 (t0) cc_final: 0.7630 (t70) REVERT: N 137 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.7034 (t) REVERT: N 165 SER cc_start: 0.7418 (OUTLIER) cc_final: 0.7084 (m) REVERT: N 170 HIS cc_start: 0.8030 (m-70) cc_final: 0.7760 (m-70) REVERT: N 175 GLU cc_start: 0.8801 (pt0) cc_final: 0.8333 (pm20) REVERT: N 176 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7759 (ttm-80) REVERT: N 180 THR cc_start: 0.8578 (m) cc_final: 0.8232 (p) outliers start: 43 outliers final: 14 residues processed: 172 average time/residue: 0.8623 time to fit residues: 159.3760 Evaluate side-chains 172 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 131 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 94 GLU 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 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 129 LEU 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 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: 10.0000 chunk 104 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.164028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.112062 restraints weight = 18100.406| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.63 r_work: 0.3289 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16529 Z= 0.225 Angle : 0.613 9.772 23622 Z= 0.352 Chirality : 0.038 0.140 2663 Planarity : 0.004 0.043 1949 Dihedral : 29.758 157.336 4679 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.82 % Allowed : 25.76 % 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 aren not related in a simple way. whole: 1.22 (0.24), residues: 1186 helix: 2.15 (0.22), residues: 548 sheet: 0.64 (0.36), residues: 214 loop : -0.91 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.016 0.002 TYR N 72 PHE 0.009 0.001 PHE N 229 TRP 0.012 0.001 TRP N 58 HIS 0.005 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00520 (16525) covalent geometry : angle 0.61321 (23614) SS BOND : bond 0.00616 ( 4) SS BOND : angle 1.03264 ( 8) hydrogen bonds : bond 0.04201 ( 828) hydrogen bonds : angle 3.49915 ( 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 187 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.412 Fit side-chains REVERT: A 79 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8245 (tttm) REVERT: A 94 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8042 (mm-30) REVERT: A 129 ARG cc_start: 0.8496 (ttt180) cc_final: 0.7549 (tpt90) REVERT: A 133 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7466 (mt-10) REVERT: B 31 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7807 (tttm) REVERT: B 91 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8478 (ttpp) REVERT: D 34 ARG cc_start: 0.6806 (ptm160) cc_final: 0.5126 (ptt180) REVERT: D 39 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8656 (m) REVERT: D 43 TYR cc_start: 0.8095 (t80) cc_final: 0.7830 (t80) REVERT: D 48 GLN cc_start: 0.8048 (tt0) cc_final: 0.7817 (tt0) REVERT: E 49 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6636 (ptp90) REVERT: E 63 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8109 (mmt-90) REVERT: E 131 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7588 (mtp85) REVERT: G 91 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: H 36 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: H 87 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7785 (mmt90) REVERT: K 103 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.6004 (tpt) REVERT: K 258 SER cc_start: 0.8668 (m) cc_final: 0.8117 (p) REVERT: K 261 LYS cc_start: 0.8533 (mttm) cc_final: 0.8020 (mtpm) REVERT: N 32 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6917 (mm-30) REVERT: N 59 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8630 (p) REVERT: N 68 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7768 (pt0) REVERT: N 95 ASP cc_start: 0.7967 (t0) cc_final: 0.7740 (t70) REVERT: N 137 SER cc_start: 0.7449 (OUTLIER) cc_final: 0.7173 (t) REVERT: N 165 SER cc_start: 0.7478 (OUTLIER) cc_final: 0.7085 (m) REVERT: N 175 GLU cc_start: 0.8780 (pt0) cc_final: 0.8494 (pm20) REVERT: N 176 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7699 (ttm-80) REVERT: N 180 THR cc_start: 0.8598 (m) cc_final: 0.8257 (p) outliers start: 39 outliers final: 17 residues processed: 173 average time/residue: 0.8291 time to fit residues: 154.1193 Evaluate side-chains 172 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 103 LEU 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 109 LEU Chi-restraints excluded: chain E residue 131 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 167 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 255 THR 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 129 LEU 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 192 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 0.0980 chunk 117 optimal weight: 8.9990 chunk 69 optimal weight: 0.3980 chunk 130 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN 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 = 0.4119 r_free = 0.4119 target = 0.165604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113813 restraints weight = 18194.831| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.61 r_work: 0.3362 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16529 Z= 0.143 Angle : 0.596 8.596 23622 Z= 0.345 Chirality : 0.036 0.198 2663 Planarity : 0.004 0.042 1949 Dihedral : 29.729 156.509 4679 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.04 % Allowed : 26.44 % 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 aren not related in a simple way. whole: 1.37 (0.25), residues: 1186 helix: 2.32 (0.22), residues: 548 sheet: 0.63 (0.36), residues: 214 loop : -0.85 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.013 0.001 TYR N 72 PHE 0.006 0.001 PHE F 61 TRP 0.008 0.001 TRP N 58 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00310 (16525) covalent geometry : angle 0.59579 (23614) SS BOND : bond 0.00513 ( 4) SS BOND : angle 0.97367 ( 8) hydrogen bonds : bond 0.03845 ( 828) hydrogen bonds : angle 3.46914 ( 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 176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.480 Fit side-chains REVERT: A 79 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8147 (tttm) REVERT: A 94 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 129 ARG cc_start: 0.8429 (ttt180) cc_final: 0.7432 (tpt90) REVERT: A 133 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7425 (mt-10) REVERT: B 31 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7621 (tttm) REVERT: B 91 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8434 (ttpp) REVERT: D 34 ARG cc_start: 0.6751 (ptm160) cc_final: 0.5101 (ptt180) REVERT: D 39 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8602 (m) REVERT: D 43 TYR cc_start: 0.8007 (t80) cc_final: 0.7738 (t80) REVERT: D 48 GLN cc_start: 0.8046 (tt0) cc_final: 0.7822 (tt0) REVERT: E 49 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6557 (ptp90) REVERT: E 59 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: E 131 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7629 (mtp85) REVERT: G 91 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: H 36 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: H 87 ARG cc_start: 0.8051 (mmt-90) cc_final: 0.7630 (mmt90) REVERT: K 103 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.6021 (tpt) REVERT: K 258 SER cc_start: 0.8641 (m) cc_final: 0.8077 (p) REVERT: K 261 LYS cc_start: 0.8457 (mttm) cc_final: 0.7914 (mtpm) REVERT: N 59 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8556 (p) REVERT: N 68 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: N 95 ASP cc_start: 0.7914 (t0) cc_final: 0.7661 (t70) REVERT: N 137 SER cc_start: 0.7342 (OUTLIER) cc_final: 0.7069 (t) REVERT: N 165 SER cc_start: 0.7442 (OUTLIER) cc_final: 0.7053 (m) REVERT: N 175 GLU cc_start: 0.8768 (pt0) cc_final: 0.8491 (pm20) REVERT: N 180 THR cc_start: 0.8576 (m) cc_final: 0.8241 (p) outliers start: 31 outliers final: 14 residues processed: 162 average time/residue: 0.8726 time to fit residues: 151.9520 Evaluate side-chains 167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 103 LEU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 131 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 K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 212 LEU 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 129 LEU Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN K 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.164379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112581 restraints weight = 18186.424| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.61 r_work: 0.3299 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16529 Z= 0.207 Angle : 0.606 10.827 23622 Z= 0.349 Chirality : 0.037 0.143 2663 Planarity : 0.004 0.041 1949 Dihedral : 29.663 156.415 4679 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.53 % Allowed : 25.76 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.25), residues: 1186 helix: 2.22 (0.22), residues: 549 sheet: 0.68 (0.37), residues: 212 loop : -0.89 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.015 0.001 TYR N 72 PHE 0.009 0.001 PHE N 229 TRP 0.011 0.001 TRP N 58 HIS 0.005 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00478 (16525) covalent geometry : angle 0.60528 (23614) SS BOND : bond 0.00539 ( 4) SS BOND : angle 1.08008 ( 8) hydrogen bonds : bond 0.04060 ( 828) hydrogen bonds : angle 3.49537 ( 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 185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.455 Fit side-chains REVERT: A 79 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8171 (tttm) REVERT: A 94 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 129 ARG cc_start: 0.8469 (ttt180) cc_final: 0.7495 (tpt90) REVERT: A 133 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7478 (mt-10) REVERT: B 31 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7815 (tttm) REVERT: B 91 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8473 (ttpp) REVERT: D 34 ARG cc_start: 0.6776 (ptm160) cc_final: 0.5094 (ptt180) REVERT: D 43 TYR cc_start: 0.8082 (t80) cc_final: 0.7810 (t80) REVERT: E 49 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6661 (ptp90) REVERT: E 59 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: E 63 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8064 (mmt-90) REVERT: E 131 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7654 (mtp85) REVERT: F 84 MET cc_start: 0.8337 (mmm) cc_final: 0.8111 (tpt) REVERT: G 91 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: H 36 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: H 87 ARG cc_start: 0.8160 (mmt-90) cc_final: 0.7815 (mmt90) REVERT: K 103 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.6058 (tpt) REVERT: K 161 LYS cc_start: 0.9071 (tttt) cc_final: 0.8744 (tptp) REVERT: K 258 SER cc_start: 0.8640 (m) cc_final: 0.8100 (p) REVERT: K 261 LYS cc_start: 0.8455 (mttm) cc_final: 0.7964 (mtpm) REVERT: N 68 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: N 95 ASP cc_start: 0.8028 (t0) cc_final: 0.7747 (t70) REVERT: N 137 SER cc_start: 0.7442 (OUTLIER) cc_final: 0.7181 (t) REVERT: N 175 GLU cc_start: 0.8717 (pt0) cc_final: 0.8508 (pm20) REVERT: N 180 THR cc_start: 0.8596 (m) cc_final: 0.8234 (p) outliers start: 36 outliers final: 15 residues processed: 169 average time/residue: 0.9253 time to fit residues: 167.5633 Evaluate side-chains 169 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 131 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 K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain N residue 33 LEU 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 129 LEU Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 76 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 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 = 0.4126 r_free = 0.4126 target = 0.166023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114417 restraints weight = 18083.314| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.59 r_work: 0.3324 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16529 Z= 0.150 Angle : 0.597 12.741 23622 Z= 0.345 Chirality : 0.036 0.183 2663 Planarity : 0.004 0.041 1949 Dihedral : 29.631 155.689 4679 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.84 % Allowed : 26.44 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.25), residues: 1186 helix: 2.33 (0.22), residues: 549 sheet: 0.71 (0.37), residues: 212 loop : -0.85 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.013 0.001 TYR N 72 PHE 0.006 0.001 PHE F 61 TRP 0.008 0.001 TRP N 58 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00331 (16525) covalent geometry : angle 0.59671 (23614) SS BOND : bond 0.00432 ( 4) SS BOND : angle 0.99183 ( 8) hydrogen bonds : bond 0.03771 ( 828) hydrogen bonds : angle 3.46607 ( 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 178 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.312 Fit side-chains REVERT: A 79 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8117 (tttm) REVERT: A 94 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 129 ARG cc_start: 0.8427 (ttt180) cc_final: 0.7399 (tpt90) REVERT: A 133 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7466 (mt-10) REVERT: B 31 LYS cc_start: 0.8427 (ttmt) cc_final: 0.7739 (tttm) REVERT: B 91 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8422 (ttpp) REVERT: D 34 ARG cc_start: 0.6672 (ptm160) cc_final: 0.5025 (ptt180) REVERT: D 43 TYR cc_start: 0.7998 (t80) cc_final: 0.7717 (t80) REVERT: E 49 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6696 (ptp90) REVERT: E 59 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: E 131 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7621 (mtp85) REVERT: G 91 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: H 36 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: H 87 ARG cc_start: 0.8069 (mmt-90) cc_final: 0.7716 (mmt90) REVERT: K 103 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.6290 (tpt) REVERT: K 161 LYS cc_start: 0.9059 (tttt) cc_final: 0.8733 (tptp) REVERT: K 258 SER cc_start: 0.8538 (m) cc_final: 0.7974 (p) REVERT: K 261 LYS cc_start: 0.8411 (mttm) cc_final: 0.7932 (mtpm) REVERT: N 25 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: N 68 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: N 95 ASP cc_start: 0.7984 (t0) cc_final: 0.7709 (t70) REVERT: N 137 SER cc_start: 0.7384 (OUTLIER) cc_final: 0.7158 (t) REVERT: N 175 GLU cc_start: 0.8727 (pt0) cc_final: 0.8485 (pm20) REVERT: N 180 THR cc_start: 0.8526 (m) cc_final: 0.8167 (p) outliers start: 29 outliers final: 16 residues processed: 165 average time/residue: 0.8818 time to fit residues: 156.1218 Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 131 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 K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU 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 129 LEU Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 0.0040 chunk 32 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 94 optimal weight: 0.0980 chunk 113 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN K 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.165158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113498 restraints weight = 18064.583| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.60 r_work: 0.3318 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16529 Z= 0.188 Angle : 0.604 12.578 23622 Z= 0.347 Chirality : 0.036 0.165 2663 Planarity : 0.004 0.041 1949 Dihedral : 29.536 154.857 4679 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.23 % Allowed : 26.15 % 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 aren not related in a simple way. whole: 1.36 (0.25), residues: 1186 helix: 2.28 (0.22), residues: 549 sheet: 0.61 (0.36), residues: 214 loop : -0.82 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.019 0.001 TYR F 88 PHE 0.008 0.001 PHE N 229 TRP 0.008 0.001 TRP N 58 HIS 0.004 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00430 (16525) covalent geometry : angle 0.60412 (23614) SS BOND : bond 0.00501 ( 4) SS BOND : angle 1.08519 ( 8) hydrogen bonds : bond 0.03915 ( 828) hydrogen bonds : angle 3.45700 ( 2122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6688.79 seconds wall clock time: 114 minutes 13.83 seconds (6853.83 seconds total)