Starting phenix.real_space_refine on Fri Jun 13 17:46:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk5_27483/06_2025/8dk5_27483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk5_27483/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dk5_27483/06_2025/8dk5_27483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk5_27483/06_2025/8dk5_27483.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk5_27483/06_2025/8dk5_27483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk5_27483/06_2025/8dk5_27483.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.48, per 1000 atoms: 0.54 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: 3.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 7.58 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: 5.94 Time building geometry restraints manager: 4.42 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: 1.000 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.480 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 PHE 0.029 0.003 PHE A 78 TYR 0.045 0.002 TYR H 41 ARG 0.012 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.13579 ( 828) hydrogen bonds : angle 6.60538 ( 2122) SS BOND : bond 0.00319 ( 4) SS BOND : angle 1.23486 ( 8) covalent geometry : bond 0.01079 (16525) covalent geometry : angle 1.11356 (23614) *********************** 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 : 1.285 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: 1.6300 time to fit residues: 447.5695 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 : 1.325 ------------------------------------------------------------------------------- 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 120 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 0.0270 chunk 129 optimal weight: 20.0000 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.170650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117058 restraints weight = 18616.322| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.77 r_work: 0.3364 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1967 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= 0.147 Angle : 0.583 7.132 23622 Z= 0.342 Chirality : 0.036 0.164 2663 Planarity : 0.004 0.076 1949 Dihedral : 29.611 154.865 4684 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.84 % Allowed : 23.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1186 helix: 1.49 (0.21), residues: 549 sheet: 0.16 (0.34), residues: 234 loop : -0.98 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 58 HIS 0.004 0.001 HIS N 170 PHE 0.005 0.001 PHE E 67 TYR 0.019 0.001 TYR H 41 ARG 0.004 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 828) hydrogen bonds : angle 3.57598 ( 2122) SS BOND : bond 0.00437 ( 4) SS BOND : angle 0.85857 ( 8) covalent geometry : bond 0.00317 (16525) covalent geometry : angle 0.58326 (23614) *********************** 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: 29 poor density : 170 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 120 MET cc_start: 0.7749 (mmt) cc_final: 0.7529 (mtt) REVERT: A 129 ARG cc_start: 0.8006 (ttt180) cc_final: 0.6905 (tpt90) REVERT: C 41 GLU cc_start: 0.7973 (tt0) cc_final: 0.7768 (pt0) REVERT: D 43 TYR cc_start: 0.7717 (t80) cc_final: 0.7290 (t80) REVERT: D 87 ARG cc_start: 0.7408 (mtp85) cc_final: 0.7059 (ttm170) REVERT: E 129 ARG cc_start: 0.7845 (tmt170) cc_final: 0.7577 (tmt170) REVERT: F 79 LYS cc_start: 0.7969 (mttt) cc_final: 0.7615 (mttm) REVERT: F 84 MET cc_start: 0.8182 (mmm) cc_final: 0.7973 (mmm) REVERT: G 73 ASN cc_start: 0.7011 (t0) cc_final: 0.6731 (t0) REVERT: G 91 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6775 (tt0) REVERT: H 36 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: H 72 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7287 (mt-10) REVERT: H 87 ARG cc_start: 0.7690 (mmt-90) cc_final: 0.7378 (mmt180) REVERT: K 84 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7470 (pm20) REVERT: K 261 LYS cc_start: 0.8248 (mttm) cc_final: 0.7729 (mtpm) REVERT: N 95 ASP cc_start: 0.7659 (t70) cc_final: 0.7370 (t0) REVERT: N 137 SER cc_start: 0.7154 (OUTLIER) cc_final: 0.6851 (t) REVERT: N 170 HIS cc_start: 0.7443 (m90) cc_final: 0.7217 (m-70) REVERT: N 175 GLU cc_start: 0.8794 (pt0) cc_final: 0.8303 (pm20) REVERT: N 180 THR cc_start: 0.8684 (m) cc_final: 0.8059 (p) REVERT: N 219 ARG cc_start: 0.7977 (mtm110) cc_final: 0.7718 (mtp180) outliers start: 29 outliers final: 12 residues processed: 189 average time/residue: 1.5690 time to fit residues: 320.6610 Evaluate side-chains 167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 175 GLU Chi-restraints excluded: chain K residue 255 THR 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 163 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 85 optimal weight: 10.0000 chunk 109 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- 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** C 112 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.169495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117702 restraints weight = 18137.797| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.64 r_work: 0.3415 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16529 Z= 0.167 Angle : 0.577 7.327 23622 Z= 0.336 Chirality : 0.036 0.141 2663 Planarity : 0.004 0.062 1949 Dihedral : 29.590 156.236 4681 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.23 % Allowed : 24.39 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1186 helix: 2.03 (0.22), residues: 552 sheet: 0.40 (0.35), residues: 234 loop : -0.86 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.007 0.001 PHE N 229 TYR 0.020 0.001 TYR H 41 ARG 0.004 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 828) hydrogen bonds : angle 3.37973 ( 2122) SS BOND : bond 0.00453 ( 4) SS BOND : angle 0.89473 ( 8) covalent geometry : bond 0.00375 (16525) covalent geometry : angle 0.57708 (23614) *********************** 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 202 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 2.180 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 120 MET cc_start: 0.8244 (mmt) cc_final: 0.8025 (mtt) REVERT: A 129 ARG cc_start: 0.8365 (ttt180) cc_final: 0.7328 (tpt90) REVERT: B 27 GLN cc_start: 0.8667 (mm110) cc_final: 0.8415 (mm-40) REVERT: D 43 TYR cc_start: 0.8046 (t80) cc_final: 0.7740 (t80) REVERT: D 87 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7346 (mmt-90) REVERT: E 125 GLN cc_start: 0.8750 (mt0) cc_final: 0.8541 (mp10) REVERT: E 129 ARG cc_start: 0.8099 (tmt170) cc_final: 0.7840 (tmt170) REVERT: F 84 MET cc_start: 0.8448 (mmm) cc_final: 0.8081 (mmm) REVERT: G 91 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: H 36 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: H 72 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7607 (mt-10) REVERT: H 87 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7509 (mmt90) REVERT: K 81 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8064 (ttpt) REVERT: K 84 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7677 (pm20) REVERT: K 258 SER cc_start: 0.8401 (m) cc_final: 0.7861 (p) REVERT: K 261 LYS cc_start: 0.8464 (mttm) cc_final: 0.7852 (mtpm) REVERT: N 32 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6556 (mm-30) REVERT: N 59 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8399 (p) REVERT: N 68 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: N 137 SER cc_start: 0.7399 (OUTLIER) cc_final: 0.7181 (t) REVERT: N 165 SER cc_start: 0.6753 (OUTLIER) cc_final: 0.6374 (m) REVERT: N 180 THR cc_start: 0.8777 (m) cc_final: 0.8360 (p) REVERT: N 219 ARG cc_start: 0.8299 (mtm110) cc_final: 0.8045 (mtp180) outliers start: 33 outliers final: 7 residues processed: 183 average time/residue: 1.8172 time to fit residues: 358.2467 Evaluate side-chains 151 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 93 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 137 SER Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 165 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 85 optimal weight: 0.0470 chunk 139 optimal weight: 5.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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** G 104 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 = 0.4113 r_free = 0.4113 target = 0.164871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112724 restraints weight = 18061.399| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.67 r_work: 0.3300 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16529 Z= 0.229 Angle : 0.619 7.601 23622 Z= 0.357 Chirality : 0.038 0.144 2663 Planarity : 0.004 0.054 1949 Dihedral : 29.865 158.344 4681 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.31 % Allowed : 23.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1186 helix: 1.92 (0.21), residues: 548 sheet: 0.75 (0.37), residues: 214 loop : -1.01 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 58 HIS 0.007 0.002 HIS N 170 PHE 0.009 0.002 PHE N 229 TYR 0.017 0.002 TYR N 72 ARG 0.004 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 828) hydrogen bonds : angle 3.57036 ( 2122) SS BOND : bond 0.00722 ( 4) SS BOND : angle 1.17202 ( 8) covalent geometry : bond 0.00528 (16525) covalent geometry : angle 0.61870 (23614) *********************** 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 200 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.329 Fit side-chains REVERT: A 94 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 120 MET cc_start: 0.8271 (mmt) cc_final: 0.8067 (mtt) REVERT: A 129 ARG cc_start: 0.8364 (ttt180) cc_final: 0.7337 (tpt90) REVERT: B 35 ARG cc_start: 0.7548 (ttm170) cc_final: 0.7322 (ttm-80) REVERT: D 34 ARG cc_start: 0.6767 (ptm160) cc_final: 0.5092 (ptt180) REVERT: D 43 TYR cc_start: 0.8054 (t80) cc_final: 0.7788 (t80) REVERT: D 48 GLN cc_start: 0.8007 (tt0) cc_final: 0.7786 (tt0) REVERT: D 62 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8607 (mp) REVERT: E 42 ARG cc_start: 0.7526 (mmp80) cc_final: 0.7299 (mtm180) REVERT: E 49 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6452 (ptp90) REVERT: E 63 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8181 (mmt-90) REVERT: E 129 ARG cc_start: 0.8130 (tmt170) cc_final: 0.7719 (tmt170) REVERT: F 45 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7074 (mtm180) REVERT: F 84 MET cc_start: 0.8504 (mmm) cc_final: 0.8204 (mmm) REVERT: F 93 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: G 91 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: H 36 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: H 87 ARG cc_start: 0.8093 (mmt-90) cc_final: 0.7635 (mmt90) REVERT: K 258 SER cc_start: 0.8535 (m) cc_final: 0.8005 (p) REVERT: K 261 LYS cc_start: 0.8284 (mttm) cc_final: 0.7938 (mtpm) REVERT: N 25 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: N 68 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: N 95 ASP cc_start: 0.7996 (t70) cc_final: 0.7729 (t70) REVERT: N 137 SER cc_start: 0.7422 (OUTLIER) cc_final: 0.7197 (t) REVERT: N 165 SER cc_start: 0.7564 (OUTLIER) cc_final: 0.7199 (m) REVERT: N 170 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7932 (m-70) REVERT: N 176 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7738 (ttm-80) REVERT: N 180 THR cc_start: 0.8588 (m) cc_final: 0.8209 (p) REVERT: N 219 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8103 (mtp-110) outliers start: 44 outliers final: 9 residues processed: 177 average time/residue: 1.8621 time to fit residues: 353.2145 Evaluate side-chains 156 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 45 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 K residue 93 THR Chi-restraints excluded: chain K residue 173 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 137 SER Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 123 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 92 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- 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 73 ASN G 104 GLN K 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114023 restraints weight = 18284.640| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.60 r_work: 0.3315 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16529 Z= 0.170 Angle : 0.588 8.003 23622 Z= 0.342 Chirality : 0.036 0.142 2663 Planarity : 0.004 0.048 1949 Dihedral : 29.776 156.821 4679 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.92 % Allowed : 25.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1186 helix: 2.14 (0.21), residues: 548 sheet: 0.68 (0.36), residues: 214 loop : -0.96 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.009 0.001 PHE K 229 TYR 0.016 0.001 TYR H 41 ARG 0.004 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 828) hydrogen bonds : angle 3.47993 ( 2122) SS BOND : bond 0.00472 ( 4) SS BOND : angle 0.88681 ( 8) covalent geometry : bond 0.00383 (16525) covalent geometry : angle 0.58807 (23614) *********************** 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 176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 1.650 Fit side-chains REVERT: A 94 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8046 (mm-30) REVERT: A 120 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7953 (mtt) REVERT: A 129 ARG cc_start: 0.8438 (ttt180) cc_final: 0.7484 (tpt90) REVERT: B 35 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7357 (ttm-80) REVERT: D 34 ARG cc_start: 0.6753 (ptm160) cc_final: 0.5020 (ptt180) REVERT: D 43 TYR cc_start: 0.8047 (t80) cc_final: 0.7798 (t80) REVERT: E 49 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6742 (ptp90) REVERT: E 63 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8039 (mmt-90) REVERT: E 131 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7620 (mtp85) REVERT: F 45 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7067 (mtm180) REVERT: F 84 MET cc_start: 0.8470 (mmm) cc_final: 0.8195 (mmm) REVERT: G 91 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: H 36 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7347 (mm-30) REVERT: H 87 ARG cc_start: 0.8086 (mmt-90) cc_final: 0.7636 (mmt90) REVERT: K 103 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.6170 (tpt) REVERT: K 111 GLU cc_start: 0.7916 (pp20) cc_final: 0.7699 (pp20) REVERT: K 258 SER cc_start: 0.8544 (m) cc_final: 0.8025 (p) REVERT: K 261 LYS cc_start: 0.8518 (mttm) cc_final: 0.8004 (mtpm) REVERT: N 25 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: N 59 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8573 (p) REVERT: N 68 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: N 95 ASP cc_start: 0.7952 (t0) cc_final: 0.7731 (t70) REVERT: N 137 SER cc_start: 0.7426 (OUTLIER) cc_final: 0.7219 (t) REVERT: N 165 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7123 (m) REVERT: N 180 THR cc_start: 0.8558 (m) cc_final: 0.8199 (p) REVERT: N 194 TYR cc_start: 0.8903 (m-80) cc_final: 0.8609 (m-80) REVERT: N 219 ARG cc_start: 0.8400 (mtm110) cc_final: 0.8144 (mtp-110) outliers start: 40 outliers final: 11 residues processed: 159 average time/residue: 2.4255 time to fit residues: 412.7893 Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET 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 165 SER Chi-restraints excluded: chain N residue 186 ASP 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 10 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 0.0030 chunk 81 optimal weight: 4.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.167034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.115248 restraints weight = 18196.882| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.60 r_work: 0.3342 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16529 Z= 0.137 Angle : 0.568 7.536 23622 Z= 0.332 Chirality : 0.035 0.176 2663 Planarity : 0.004 0.044 1949 Dihedral : 29.702 155.878 4679 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.33 % Allowed : 26.54 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1186 helix: 2.32 (0.22), residues: 548 sheet: 0.66 (0.36), residues: 214 loop : -0.92 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 PHE 0.006 0.001 PHE K 229 TYR 0.013 0.001 TYR H 41 ARG 0.003 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 828) hydrogen bonds : angle 3.43821 ( 2122) SS BOND : bond 0.00369 ( 4) SS BOND : angle 0.80692 ( 8) covalent geometry : bond 0.00296 (16525) covalent geometry : angle 0.56831 (23614) *********************** 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 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.189 Fit side-chains REVERT: A 94 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8006 (mm-30) REVERT: A 120 MET cc_start: 0.8146 (mmt) cc_final: 0.7880 (mtt) REVERT: A 129 ARG cc_start: 0.8417 (ttt180) cc_final: 0.7457 (tpt90) REVERT: C 91 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: D 34 ARG cc_start: 0.6680 (ptm160) cc_final: 0.4978 (ptt180) REVERT: D 43 TYR cc_start: 0.7998 (t80) cc_final: 0.7717 (t80) REVERT: E 49 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6747 (ptp90) REVERT: E 63 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7983 (mmt-90) REVERT: E 129 ARG cc_start: 0.7989 (tmt170) cc_final: 0.7655 (tmt170) REVERT: F 45 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.6993 (mtm180) REVERT: F 84 MET cc_start: 0.8473 (mmm) cc_final: 0.8236 (mmm) REVERT: G 91 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: H 36 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: H 87 ARG cc_start: 0.8044 (mmt-90) cc_final: 0.7605 (mmt90) REVERT: K 111 GLU cc_start: 0.7948 (pp20) cc_final: 0.7689 (pp20) REVERT: K 169 MET cc_start: 0.8275 (ppp) cc_final: 0.7942 (ppp) REVERT: K 258 SER cc_start: 0.8524 (m) cc_final: 0.8002 (p) REVERT: K 261 LYS cc_start: 0.8489 (mttm) cc_final: 0.7819 (mtpm) REVERT: N 59 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8485 (p) REVERT: N 68 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: N 95 ASP cc_start: 0.7950 (t0) cc_final: 0.7689 (t70) REVERT: N 137 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.7198 (t) REVERT: N 165 SER cc_start: 0.7431 (OUTLIER) cc_final: 0.7043 (m) REVERT: N 176 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7697 (ttm-80) REVERT: N 180 THR cc_start: 0.8564 (m) cc_final: 0.8213 (p) REVERT: N 194 TYR cc_start: 0.8905 (m-80) cc_final: 0.8638 (m-80) REVERT: N 219 ARG cc_start: 0.8367 (mtm110) cc_final: 0.8116 (mtp-110) outliers start: 34 outliers final: 10 residues processed: 162 average time/residue: 1.7960 time to fit residues: 313.7549 Evaluate side-chains 164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 GLU 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 F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 162 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 129 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.167732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116019 restraints weight = 18175.676| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.61 r_work: 0.3349 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3486 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= 0.150 Angle : 0.557 7.986 23622 Z= 0.325 Chirality : 0.035 0.145 2663 Planarity : 0.004 0.041 1949 Dihedral : 29.492 155.076 4679 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.43 % Allowed : 26.44 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1186 helix: 2.49 (0.21), residues: 549 sheet: 0.70 (0.37), residues: 214 loop : -0.89 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.003 0.001 HIS H 50 PHE 0.006 0.001 PHE F 61 TYR 0.014 0.001 TYR N 72 ARG 0.004 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 828) hydrogen bonds : angle 3.32680 ( 2122) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.87980 ( 8) covalent geometry : bond 0.00335 (16525) covalent geometry : angle 0.55659 (23614) *********************** 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 180 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.421 Fit side-chains REVERT: A 94 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 120 MET cc_start: 0.8143 (mmt) cc_final: 0.7858 (mtt) REVERT: A 129 ARG cc_start: 0.8429 (ttt180) cc_final: 0.7454 (tpt90) REVERT: C 24 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: D 34 ARG cc_start: 0.6350 (ptm160) cc_final: 0.4706 (ptt180) REVERT: D 43 TYR cc_start: 0.8001 (t80) cc_final: 0.7691 (t80) REVERT: E 49 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6813 (ptp90) REVERT: E 63 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7969 (mmt-90) REVERT: E 129 ARG cc_start: 0.8033 (tmt170) cc_final: 0.7760 (tmt170) REVERT: E 131 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7654 (mtp85) REVERT: G 91 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: H 36 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: H 87 ARG cc_start: 0.8016 (mmt-90) cc_final: 0.7581 (mmt90) REVERT: K 84 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7681 (pm20) REVERT: K 111 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7642 (pp20) REVERT: K 258 SER cc_start: 0.8443 (m) cc_final: 0.7918 (p) REVERT: K 261 LYS cc_start: 0.8435 (mttm) cc_final: 0.7924 (mtpm) REVERT: N 95 ASP cc_start: 0.7948 (t0) cc_final: 0.7672 (t70) REVERT: N 165 SER cc_start: 0.7277 (OUTLIER) cc_final: 0.6916 (m) REVERT: N 176 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7740 (ttm-80) REVERT: N 180 THR cc_start: 0.8597 (m) cc_final: 0.8240 (p) REVERT: N 219 ARG cc_start: 0.8326 (mtm110) cc_final: 0.8108 (mtp-110) outliers start: 35 outliers final: 12 residues processed: 165 average time/residue: 1.8059 time to fit residues: 320.7103 Evaluate side-chains 151 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN 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 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 25 GLN Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 162 MET 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 107 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.168180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116572 restraints weight = 18145.257| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.60 r_work: 0.3354 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16529 Z= 0.148 Angle : 0.557 7.795 23622 Z= 0.325 Chirality : 0.035 0.148 2663 Planarity : 0.003 0.040 1949 Dihedral : 29.467 155.139 4679 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.23 % Allowed : 26.74 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1186 helix: 2.56 (0.21), residues: 548 sheet: 0.68 (0.37), residues: 214 loop : -0.84 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 PHE 0.007 0.001 PHE K 229 TYR 0.013 0.001 TYR N 72 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 828) hydrogen bonds : angle 3.33069 ( 2122) SS BOND : bond 0.00326 ( 4) SS BOND : angle 0.83042 ( 8) covalent geometry : bond 0.00330 (16525) covalent geometry : angle 0.55687 (23614) *********************** 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 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7974 (mm-30) REVERT: A 120 MET cc_start: 0.8169 (mmt) cc_final: 0.7898 (mtt) REVERT: A 129 ARG cc_start: 0.8473 (ttt180) cc_final: 0.7527 (tpt90) REVERT: C 24 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: D 34 ARG cc_start: 0.6425 (ptm160) cc_final: 0.4763 (ptt180) REVERT: D 43 TYR cc_start: 0.8071 (t80) cc_final: 0.7743 (t80) REVERT: E 49 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6845 (ptp90) REVERT: E 63 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8005 (mmt-90) REVERT: E 129 ARG cc_start: 0.8083 (tmt170) cc_final: 0.7769 (tmt170) REVERT: G 91 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: H 36 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: H 87 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7632 (mmt90) REVERT: K 84 GLU cc_start: 0.8645 (mm-30) cc_final: 0.7780 (pm20) REVERT: K 111 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: K 169 MET cc_start: 0.8169 (ppp) cc_final: 0.7961 (ppp) REVERT: K 258 SER cc_start: 0.8429 (m) cc_final: 0.7915 (p) REVERT: K 261 LYS cc_start: 0.8540 (mttm) cc_final: 0.7915 (mtpm) REVERT: N 32 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6819 (mm-30) REVERT: N 68 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: N 95 ASP cc_start: 0.7965 (t0) cc_final: 0.7697 (t70) REVERT: N 165 SER cc_start: 0.7216 (OUTLIER) cc_final: 0.6850 (m) REVERT: N 169 MET cc_start: 0.7497 (ptt) cc_final: 0.7085 (ptt) REVERT: N 176 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7752 (ttm-80) REVERT: N 180 THR cc_start: 0.8623 (m) cc_final: 0.8276 (p) REVERT: N 263 GLU cc_start: 0.8222 (pm20) cc_final: 0.7780 (pm20) outliers start: 33 outliers final: 14 residues processed: 159 average time/residue: 1.8172 time to fit residues: 312.2798 Evaluate side-chains 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 41 GLU 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 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 25 GLN Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 111 GLU 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 162 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 116 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 71 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.168460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116984 restraints weight = 18244.274| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.59 r_work: 0.3407 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16529 Z= 0.146 Angle : 0.559 7.727 23622 Z= 0.327 Chirality : 0.035 0.146 2663 Planarity : 0.004 0.039 1949 Dihedral : 29.421 155.071 4679 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.94 % Allowed : 26.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1186 helix: 2.60 (0.21), residues: 549 sheet: 0.67 (0.36), residues: 214 loop : -0.84 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 58 HIS 0.003 0.001 HIS H 50 PHE 0.006 0.001 PHE F 61 TYR 0.014 0.001 TYR N 72 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 828) hydrogen bonds : angle 3.30161 ( 2122) SS BOND : bond 0.00330 ( 4) SS BOND : angle 0.99000 ( 8) covalent geometry : bond 0.00324 (16525) covalent geometry : angle 0.55907 (23614) *********************** 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 175 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 120 MET cc_start: 0.8122 (mmt) cc_final: 0.7847 (mtt) REVERT: A 129 ARG cc_start: 0.8426 (ttt180) cc_final: 0.7456 (tpt90) REVERT: B 27 GLN cc_start: 0.8647 (mm110) cc_final: 0.8420 (mm110) REVERT: C 24 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.6723 (mp10) REVERT: D 34 ARG cc_start: 0.6402 (ptm160) cc_final: 0.4748 (ptt180) REVERT: D 43 TYR cc_start: 0.7975 (t80) cc_final: 0.7616 (t80) REVERT: E 49 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6769 (ptp90) REVERT: E 63 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7950 (mmt-90) REVERT: G 91 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: H 36 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7425 (mm-30) REVERT: H 87 ARG cc_start: 0.7986 (mmt-90) cc_final: 0.7561 (mmt90) REVERT: K 84 GLU cc_start: 0.8626 (mm-30) cc_final: 0.7741 (pm20) REVERT: K 111 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: K 169 MET cc_start: 0.8193 (ppp) cc_final: 0.7975 (ppp) REVERT: K 258 SER cc_start: 0.8390 (m) cc_final: 0.7888 (p) REVERT: K 261 LYS cc_start: 0.8483 (mttm) cc_final: 0.7843 (mtpm) REVERT: N 32 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6833 (mm-30) REVERT: N 68 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7832 (pt0) REVERT: N 95 ASP cc_start: 0.7978 (t0) cc_final: 0.7685 (t70) REVERT: N 176 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7752 (ttm-80) REVERT: N 180 THR cc_start: 0.8607 (m) cc_final: 0.8203 (p) REVERT: N 263 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7882 (pm20) outliers start: 30 outliers final: 13 residues processed: 162 average time/residue: 1.6931 time to fit residues: 295.8731 Evaluate side-chains 164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN 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 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 25 GLN Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 111 GLU 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 162 MET Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.162364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110130 restraints weight = 18210.514| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.67 r_work: 0.3263 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 16529 Z= 0.293 Angle : 0.657 12.462 23622 Z= 0.374 Chirality : 0.041 0.143 2663 Planarity : 0.004 0.041 1949 Dihedral : 29.887 158.016 4679 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.84 % Allowed : 26.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1186 helix: 2.01 (0.21), residues: 548 sheet: 0.73 (0.37), residues: 198 loop : -1.07 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 58 HIS 0.006 0.001 HIS N 249 PHE 0.012 0.002 PHE F 100 TYR 0.019 0.002 TYR N 72 ARG 0.007 0.001 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 828) hydrogen bonds : angle 3.64672 ( 2122) SS BOND : bond 0.00679 ( 4) SS BOND : angle 1.35162 ( 8) covalent geometry : bond 0.00686 (16525) covalent geometry : angle 0.65699 (23614) ********************** 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 168 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8204 (tttm) REVERT: A 94 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 115 LYS cc_start: 0.8500 (mttt) cc_final: 0.8058 (mtmp) REVERT: A 129 ARG cc_start: 0.8399 (ttt180) cc_final: 0.7307 (tpt90) REVERT: B 35 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7336 (ttm-80) REVERT: B 91 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8404 (ttpp) REVERT: C 24 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: D 34 ARG cc_start: 0.6721 (ptm160) cc_final: 0.5010 (ptt180) REVERT: D 43 TYR cc_start: 0.7998 (t80) cc_final: 0.7762 (t80) REVERT: E 49 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6470 (ptp90) REVERT: E 63 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8283 (mmt-90) REVERT: E 131 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7532 (mtp85) REVERT: G 91 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: H 36 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: H 87 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7696 (mmt90) REVERT: K 111 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7650 (pp20) REVERT: K 258 SER cc_start: 0.8567 (m) cc_final: 0.8041 (p) REVERT: K 261 LYS cc_start: 0.8448 (mttm) cc_final: 0.7947 (mtpm) REVERT: N 32 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7082 (mm-30) REVERT: N 68 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: N 95 ASP cc_start: 0.7946 (t0) cc_final: 0.7716 (t70) REVERT: N 176 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7798 (ttm-80) REVERT: N 180 THR cc_start: 0.8591 (m) cc_final: 0.8081 (p) REVERT: N 263 GLU cc_start: 0.8250 (pm20) cc_final: 0.7852 (pm20) outliers start: 29 outliers final: 12 residues processed: 156 average time/residue: 1.9390 time to fit residues: 324.3902 Evaluate side-chains 156 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN 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 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 65 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 111 GLU 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 162 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 22 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** D 96 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.165218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113534 restraints weight = 18114.865| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.62 r_work: 0.3319 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16529 Z= 0.146 Angle : 0.612 11.718 23622 Z= 0.354 Chirality : 0.037 0.229 2663 Planarity : 0.004 0.040 1949 Dihedral : 29.825 156.295 4679 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.64 % Allowed : 27.33 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1186 helix: 2.21 (0.21), residues: 548 sheet: 0.73 (0.37), residues: 198 loop : -1.02 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 58 HIS 0.003 0.001 HIS K 249 PHE 0.005 0.001 PHE F 61 TYR 0.014 0.001 TYR H 41 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 828) hydrogen bonds : angle 3.56869 ( 2122) SS BOND : bond 0.00490 ( 4) SS BOND : angle 0.99216 ( 8) covalent geometry : bond 0.00321 (16525) covalent geometry : angle 0.61138 (23614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14137.91 seconds wall clock time: 247 minutes 37.78 seconds (14857.78 seconds total)