Starting phenix.real_space_refine on Sun Aug 24 03:39:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ys5_10892/08_2025/6ys5_10892.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ys5_10892/08_2025/6ys5_10892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ys5_10892/08_2025/6ys5_10892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ys5_10892/08_2025/6ys5_10892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ys5_10892/08_2025/6ys5_10892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ys5_10892/08_2025/6ys5_10892.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 477 5.49 5 Mg 24 5.21 5 S 24 5.16 5 C 8718 2.51 5 N 3115 2.21 5 O 4506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16864 Number of models: 1 Model: "" Number of chains: 13 Chain: "3" Number of atoms: 9676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 9676 Classifications: {'RNA': 453} Modifications used: {'rna2p_pur': 35, 'rna2p_pyr': 39, 'rna3p_pur': 208, 'rna3p_pyr': 171} Link IDs: {'rna2p': 74, 'rna3p': 378} Chain breaks: 1 Chain: "7" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 428 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "9" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Classifications: {'RNA': 4} Modifications used: {'rna3p_pyr': 4} Link IDs: {'rna3p': 3} Chain: "d" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1649 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "h" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "j" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "k" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 797 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "n" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "o" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 791 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 650 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "3" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Unusual residues: {' MG': 22} Classifications: {'undetermined': 22} Link IDs: {None: 21} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.19 Number of scatterers: 16864 At special positions: 0 Unit cell: (116.63, 123.05, 128.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 477 15.00 Mg 24 11.99 O 4506 8.00 N 3115 7.00 C 8718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 172.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 45.8% alpha, 16.9% beta 135 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'd' and resid 8 through 12 removed outlier: 3.903A pdb=" N LEU d 12 " --> pdb=" O GLY d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 47 removed outlier: 3.534A pdb=" N GLN d 38 " --> pdb=" O LEU d 34 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL d 39 " --> pdb=" O LYS d 35 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS d 45 " --> pdb=" O GLU d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 72 through 78 removed outlier: 3.810A pdb=" N VAL d 76 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 96 removed outlier: 3.549A pdb=" N GLN d 88 " --> pdb=" O ILE d 84 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG d 89 " --> pdb=" O GLU d 85 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN d 93 " --> pdb=" O ARG d 89 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE d 94 " --> pdb=" O GLU d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 125 removed outlier: 3.523A pdb=" N VAL d 116 " --> pdb=" O ASP d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 143 removed outlier: 3.658A pdb=" N ARG d 143 " --> pdb=" O GLN d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 160 removed outlier: 3.524A pdb=" N GLY d 159 " --> pdb=" O ARG d 156 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA d 160 " --> pdb=" O LEU d 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 156 through 160' Processing helix chain 'h' and resid 20 through 31 removed outlier: 3.884A pdb=" N ALA h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS h 29 " --> pdb=" O LYS h 25 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL h 30 " --> pdb=" O PHE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 53 removed outlier: 3.531A pdb=" N ALA h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU h 52 " --> pdb=" O GLU h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 70 removed outlier: 3.692A pdb=" N GLU h 63 " --> pdb=" O VAL h 59 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU h 67 " --> pdb=" O GLU h 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS h 68 " --> pdb=" O THR h 64 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL h 69 " --> pdb=" O THR h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 108 Processing helix chain 'h' and resid 115 through 129 removed outlier: 3.661A pdb=" N ALA h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU h 125 " --> pdb=" O ALA h 121 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU h 129 " --> pdb=" O LEU h 125 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 144 removed outlier: 3.525A pdb=" N MET h 144 " --> pdb=" O ASP h 140 " (cutoff:3.500A) Processing helix chain 'j' and resid 32 through 37 Processing helix chain 'j' and resid 39 through 47 removed outlier: 3.825A pdb=" N ARG j 43 " --> pdb=" O ARG j 39 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET j 44 " --> pdb=" O GLU j 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL j 45 " --> pdb=" O THR j 41 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 53 removed outlier: 3.542A pdb=" N GLU j 51 " --> pdb=" O ARG j 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 89 removed outlier: 3.671A pdb=" N ALA j 88 " --> pdb=" O ALA j 84 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 99 Processing helix chain 'k' and resid 14 through 32 removed outlier: 3.689A pdb=" N GLN k 20 " --> pdb=" O ARG k 16 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU k 27 " --> pdb=" O GLN k 23 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR k 28 " --> pdb=" O GLU k 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR k 32 " --> pdb=" O THR k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 89 Processing helix chain 'n' and resid 14 through 19 Processing helix chain 'n' and resid 20 through 22 No H-bonds generated for 'chain 'n' and resid 20 through 22' Processing helix chain 'n' and resid 26 through 38 removed outlier: 3.641A pdb=" N ALA n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 48 removed outlier: 3.524A pdb=" N LEU n 48 " --> pdb=" O ILE n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 61 removed outlier: 4.126A pdb=" N ALA n 55 " --> pdb=" O ALA n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 65 through 84 removed outlier: 3.507A pdb=" N ASN n 76 " --> pdb=" O GLU n 72 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE n 77 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS n 78 " --> pdb=" O SER n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 85 through 93 Processing helix chain 'o' and resid 3 through 20 removed outlier: 3.727A pdb=" N ILE o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN o 8 " --> pdb=" O LYS o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 32 removed outlier: 3.688A pdb=" N ARG o 24 " --> pdb=" O TYR o 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 49 removed outlier: 3.676A pdb=" N MET o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 51 No H-bonds generated for 'chain 'o' and resid 50 through 51' Processing helix chain 'o' and resid 52 through 60 Proline residue: o 57 - end of helix removed outlier: 3.591A pdb=" N LEU o 60 " --> pdb=" O PRO o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 90 removed outlier: 3.515A pdb=" N ASP o 86 " --> pdb=" O ASN o 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN o 90 " --> pdb=" O ASP o 86 " (cutoff:3.500A) Processing helix chain 't' and resid 12 through 26 removed outlier: 3.538A pdb=" N ALA t 24 " --> pdb=" O GLU t 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER t 25 " --> pdb=" O ALA t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 75 removed outlier: 3.537A pdb=" N ALA t 75 " --> pdb=" O GLY t 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.637A pdb=" N ASN d 54 " --> pdb=" O SER d 69 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA d 64 " --> pdb=" O GLN d 100 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER d 102 " --> pdb=" O ALA d 64 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL d 66 " --> pdb=" O SER d 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 165 through 171 removed outlier: 3.617A pdb=" N GLY d 148 " --> pdb=" O PHE d 203 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP d 181 " --> pdb=" O ARG d 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'j' and resid 4 through 7 removed outlier: 6.439A pdb=" N LYS j 25 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE j 63 " --> pdb=" O LYS j 25 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL j 27 " --> pdb=" O ILE j 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.824A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.824A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'n' and resid 3 through 4 Processing sheet with id=AA7, first strand: chain 't' and resid 31 through 33 284 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2376 1.32 - 1.45: 7110 1.45 - 1.57: 7656 1.57 - 1.69: 950 1.69 - 1.81: 45 Bond restraints: 18137 Sorted by residual: bond pdb=" CA ARG n 107 " pdb=" C ARG n 107 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.72e-02 3.38e+03 4.04e+00 bond pdb=" C ALA n 106 " pdb=" N ARG n 107 " ideal model delta sigma weight residual 1.333 1.309 0.024 1.56e-02 4.11e+03 2.39e+00 bond pdb=" CG ARG j 120 " pdb=" CD ARG j 120 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CB GLU o 14 " pdb=" CG GLU o 14 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB ARG j 122 " pdb=" CG ARG j 122 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.01e+00 ... (remaining 18132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 25516 1.50 - 3.00: 1145 3.00 - 4.50: 127 4.50 - 6.00: 19 6.00 - 7.50: 5 Bond angle restraints: 26812 Sorted by residual: angle pdb=" C PRO k 55 " pdb=" N HIS k 56 " pdb=" CA HIS k 56 " ideal model delta sigma weight residual 122.44 116.36 6.08 1.19e+00 7.06e-01 2.61e+01 angle pdb=" N HIS k 56 " pdb=" CA HIS k 56 " pdb=" C HIS k 56 " ideal model delta sigma weight residual 111.02 117.89 -6.87 1.52e+00 4.33e-01 2.04e+01 angle pdb=" CA ARG n 107 " pdb=" C ARG n 107 " pdb=" N THR n 108 " ideal model delta sigma weight residual 118.59 124.29 -5.70 1.63e+00 3.76e-01 1.22e+01 angle pdb=" C2' A 3 955 " pdb=" C1' A 3 955 " pdb=" N9 A 3 955 " ideal model delta sigma weight residual 112.00 117.21 -5.21 1.50e+00 4.44e-01 1.21e+01 angle pdb=" C2' G 31353 " pdb=" C1' G 31353 " pdb=" N9 G 31353 " ideal model delta sigma weight residual 112.00 116.98 -4.98 1.50e+00 4.44e-01 1.10e+01 ... (remaining 26807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 10385 34.83 - 69.65: 1080 69.65 - 104.48: 137 104.48 - 139.30: 3 139.30 - 174.13: 7 Dihedral angle restraints: 11612 sinusoidal: 9176 harmonic: 2436 Sorted by residual: dihedral pdb=" O4' C 3 964 " pdb=" C1' C 3 964 " pdb=" N1 C 3 964 " pdb=" C2 C 3 964 " ideal model delta sinusoidal sigma weight residual 200.00 40.76 159.24 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U 31156 " pdb=" C1' U 31156 " pdb=" N1 U 31156 " pdb=" C2 U 31156 " ideal model delta sinusoidal sigma weight residual -128.00 46.13 -174.13 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U 3 957 " pdb=" C1' U 3 957 " pdb=" N1 U 3 957 " pdb=" C2 U 3 957 " ideal model delta sinusoidal sigma weight residual 232.00 58.17 173.83 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 11609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2592 0.047 - 0.095: 638 0.095 - 0.142: 151 0.142 - 0.189: 26 0.189 - 0.236: 6 Chirality restraints: 3413 Sorted by residual: chirality pdb=" C1' G 31353 " pdb=" O4' G 31353 " pdb=" C2' G 31353 " pdb=" N9 G 31353 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C3' U 7 27 " pdb=" C4' U 7 27 " pdb=" O3' U 7 27 " pdb=" C2' U 7 27 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1' C 31155 " pdb=" O4' C 31155 " pdb=" C2' C 31155 " pdb=" N1 C 31155 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3410 not shown) Planarity restraints: 1645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 3 955 " 0.047 2.00e-02 2.50e+03 2.20e-02 1.33e+01 pdb=" N9 A 3 955 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A 3 955 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A 3 955 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 3 955 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A 3 955 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A 3 955 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A 3 955 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 3 955 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A 3 955 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 3 955 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 31354 " -0.042 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 A 31354 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A 31354 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A 31354 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A 31354 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A 31354 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 31354 " 0.011 2.00e-02 2.50e+03 pdb=" C4 A 31354 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 31353 " -0.038 2.00e-02 2.50e+03 1.71e-02 8.82e+00 pdb=" N9 G 31353 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G 31353 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 31353 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 31353 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 31353 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G 31353 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G 31353 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 31353 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 31353 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G 31353 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 31353 " 0.001 2.00e-02 2.50e+03 ... (remaining 1642 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 59 2.48 - 3.09: 10419 3.09 - 3.69: 28528 3.69 - 4.30: 45757 4.30 - 4.90: 62981 Nonbonded interactions: 147744 Sorted by model distance: nonbonded pdb=" O6 G 31105 " pdb="MG MG 31608 " model vdw 1.880 2.170 nonbonded pdb=" OP1 U 31196 " pdb="MG MG 31606 " model vdw 1.981 2.170 nonbonded pdb=" O LYS h 114 " pdb=" NH1 ARG h 119 " model vdw 2.056 3.120 nonbonded pdb=" OP2 G 31301 " pdb="MG MG 31620 " model vdw 2.056 2.170 nonbonded pdb=" OP1 G 3 990 " pdb="MG MG 31614 " model vdw 2.064 2.170 ... (remaining 147739 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.760 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 18137 Z= 0.363 Angle : 0.721 7.502 26812 Z= 0.392 Chirality : 0.046 0.236 3413 Planarity : 0.005 0.042 1645 Dihedral : 22.533 174.129 10038 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.15 % Allowed : 18.10 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.24), residues: 836 helix: -2.42 (0.22), residues: 344 sheet: 0.17 (0.44), residues: 125 loop : -2.42 (0.26), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG j 107 TYR 0.014 0.002 TYR d 29 PHE 0.012 0.002 PHE d 42 TRP 0.018 0.003 TRP o 101 HIS 0.007 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00735 (18137) covalent geometry : angle 0.72128 (26812) hydrogen bonds : bond 0.12427 ( 621) hydrogen bonds : angle 4.68476 ( 1391) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.364 Fit side-chains REVERT: d 11 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8635 (ptp-170) REVERT: d 110 ASP cc_start: 0.8014 (m-30) cc_final: 0.7761 (m-30) REVERT: d 152 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: d 187 MET cc_start: 0.8303 (mmm) cc_final: 0.7661 (tpt) REVERT: h 3 ARG cc_start: 0.6482 (mtm-85) cc_final: 0.6222 (mtm-85) REVERT: h 10 ARG cc_start: 0.7570 (ttm110) cc_final: 0.7360 (ttm110) REVERT: h 62 PHE cc_start: 0.8326 (t80) cc_final: 0.8018 (t80) REVERT: j 40 GLU cc_start: 0.7673 (pp20) cc_final: 0.7391 (pp20) REVERT: k 47 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: n 79 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7223 (ttm110) REVERT: n 107 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7649 (mmp80) REVERT: o 85 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8081 (ttt180) outliers start: 49 outliers final: 26 residues processed: 204 average time/residue: 0.6755 time to fit residues: 150.5214 Evaluate side-chains 182 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 11 ARG Chi-restraints excluded: chain d residue 34 LEU Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 93 ASN Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 56 THR Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 107 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 85 ARG Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.0070 chunk 129 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 6 HIS d 54 ASN d 104 ASN d 176 HIS h 29 HIS j 4 ASN j 30 ASN j 35 GLN j 73 GLN j 79 HIS j 124 GLN k 15 HIS k 50 ASN k 58 ASN k 64 GLN k 99 GLN n 76 ASN n 105 ASN o 8 ASN o 71 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097312 restraints weight = 20526.938| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 0.81 r_work: 0.2747 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18137 Z= 0.139 Angle : 0.539 6.871 26812 Z= 0.287 Chirality : 0.036 0.217 3413 Planarity : 0.005 0.038 1645 Dihedral : 22.395 176.392 8429 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.36 % Allowed : 24.67 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.27), residues: 836 helix: -0.80 (0.28), residues: 337 sheet: 0.97 (0.46), residues: 123 loop : -1.94 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 72 TYR 0.007 0.001 TYR k 70 PHE 0.010 0.001 PHE h 61 TRP 0.015 0.002 TRP o 101 HIS 0.007 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00277 (18137) covalent geometry : angle 0.53868 (26812) hydrogen bonds : bond 0.04779 ( 621) hydrogen bonds : angle 3.43787 ( 1391) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.354 Fit side-chains REVERT: h 10 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7675 (ttm110) REVERT: j 45 VAL cc_start: 0.9220 (t) cc_final: 0.9016 (t) REVERT: k 85 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: n 79 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7910 (ttm110) REVERT: o 41 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8086 (mtp85) outliers start: 23 outliers final: 14 residues processed: 177 average time/residue: 0.6151 time to fit residues: 119.9623 Evaluate side-chains 167 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 3 GLN h 54 ASN k 64 GLN k 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.126084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.093673 restraints weight = 20680.643| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 0.76 r_work: 0.2681 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18137 Z= 0.245 Angle : 0.611 7.058 26812 Z= 0.320 Chirality : 0.040 0.228 3413 Planarity : 0.005 0.039 1645 Dihedral : 22.362 175.510 8382 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 6.13 % Allowed : 23.21 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.28), residues: 836 helix: -0.45 (0.28), residues: 335 sheet: 1.19 (0.47), residues: 123 loop : -1.76 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG n 3 TYR 0.011 0.002 TYR d 29 PHE 0.011 0.002 PHE h 61 TRP 0.016 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00502 (18137) covalent geometry : angle 0.61132 (26812) hydrogen bonds : bond 0.05933 ( 621) hydrogen bonds : angle 3.46140 ( 1391) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.373 Fit side-chains REVERT: d 152 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: h 5 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5177 (mmt90) REVERT: h 10 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7665 (ttm110) REVERT: j 26 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8662 (tt) REVERT: j 45 VAL cc_start: 0.9223 (t) cc_final: 0.9009 (t) REVERT: k 47 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: k 85 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: n 71 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7877 (ttm-80) REVERT: n 78 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8008 (mtpp) REVERT: n 79 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7914 (ttm110) outliers start: 42 outliers final: 28 residues processed: 180 average time/residue: 0.6522 time to fit residues: 129.1657 Evaluate side-chains 181 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 51 MET Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 78 LYS Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Chi-restraints excluded: chain t residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 61 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.095225 restraints weight = 20572.640| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 0.74 r_work: 0.2723 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18137 Z= 0.174 Angle : 0.558 6.948 26812 Z= 0.295 Chirality : 0.037 0.223 3413 Planarity : 0.005 0.039 1645 Dihedral : 22.298 175.900 8382 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.99 % Allowed : 24.82 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.28), residues: 836 helix: -0.17 (0.29), residues: 339 sheet: 1.32 (0.47), residues: 128 loop : -1.61 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG h 119 TYR 0.009 0.001 TYR d 29 PHE 0.012 0.001 PHE h 61 TRP 0.014 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00354 (18137) covalent geometry : angle 0.55818 (26812) hydrogen bonds : bond 0.05136 ( 621) hydrogen bonds : angle 3.33489 ( 1391) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.396 Fit side-chains REVERT: d 152 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: h 5 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5120 (mmt90) REVERT: h 10 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7627 (ttm110) REVERT: h 48 GLU cc_start: 0.6965 (pt0) cc_final: 0.6457 (pm20) REVERT: j 26 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8442 (tt) REVERT: j 40 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7642 (tm-30) REVERT: j 45 VAL cc_start: 0.9209 (t) cc_final: 0.8977 (t) REVERT: k 47 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7576 (pt0) REVERT: k 60 ASP cc_start: 0.8867 (m-30) cc_final: 0.8602 (m-30) REVERT: k 85 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7399 (m-30) REVERT: n 71 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7861 (ttm-80) REVERT: n 79 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7811 (ttm170) REVERT: n 113 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.7020 (mtt180) REVERT: o 41 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8145 (mtp85) outliers start: 41 outliers final: 29 residues processed: 178 average time/residue: 0.6750 time to fit residues: 132.4727 Evaluate side-chains 179 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Chi-restraints excluded: chain t residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.096805 restraints weight = 20464.767| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 0.75 r_work: 0.2728 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18137 Z= 0.163 Angle : 0.541 7.132 26812 Z= 0.286 Chirality : 0.037 0.220 3413 Planarity : 0.004 0.038 1645 Dihedral : 22.237 176.284 8382 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 6.57 % Allowed : 24.67 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.29), residues: 836 helix: 0.04 (0.29), residues: 343 sheet: 1.44 (0.47), residues: 128 loop : -1.52 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 108 TYR 0.008 0.001 TYR k 70 PHE 0.014 0.001 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00331 (18137) covalent geometry : angle 0.54127 (26812) hydrogen bonds : bond 0.04970 ( 621) hydrogen bonds : angle 3.24560 ( 1391) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: d 140 ASN cc_start: 0.8869 (t0) cc_final: 0.8632 (t0) REVERT: d 152 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: h 5 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5118 (mmt90) REVERT: h 10 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7634 (ttm110) REVERT: j 40 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7803 (tm-30) REVERT: j 45 VAL cc_start: 0.9183 (t) cc_final: 0.8936 (t) REVERT: j 51 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7821 (pp20) REVERT: k 47 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: k 60 ASP cc_start: 0.8854 (m-30) cc_final: 0.8575 (m-30) REVERT: k 85 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: n 71 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7865 (ttm-80) REVERT: n 79 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7835 (ttm170) REVERT: n 108 THR cc_start: 0.8878 (t) cc_final: 0.8666 (m) REVERT: n 113 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7093 (mtt180) REVERT: t 18 LYS cc_start: 0.9009 (mttt) cc_final: 0.8759 (mttm) outliers start: 45 outliers final: 29 residues processed: 177 average time/residue: 0.6443 time to fit residues: 126.0053 Evaluate side-chains 180 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 8 ASN Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Chi-restraints excluded: chain t residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 84 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 0.0170 chunk 120 optimal weight: 0.1980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.099236 restraints weight = 20550.810| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 0.74 r_work: 0.2753 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 18137 Z= 0.107 Angle : 0.517 6.828 26812 Z= 0.275 Chirality : 0.035 0.215 3413 Planarity : 0.004 0.037 1645 Dihedral : 22.226 176.707 8379 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.38 % Allowed : 27.74 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.29), residues: 836 helix: 0.27 (0.29), residues: 343 sheet: 1.66 (0.49), residues: 123 loop : -1.46 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 72 TYR 0.007 0.001 TYR k 70 PHE 0.018 0.001 PHE h 61 TRP 0.011 0.002 TRP o 101 HIS 0.002 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00213 (18137) covalent geometry : angle 0.51701 (26812) hydrogen bonds : bond 0.04547 ( 621) hydrogen bonds : angle 3.19936 ( 1391) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.374 Fit side-chains REVERT: d 27 LYS cc_start: 0.9014 (ptmt) cc_final: 0.8780 (ttpt) REVERT: d 54 ASN cc_start: 0.8672 (t0) cc_final: 0.8433 (t0) REVERT: d 140 ASN cc_start: 0.8852 (t0) cc_final: 0.8627 (t0) REVERT: d 152 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: h 5 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5234 (mmt90) REVERT: h 10 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7563 (ttm110) REVERT: h 48 GLU cc_start: 0.6883 (pt0) cc_final: 0.6352 (pm20) REVERT: j 40 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7600 (tm-30) REVERT: j 45 VAL cc_start: 0.9162 (t) cc_final: 0.8892 (t) REVERT: j 51 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7839 (pp20) REVERT: k 47 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: k 60 ASP cc_start: 0.8857 (m-30) cc_final: 0.8586 (m-30) REVERT: k 85 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: n 3 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.6682 (ttm-80) REVERT: n 8 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7049 (m-40) REVERT: n 71 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7873 (ttm-80) REVERT: n 79 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7838 (ttm170) REVERT: t 18 LYS cc_start: 0.8962 (mttt) cc_final: 0.8715 (mttm) outliers start: 30 outliers final: 17 residues processed: 167 average time/residue: 0.6883 time to fit residues: 126.4192 Evaluate side-chains 168 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 8 ASN Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.097705 restraints weight = 20381.636| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 0.78 r_work: 0.2730 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18137 Z= 0.159 Angle : 0.537 6.739 26812 Z= 0.283 Chirality : 0.036 0.220 3413 Planarity : 0.005 0.078 1645 Dihedral : 22.174 176.554 8379 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.40 % Allowed : 26.57 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.29), residues: 836 helix: 0.29 (0.28), residues: 348 sheet: 1.56 (0.48), residues: 128 loop : -1.43 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG d 143 TYR 0.008 0.001 TYR j 59 PHE 0.017 0.001 PHE h 61 TRP 0.012 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00324 (18137) covalent geometry : angle 0.53657 (26812) hydrogen bonds : bond 0.04923 ( 621) hydrogen bonds : angle 3.16528 ( 1391) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.238 Fit side-chains REVERT: d 27 LYS cc_start: 0.9015 (ptmt) cc_final: 0.8772 (ttpt) REVERT: d 140 ASN cc_start: 0.8839 (t0) cc_final: 0.8616 (t0) REVERT: d 152 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: h 5 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5102 (mmt90) REVERT: h 10 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7606 (ttm110) REVERT: h 48 GLU cc_start: 0.6885 (pt0) cc_final: 0.6419 (pm20) REVERT: j 45 VAL cc_start: 0.9005 (t) cc_final: 0.8755 (t) REVERT: j 51 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7837 (pp20) REVERT: k 47 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: k 60 ASP cc_start: 0.8894 (m-30) cc_final: 0.8585 (m-30) REVERT: k 85 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: n 3 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6636 (ttm-80) REVERT: n 8 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7048 (m-40) REVERT: n 71 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7842 (ttm-80) REVERT: n 79 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7862 (ttm170) outliers start: 37 outliers final: 26 residues processed: 167 average time/residue: 0.6761 time to fit residues: 124.3838 Evaluate side-chains 171 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 93 ASN Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 8 ASN Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.090922 restraints weight = 20627.635| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 0.87 r_work: 0.2637 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 18137 Z= 0.379 Angle : 0.731 7.258 26812 Z= 0.375 Chirality : 0.046 0.241 3413 Planarity : 0.006 0.052 1645 Dihedral : 22.417 173.913 8379 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.72 % Allowed : 25.69 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.28), residues: 836 helix: 0.02 (0.28), residues: 341 sheet: 1.36 (0.47), residues: 128 loop : -1.50 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG d 143 TYR 0.013 0.002 TYR d 29 PHE 0.021 0.002 PHE h 61 TRP 0.014 0.003 TRP o 101 HIS 0.007 0.002 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00776 (18137) covalent geometry : angle 0.73114 (26812) hydrogen bonds : bond 0.07344 ( 621) hydrogen bonds : angle 3.49891 ( 1391) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: d 93 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8321 (t0) REVERT: d 140 ASN cc_start: 0.8930 (t0) cc_final: 0.8657 (t0) REVERT: d 152 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: d 166 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: h 5 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.5175 (mmt90) REVERT: h 10 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7784 (ttm110) REVERT: h 68 LYS cc_start: 0.7944 (tppt) cc_final: 0.7294 (tptm) REVERT: j 51 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7932 (pp20) REVERT: k 47 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: k 85 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: n 78 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8096 (ttpp) REVERT: n 79 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7887 (ttm170) REVERT: n 113 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7177 (mtt180) REVERT: o 6 MET cc_start: 0.8886 (mmm) cc_final: 0.8667 (mmm) REVERT: t 63 THR cc_start: 0.9224 (m) cc_final: 0.8951 (m) outliers start: 46 outliers final: 31 residues processed: 170 average time/residue: 0.6766 time to fit residues: 126.9888 Evaluate side-chains 179 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 51 MET Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 93 ASN Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain k residue 100 ILE Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 78 LYS Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 38 ASP Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 123 GLN k 64 GLN k 99 GLN t 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.095201 restraints weight = 20479.529| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 0.82 r_work: 0.2699 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18137 Z= 0.175 Angle : 0.564 6.698 26812 Z= 0.299 Chirality : 0.038 0.223 3413 Planarity : 0.005 0.053 1645 Dihedral : 22.231 174.936 8379 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.11 % Allowed : 27.15 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.29), residues: 836 helix: 0.28 (0.28), residues: 347 sheet: 1.43 (0.47), residues: 128 loop : -1.35 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG d 143 TYR 0.009 0.001 TYR d 29 PHE 0.024 0.001 PHE h 61 TRP 0.014 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00355 (18137) covalent geometry : angle 0.56401 (26812) hydrogen bonds : bond 0.05085 ( 621) hydrogen bonds : angle 3.29700 ( 1391) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.410 Fit side-chains REVERT: d 140 ASN cc_start: 0.8867 (t0) cc_final: 0.8623 (t0) REVERT: d 166 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: h 5 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.5090 (mmt90) REVERT: h 10 ARG cc_start: 0.8339 (ttm110) cc_final: 0.7716 (ttm110) REVERT: h 48 GLU cc_start: 0.6958 (pt0) cc_final: 0.6579 (pm20) REVERT: h 68 LYS cc_start: 0.7891 (tppt) cc_final: 0.7288 (tptm) REVERT: j 51 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: k 47 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7622 (pt0) REVERT: k 48 ARG cc_start: 0.8917 (mtt180) cc_final: 0.8709 (mtt180) REVERT: k 60 ASP cc_start: 0.8927 (m-30) cc_final: 0.8638 (m-30) REVERT: k 85 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: n 79 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7857 (ttm170) REVERT: n 113 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7200 (mtt180) REVERT: t 18 LYS cc_start: 0.9011 (mttt) cc_final: 0.8748 (mttm) REVERT: t 63 THR cc_start: 0.9228 (m) cc_final: 0.8968 (m) outliers start: 35 outliers final: 23 residues processed: 161 average time/residue: 0.7003 time to fit residues: 124.0548 Evaluate side-chains 163 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 38 ASP Chi-restraints excluded: chain t residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 110 optimal weight: 0.0020 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 123 GLN k 64 GLN k 99 GLN t 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095455 restraints weight = 20322.186| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 0.75 r_work: 0.2687 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18137 Z= 0.207 Angle : 0.584 6.681 26812 Z= 0.307 Chirality : 0.039 0.225 3413 Planarity : 0.005 0.051 1645 Dihedral : 22.236 174.979 8379 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.96 % Allowed : 27.74 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.29), residues: 836 helix: 0.27 (0.28), residues: 348 sheet: 1.35 (0.45), residues: 140 loop : -1.36 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG d 143 TYR 0.011 0.002 TYR j 59 PHE 0.024 0.002 PHE h 61 TRP 0.014 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00422 (18137) covalent geometry : angle 0.58390 (26812) hydrogen bonds : bond 0.05451 ( 621) hydrogen bonds : angle 3.29536 ( 1391) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.428 Fit side-chains REVERT: d 140 ASN cc_start: 0.8874 (t0) cc_final: 0.8630 (t0) REVERT: d 166 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: h 5 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5108 (mmt90) REVERT: h 10 ARG cc_start: 0.8342 (ttm110) cc_final: 0.7695 (ttm110) REVERT: h 48 GLU cc_start: 0.6948 (pt0) cc_final: 0.6485 (pm20) REVERT: h 68 LYS cc_start: 0.7910 (tppt) cc_final: 0.7366 (tptm) REVERT: j 51 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7882 (pp20) REVERT: k 47 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: k 60 ASP cc_start: 0.8928 (m-30) cc_final: 0.8637 (m-30) REVERT: k 85 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: n 78 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8194 (ttpp) REVERT: n 79 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7869 (ttm170) REVERT: n 113 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7214 (mtt180) REVERT: t 63 THR cc_start: 0.9237 (m) cc_final: 0.8971 (m) outliers start: 34 outliers final: 26 residues processed: 157 average time/residue: 0.6380 time to fit residues: 110.3716 Evaluate side-chains 165 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain k residue 100 ILE Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 78 LYS Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 38 ASP Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 55 optimal weight: 0.0970 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 123 GLN k 64 GLN k 99 GLN t 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.096048 restraints weight = 20300.055| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 0.78 r_work: 0.2722 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18137 Z= 0.126 Angle : 0.554 11.735 26812 Z= 0.293 Chirality : 0.036 0.221 3413 Planarity : 0.005 0.084 1645 Dihedral : 22.244 175.416 8379 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.96 % Allowed : 27.74 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.29), residues: 836 helix: 0.42 (0.28), residues: 347 sheet: 1.51 (0.46), residues: 135 loop : -1.26 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG d 143 TYR 0.011 0.001 TYR j 59 PHE 0.024 0.001 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00255 (18137) covalent geometry : angle 0.55376 (26812) hydrogen bonds : bond 0.04840 ( 621) hydrogen bonds : angle 3.26604 ( 1391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5057.32 seconds wall clock time: 87 minutes 6.76 seconds (5226.76 seconds total)