Starting phenix.real_space_refine on Tue Dec 31 08:55:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk5_27483/12_2024/8dk5_27483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk5_27483/12_2024/8dk5_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_27483/12_2024/8dk5_27483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk5_27483/12_2024/8dk5_27483.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk5_27483/12_2024/8dk5_27483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk5_27483/12_2024/8dk5_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.08, per 1000 atoms: 0.58 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: 3.78 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: 6.71 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: 6.37 Time building geometry restraints manager: 4.08 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: 0.560 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.590 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.560 ------------------------------------------------------------------------------- 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 16525 Z= 0.613 Angle : 1.114 29.781 23614 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 *********************** 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 : 1.255 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: 1.7328 time to fit residues: 475.5932 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 : 1.383 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 16525 Z= 0.177 Angle : 0.583 7.132 23614 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 *********************** 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 : 1.217 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 129 ARG cc_start: 0.7912 (ttt180) cc_final: 0.7547 (tpt90) REVERT: D 43 TYR cc_start: 0.7887 (t80) cc_final: 0.7533 (t80) REVERT: F 79 LYS cc_start: 0.8232 (mttt) cc_final: 0.7904 (mttm) REVERT: G 73 ASN cc_start: 0.7564 (t0) cc_final: 0.7324 (t0) REVERT: G 91 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: H 36 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: H 72 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7156 (mt-10) REVERT: H 87 ARG cc_start: 0.7857 (mmt-90) cc_final: 0.7568 (mmt180) REVERT: H 96 GLN cc_start: 0.8597 (tt0) cc_final: 0.8354 (tt0) REVERT: K 84 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7579 (pm20) REVERT: K 161 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8647 (tttt) REVERT: K 261 LYS cc_start: 0.8584 (mttm) cc_final: 0.8143 (mtpm) REVERT: N 137 SER cc_start: 0.7706 (OUTLIER) cc_final: 0.7421 (t) REVERT: N 180 THR cc_start: 0.8840 (m) cc_final: 0.8323 (p) outliers start: 29 outliers final: 12 residues processed: 189 average time/residue: 1.6719 time to fit residues: 341.0959 Evaluate side-chains 167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 161 LYS 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 72 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 GLN N 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16525 Z= 0.336 Angle : 0.634 7.849 23614 Z= 0.365 Chirality : 0.039 0.150 2663 Planarity : 0.005 0.064 1949 Dihedral : 29.954 158.229 4681 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.60 % Allowed : 23.60 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.24), residues: 1186 helix: 1.71 (0.21), residues: 550 sheet: 0.27 (0.34), residues: 234 loop : -1.01 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 58 HIS 0.007 0.001 HIS N 249 PHE 0.009 0.002 PHE N 229 TYR 0.021 0.002 TYR H 41 ARG 0.004 0.001 ARG N 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.311 Fit side-chains REVERT: A 94 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 129 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7680 (tpt90) REVERT: A 133 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 32 ARG cc_start: 0.8816 (ttp-170) cc_final: 0.8606 (ttp-170) REVERT: D 43 TYR cc_start: 0.7861 (t80) cc_final: 0.7637 (t80) REVERT: E 63 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8027 (mmt-90) REVERT: F 45 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7235 (mtm180) REVERT: G 91 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: H 36 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: H 48 GLN cc_start: 0.8222 (tt0) cc_final: 0.8012 (tt0) REVERT: H 87 ARG cc_start: 0.8000 (mmt-90) cc_final: 0.7619 (mmt90) REVERT: K 81 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8183 (ttpt) REVERT: K 161 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8715 (tttt) REVERT: K 169 MET cc_start: 0.8048 (ppp) cc_final: 0.7761 (pmm) REVERT: K 258 SER cc_start: 0.8485 (m) cc_final: 0.7995 (p) REVERT: K 261 LYS cc_start: 0.8614 (mttm) cc_final: 0.8193 (mtpm) REVERT: N 23 GLU cc_start: 0.7348 (tt0) cc_final: 0.6986 (tt0) REVERT: N 25 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7655 (mp10) REVERT: N 68 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7633 (pt0) REVERT: N 165 SER cc_start: 0.7011 (OUTLIER) cc_final: 0.6723 (m) REVERT: N 176 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7468 (ttm-80) REVERT: N 180 THR cc_start: 0.8659 (m) cc_final: 0.8321 (p) REVERT: N 263 GLU cc_start: 0.7529 (pp20) cc_final: 0.6925 (tm-30) outliers start: 47 outliers final: 11 residues processed: 191 average time/residue: 1.9220 time to fit residues: 393.1940 Evaluate side-chains 165 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 87 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 G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 73 ASN K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16525 Z= 0.177 Angle : 0.555 7.641 23614 Z= 0.325 Chirality : 0.034 0.144 2663 Planarity : 0.004 0.053 1949 Dihedral : 29.472 154.614 4679 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.04 % Allowed : 25.76 % Favored : 71.20 % 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: 1.29 (0.24), residues: 1186 helix: 2.23 (0.22), residues: 553 sheet: 0.35 (0.35), residues: 234 loop : -0.80 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 69 HIS 0.003 0.001 HIS H 50 PHE 0.006 0.001 PHE N 229 TYR 0.016 0.001 TYR H 41 ARG 0.004 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.338 Fit side-chains REVERT: A 94 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 129 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7663 (tpt90) REVERT: B 31 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7888 (tttm) REVERT: D 34 ARG cc_start: 0.6865 (ptm160) cc_final: 0.5156 (ptt180) REVERT: D 43 TYR cc_start: 0.7841 (t80) cc_final: 0.7511 (t80) REVERT: G 91 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: H 36 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: H 87 ARG cc_start: 0.7908 (mmt-90) cc_final: 0.7552 (mmt90) REVERT: K 84 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7700 (pm20) REVERT: K 161 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8609 (tptm) REVERT: K 258 SER cc_start: 0.8347 (m) cc_final: 0.7879 (p) REVERT: K 261 LYS cc_start: 0.8547 (mttm) cc_final: 0.8020 (mtpm) REVERT: N 165 SER cc_start: 0.6570 (OUTLIER) cc_final: 0.6217 (m) REVERT: N 180 THR cc_start: 0.8751 (m) cc_final: 0.8452 (p) REVERT: N 263 GLU cc_start: 0.7154 (pp20) cc_final: 0.6782 (tm-30) outliers start: 31 outliers final: 5 residues processed: 177 average time/residue: 1.7137 time to fit residues: 326.9295 Evaluate side-chains 149 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16525 Z= 0.338 Angle : 0.616 7.992 23614 Z= 0.355 Chirality : 0.038 0.142 2663 Planarity : 0.004 0.049 1949 Dihedral : 29.785 157.627 4679 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.02 % Allowed : 25.56 % 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: 1.12 (0.24), residues: 1186 helix: 2.04 (0.22), residues: 548 sheet: 0.70 (0.37), residues: 214 loop : -1.00 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 58 HIS 0.006 0.001 HIS H 50 PHE 0.010 0.002 PHE N 229 TYR 0.017 0.002 TYR N 72 ARG 0.005 0.000 ARG F 95 *********************** 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 188 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.347 Fit side-chains REVERT: A 94 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 129 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7692 (tpt90) REVERT: B 31 LYS cc_start: 0.8532 (ttmt) cc_final: 0.7974 (tttm) REVERT: D 34 ARG cc_start: 0.7285 (ptm160) cc_final: 0.5561 (ptt180) REVERT: D 43 TYR cc_start: 0.7808 (t80) cc_final: 0.7543 (t80) REVERT: D 87 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7310 (ttm170) REVERT: E 49 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6238 (ptp90) REVERT: E 63 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8050 (mmt-90) REVERT: E 131 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7459 (mtp85) REVERT: G 91 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: H 36 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: H 87 ARG cc_start: 0.7995 (mmt-90) cc_final: 0.7654 (mmt90) REVERT: K 258 SER cc_start: 0.8481 (m) cc_final: 0.8014 (p) REVERT: K 261 LYS cc_start: 0.8467 (mttm) cc_final: 0.8157 (mtpm) REVERT: N 25 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: N 68 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: N 165 SER cc_start: 0.7123 (OUTLIER) cc_final: 0.6794 (m) REVERT: N 180 THR cc_start: 0.8630 (m) cc_final: 0.8321 (p) REVERT: N 263 GLU cc_start: 0.7247 (pp20) cc_final: 0.6880 (tm-30) outliers start: 41 outliers final: 9 residues processed: 167 average time/residue: 1.9031 time to fit residues: 340.6827 Evaluate side-chains 155 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 87 ARG 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 93 THR Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 165 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 72 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16525 Z= 0.195 Angle : 0.587 8.132 23614 Z= 0.342 Chirality : 0.036 0.157 2663 Planarity : 0.004 0.044 1949 Dihedral : 29.730 156.457 4679 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.13 % Allowed : 27.23 % Favored : 69.64 % 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: 1.24 (0.24), residues: 1186 helix: 2.21 (0.22), residues: 548 sheet: 0.59 (0.36), residues: 214 loop : -0.94 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 58 HIS 0.003 0.001 HIS H 50 PHE 0.008 0.001 PHE K 229 TYR 0.013 0.001 TYR H 41 ARG 0.004 0.000 ARG C 71 *********************** 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 181 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.394 Fit side-chains REVERT: A 94 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 129 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7636 (tpt90) REVERT: B 31 LYS cc_start: 0.8483 (ttmt) cc_final: 0.7829 (tttm) REVERT: D 34 ARG cc_start: 0.7247 (ptm160) cc_final: 0.5545 (ptt180) REVERT: D 43 TYR cc_start: 0.7779 (t80) cc_final: 0.7505 (t80) REVERT: E 49 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6488 (ptp90) REVERT: E 131 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7379 (mtp85) REVERT: F 45 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7220 (mtm180) REVERT: G 91 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: H 36 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: H 87 ARG cc_start: 0.7936 (mmt-90) cc_final: 0.7602 (mmt90) REVERT: H 96 GLN cc_start: 0.8657 (tt0) cc_final: 0.8393 (tt0) REVERT: K 161 LYS cc_start: 0.8978 (tttt) cc_final: 0.8689 (tptm) REVERT: K 258 SER cc_start: 0.8464 (m) cc_final: 0.7998 (p) REVERT: K 261 LYS cc_start: 0.8550 (mttm) cc_final: 0.8109 (mtpm) REVERT: N 25 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: N 165 SER cc_start: 0.7038 (OUTLIER) cc_final: 0.6700 (m) REVERT: N 180 THR cc_start: 0.8626 (m) cc_final: 0.8334 (p) REVERT: N 263 GLU cc_start: 0.7170 (pp20) cc_final: 0.6910 (tm-30) outliers start: 32 outliers final: 12 residues processed: 163 average time/residue: 1.9994 time to fit residues: 352.2930 Evaluate side-chains 158 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 77 optimal weight: 0.1980 chunk 137 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 84 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16525 Z= 0.244 Angle : 0.581 7.886 23614 Z= 0.337 Chirality : 0.036 0.143 2663 Planarity : 0.004 0.042 1949 Dihedral : 29.557 155.939 4679 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.53 % Allowed : 26.84 % Favored : 69.64 % 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: 1.33 (0.24), residues: 1186 helix: 2.31 (0.21), residues: 548 sheet: 0.56 (0.36), residues: 214 loop : -0.88 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 PHE 0.007 0.001 PHE N 229 TYR 0.015 0.001 TYR N 72 ARG 0.005 0.000 ARG C 71 *********************** 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 191 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 1.328 Fit side-chains REVERT: A 94 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 129 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7675 (tpt90) REVERT: B 31 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7836 (tttm) REVERT: C 24 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: D 34 ARG cc_start: 0.7253 (ptm160) cc_final: 0.5551 (ptt180) REVERT: D 43 TYR cc_start: 0.7784 (t80) cc_final: 0.7482 (t80) REVERT: D 62 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8548 (mp) REVERT: D 87 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: E 49 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6537 (ptp90) REVERT: E 131 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7504 (mtp85) REVERT: F 45 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7197 (mtm180) REVERT: G 91 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: H 36 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: H 87 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7693 (mmt90) REVERT: K 84 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7650 (pm20) REVERT: K 103 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6028 (tpt) REVERT: K 258 SER cc_start: 0.8405 (m) cc_final: 0.7933 (p) REVERT: K 261 LYS cc_start: 0.8536 (mttm) cc_final: 0.8118 (mtpm) REVERT: N 32 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7014 (mm-30) REVERT: N 165 SER cc_start: 0.6970 (OUTLIER) cc_final: 0.6616 (m) REVERT: N 180 THR cc_start: 0.8629 (m) cc_final: 0.8345 (p) REVERT: N 263 GLU cc_start: 0.7240 (pp20) cc_final: 0.7012 (tm-30) outliers start: 36 outliers final: 10 residues processed: 174 average time/residue: 1.8497 time to fit residues: 345.1309 Evaluate side-chains 164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 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 K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 N 170 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16525 Z= 0.239 Angle : 0.581 9.331 23614 Z= 0.337 Chirality : 0.036 0.147 2663 Planarity : 0.004 0.040 1949 Dihedral : 29.467 155.288 4679 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.23 % Allowed : 27.03 % Favored : 69.74 % 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: 1.39 (0.25), residues: 1186 helix: 2.36 (0.22), residues: 548 sheet: 0.56 (0.36), residues: 214 loop : -0.83 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.004 0.001 HIS N 249 PHE 0.007 0.001 PHE N 229 TYR 0.014 0.001 TYR N 72 ARG 0.006 0.000 ARG C 71 *********************** 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 190 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.308 Fit side-chains REVERT: A 79 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8166 (tttm) REVERT: A 94 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 129 ARG cc_start: 0.8045 (ttt180) cc_final: 0.7672 (tpt90) REVERT: B 31 LYS cc_start: 0.8495 (ttmt) cc_final: 0.7955 (tttm) REVERT: B 91 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8403 (ttpp) REVERT: C 24 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: D 34 ARG cc_start: 0.7326 (ptm160) cc_final: 0.5568 (ptt180) REVERT: D 43 TYR cc_start: 0.7756 (t80) cc_final: 0.7453 (t80) REVERT: D 87 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7268 (ttm170) REVERT: E 49 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6545 (ptp90) REVERT: E 63 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7955 (mmt-90) REVERT: E 131 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7497 (mtp85) REVERT: F 45 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7172 (mtm180) REVERT: G 91 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: H 36 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: H 87 ARG cc_start: 0.7959 (mmt-90) cc_final: 0.7702 (mmt90) REVERT: K 84 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7661 (pm20) REVERT: K 103 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.6006 (tpt) REVERT: K 161 LYS cc_start: 0.8928 (tttt) cc_final: 0.8616 (tptm) REVERT: K 258 SER cc_start: 0.8383 (m) cc_final: 0.7920 (p) REVERT: K 261 LYS cc_start: 0.8590 (mttm) cc_final: 0.8092 (mtpm) REVERT: N 68 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7517 (pt0) REVERT: N 84 GLU cc_start: 0.8084 (tp30) cc_final: 0.7395 (pm20) REVERT: N 165 SER cc_start: 0.6989 (OUTLIER) cc_final: 0.6592 (m) REVERT: N 180 THR cc_start: 0.8625 (m) cc_final: 0.8339 (p) REVERT: N 263 GLU cc_start: 0.7199 (pp20) cc_final: 0.6973 (tm-30) outliers start: 33 outliers final: 13 residues processed: 178 average time/residue: 1.8611 time to fit residues: 356.2232 Evaluate side-chains 167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 87 ARG 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 90 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 223 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16525 Z= 0.362 Angle : 0.644 10.771 23614 Z= 0.367 Chirality : 0.039 0.192 2663 Planarity : 0.004 0.052 1949 Dihedral : 29.762 156.695 4679 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.62 % Allowed : 26.93 % Favored : 69.44 % 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: 1.08 (0.24), residues: 1186 helix: 2.03 (0.22), residues: 548 sheet: 0.72 (0.37), residues: 198 loop : -1.01 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 58 HIS 0.006 0.001 HIS N 249 PHE 0.010 0.002 PHE N 229 TYR 0.019 0.002 TYR F 88 ARG 0.005 0.000 ARG F 95 *********************** 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 178 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.272 Fit side-chains REVERT: A 79 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8295 (tttm) REVERT: A 94 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 115 LYS cc_start: 0.8435 (mttt) cc_final: 0.8209 (mtmp) REVERT: A 129 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7618 (tpt90) REVERT: B 31 LYS cc_start: 0.8531 (ttmt) cc_final: 0.7970 (tttm) REVERT: B 91 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8437 (ttpp) REVERT: C 24 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: D 34 ARG cc_start: 0.7420 (ptm160) cc_final: 0.5627 (ptt180) REVERT: D 43 TYR cc_start: 0.7816 (t80) cc_final: 0.7602 (t80) REVERT: D 87 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7397 (ttm170) REVERT: E 49 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6298 (ptp90) REVERT: E 63 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8030 (mmt-90) REVERT: E 131 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7427 (mtp85) REVERT: F 35 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7423 (mtm-85) REVERT: F 45 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7089 (mtm180) REVERT: G 91 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: H 36 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: H 87 ARG cc_start: 0.8008 (mmt-90) cc_final: 0.7758 (mmt90) REVERT: K 103 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.5938 (tpt) REVERT: K 258 SER cc_start: 0.8498 (m) cc_final: 0.8020 (p) REVERT: K 261 LYS cc_start: 0.8468 (mttm) cc_final: 0.8173 (mtpm) REVERT: N 68 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: N 165 SER cc_start: 0.7289 (OUTLIER) cc_final: 0.6913 (m) REVERT: N 180 THR cc_start: 0.8585 (m) cc_final: 0.8298 (p) REVERT: N 263 GLU cc_start: 0.7253 (pp20) cc_final: 0.6991 (tm-30) outliers start: 37 outliers final: 12 residues processed: 163 average time/residue: 1.9884 time to fit residues: 346.8013 Evaluate side-chains 161 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 87 ARG 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 F residue 45 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 165 SER 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 135 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.0010 chunk 142 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16525 Z= 0.247 Angle : 0.621 11.769 23614 Z= 0.358 Chirality : 0.037 0.191 2663 Planarity : 0.004 0.043 1949 Dihedral : 29.724 155.979 4679 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.64 % Allowed : 28.01 % Favored : 69.34 % 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: 1.16 (0.24), residues: 1186 helix: 2.10 (0.22), residues: 548 sheet: 0.51 (0.37), residues: 214 loop : -0.87 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 58 HIS 0.004 0.001 HIS K 170 PHE 0.007 0.001 PHE N 229 TYR 0.014 0.001 TYR N 72 ARG 0.004 0.000 ARG C 71 ********************** 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 170 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.235 Fit side-chains REVERT: A 79 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8253 (tttm) REVERT: A 94 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 115 LYS cc_start: 0.8417 (mttt) cc_final: 0.8194 (mtmp) REVERT: A 129 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7588 (tpt90) REVERT: B 31 LYS cc_start: 0.8520 (ttmt) cc_final: 0.7967 (tttm) REVERT: B 91 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8429 (ttpp) REVERT: C 24 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: D 34 ARG cc_start: 0.7430 (ptm160) cc_final: 0.5632 (ptt180) REVERT: D 43 TYR cc_start: 0.7789 (t80) cc_final: 0.7532 (t80) REVERT: D 87 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7300 (ttm170) REVERT: E 49 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6205 (ptp90) REVERT: E 63 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7952 (mmt-90) REVERT: E 131 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7338 (mtp85) REVERT: F 45 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7139 (mtm180) REVERT: G 91 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: H 36 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: H 87 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7729 (mmt90) REVERT: H 96 GLN cc_start: 0.8719 (tt0) cc_final: 0.8459 (tt0) REVERT: K 103 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.5935 (tpt) REVERT: K 258 SER cc_start: 0.8492 (m) cc_final: 0.8013 (p) REVERT: K 261 LYS cc_start: 0.8569 (mttm) cc_final: 0.8156 (mtpm) REVERT: N 68 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: N 165 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6864 (m) REVERT: N 180 THR cc_start: 0.8582 (m) cc_final: 0.8302 (p) REVERT: N 263 GLU cc_start: 0.7259 (pp20) cc_final: 0.7020 (tm-30) outliers start: 27 outliers final: 10 residues processed: 159 average time/residue: 1.9394 time to fit residues: 330.2499 Evaluate side-chains 161 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 87 ARG 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 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 K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 170 HIS 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 120 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 14 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.160716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106478 restraints weight = 18389.456| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.69 r_work: 0.3213 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16525 Z= 0.201 Angle : 0.618 12.905 23614 Z= 0.355 Chirality : 0.036 0.140 2663 Planarity : 0.004 0.040 1949 Dihedral : 29.690 155.485 4679 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.45 % Allowed : 28.11 % Favored : 69.44 % 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: 1.27 (0.25), residues: 1186 helix: 2.22 (0.22), residues: 548 sheet: 0.49 (0.37), residues: 214 loop : -0.83 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.003 0.001 HIS N 249 PHE 0.006 0.001 PHE F 100 TYR 0.013 0.001 TYR H 41 ARG 0.004 0.000 ARG C 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5783.31 seconds wall clock time: 104 minutes 11.40 seconds (6251.40 seconds total)