Starting phenix.real_space_refine on Thu Mar 5 03:09:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afh_11765/03_2026/7afh_11765_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afh_11765/03_2026/7afh_11765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7afh_11765/03_2026/7afh_11765_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afh_11765/03_2026/7afh_11765_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7afh_11765/03_2026/7afh_11765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afh_11765/03_2026/7afh_11765.map" } resolution = 3.59 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= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 11 5.21 5 S 28 5.16 5 C 9820 2.51 5 N 3442 2.21 5 O 4724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18482 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 211, 'rna3p_pyr': 171} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.51, per 1000 atoms: 0.19 Number of scatterers: 18482 At special positions: 0 Unit cell: (116.095, 116.095, 158.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 11 11.99 O 4724 8.00 N 3442 7.00 C 9820 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: 1.53 Conformation dependent library (CDL) restraints added in 437.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 50.0% alpha, 14.9% beta 130 base pairs and 210 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.586A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.226A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.781A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 4.003A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.294A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.584A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 133 through 147 Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 3.676A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.872A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.845A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 4.497A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.577A pdb=" N TYR N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 51 removed outlier: 3.864A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 56 Processing helix chain 'N' and resid 82 through 90 Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.722A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.400A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 170 removed outlier: 5.953A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 11 removed outlier: 3.738A pdb=" N GLY I 10 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 40 through 51 removed outlier: 4.678A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 40 through 51 removed outlier: 4.678A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 5.808A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 299 hydrogen bonds 378 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 210 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.99 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: 2703 1.32 - 1.45: 7435 1.45 - 1.57: 8660 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19762 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.457 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N VAL M 65 " pdb=" CA VAL M 65 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N ILE J 40 " pdb=" CA ILE J 40 " ideal model delta sigma weight residual 1.460 1.493 -0.033 9.30e-03 1.16e+04 1.23e+01 bond pdb=" N VAL J 51 " pdb=" CA VAL J 51 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.14e-02 7.69e+03 1.21e+01 bond pdb=" C6 2MG 11207 " pdb=" N1 2MG 11207 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 19757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 27573 1.92 - 3.83: 1188 3.83 - 5.75: 108 5.75 - 7.67: 17 7.67 - 9.59: 11 Bond angle restraints: 28897 Sorted by residual: angle pdb=" C HIS M 14 " pdb=" CA HIS M 14 " pdb=" CB HIS M 14 " ideal model delta sigma weight residual 109.62 118.70 -9.08 1.79e+00 3.12e-01 2.57e+01 angle pdb=" CA GLY B 124 " pdb=" C GLY B 124 " pdb=" O GLY B 124 " ideal model delta sigma weight residual 121.30 116.92 4.38 9.80e-01 1.04e+00 1.99e+01 angle pdb=" N SER I 93 " pdb=" CA SER I 93 " pdb=" C SER I 93 " ideal model delta sigma weight residual 112.90 107.06 5.84 1.31e+00 5.83e-01 1.99e+01 angle pdb=" C GLU M 66 " pdb=" CA GLU M 66 " pdb=" CB GLU M 66 " ideal model delta sigma weight residual 116.63 111.47 5.16 1.16e+00 7.43e-01 1.98e+01 angle pdb=" CA GLY M 26 " pdb=" C GLY M 26 " pdb=" O GLY M 26 " ideal model delta sigma weight residual 122.28 117.92 4.36 1.00e+00 1.00e+00 1.90e+01 ... (remaining 28892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 11300 35.21 - 70.41: 1162 70.41 - 105.62: 157 105.62 - 140.82: 5 140.82 - 176.03: 4 Dihedral angle restraints: 12628 sinusoidal: 9473 harmonic: 3155 Sorted by residual: dihedral pdb=" C4' G 11279 " pdb=" C3' G 11279 " pdb=" C2' G 11279 " pdb=" C1' G 11279 " ideal model delta sinusoidal sigma weight residual -35.00 35.37 -70.37 1 8.00e+00 1.56e-02 9.96e+01 dihedral pdb=" C5' G 11279 " pdb=" C4' G 11279 " pdb=" C3' G 11279 " pdb=" O3' G 11279 " ideal model delta sinusoidal sigma weight residual 147.00 81.41 65.59 1 8.00e+00 1.56e-02 8.80e+01 dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual -160.00 16.03 -176.03 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 12625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3092 0.066 - 0.131: 417 0.131 - 0.197: 75 0.197 - 0.263: 17 0.263 - 0.328: 3 Chirality restraints: 3604 Sorted by residual: chirality pdb=" C3' G 11279 " pdb=" C4' G 11279 " pdb=" O3' G 11279 " pdb=" C2' G 11279 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA THR B 125 " pdb=" N THR B 125 " pdb=" C THR B 125 " pdb=" CB THR B 125 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA HIS M 14 " pdb=" N HIS M 14 " pdb=" C HIS M 14 " pdb=" CB HIS M 14 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3601 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " -0.062 2.00e-02 2.50e+03 1.14e-01 4.23e+02 pdb=" N9 2MG 1 966 " -0.010 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " 0.056 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " 0.077 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " 0.024 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " 0.010 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " 0.058 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " -0.056 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " -0.112 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " -0.166 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " -0.097 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " -0.034 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " 0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " 0.027 2.00e-02 2.50e+03 3.94e-02 5.05e+01 pdb=" N9 2MG 11207 " -0.006 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " -0.018 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " -0.024 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " -0.005 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " -0.006 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " -0.020 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " 0.018 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " 0.038 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " 0.058 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " 0.035 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " 0.010 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN N 60 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C GLN N 60 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN N 60 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG N 61 " 0.015 2.00e-02 2.50e+03 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 267 2.38 - 3.01: 11503 3.01 - 3.64: 38143 3.64 - 4.27: 54012 4.27 - 4.90: 74536 Nonbonded interactions: 178461 Sorted by model distance: nonbonded pdb=" O3' G 11365 " pdb="MG MG 11606 " model vdw 1.752 2.170 nonbonded pdb=" O3' G 11242 " pdb="MG MG 11610 " model vdw 1.796 2.170 nonbonded pdb=" OP1 U 11199 " pdb="MG MG 11609 " model vdw 1.842 2.170 nonbonded pdb=" OP1 C 11054 " pdb="MG MG 11608 " model vdw 1.849 2.170 nonbonded pdb=" OP1 A 1 964 " pdb="MG MG 11609 " model vdw 1.857 2.170 ... (remaining 178456 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 group one per residue 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.860 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.009 0.151 19763 Z= 0.506 Angle : 0.894 9.586 28897 Z= 0.539 Chirality : 0.050 0.328 3604 Planarity : 0.005 0.114 1988 Dihedral : 22.890 176.029 10586 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 32.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.24), residues: 1087 helix: -1.42 (0.22), residues: 478 sheet: -1.84 (0.36), residues: 162 loop : -1.82 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 99 TYR 0.016 0.002 TYR I 64 PHE 0.016 0.002 PHE C 37 TRP 0.009 0.002 TRP C 201 HIS 0.006 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00866 (19762) covalent geometry : angle 0.89391 (28897) hydrogen bonds : bond 0.26020 ( 738) hydrogen bonds : angle 9.01883 ( 1629) metal coordination : bond 0.15062 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.8038 (t-100) cc_final: 0.7798 (t-100) REVERT: C 183 ASP cc_start: 0.8739 (t0) cc_final: 0.8405 (t0) REVERT: J 91 ASP cc_start: 0.8061 (p0) cc_final: 0.7780 (p0) REVERT: J 97 ASP cc_start: 0.8734 (t70) cc_final: 0.8515 (t0) REVERT: M 34 LEU cc_start: 0.9321 (tp) cc_final: 0.9049 (tp) REVERT: M 81 MET cc_start: 0.9185 (mtp) cc_final: 0.8691 (ttm) REVERT: N 67 THR cc_start: 0.8772 (p) cc_final: 0.8097 (t) REVERT: S 66 MET cc_start: 0.8908 (mtp) cc_final: 0.8610 (mtp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1722 time to fit residues: 60.5662 Evaluate side-chains 135 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.038737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.028228 restraints weight = 161201.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.028820 restraints weight = 76392.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.029146 restraints weight = 52862.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.029267 restraints weight = 44998.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.029268 restraints weight = 42054.302| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19763 Z= 0.165 Angle : 0.684 13.799 28897 Z= 0.348 Chirality : 0.038 0.263 3604 Planarity : 0.005 0.055 1988 Dihedral : 23.627 178.893 8369 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.51 % Allowed : 17.43 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.24), residues: 1087 helix: -0.53 (0.22), residues: 498 sheet: -1.41 (0.37), residues: 157 loop : -1.28 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 3 TYR 0.014 0.002 TYR I 90 PHE 0.026 0.002 PHE B 198 TRP 0.013 0.001 TRP C 201 HIS 0.004 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00322 (19762) covalent geometry : angle 0.68356 (28897) hydrogen bonds : bond 0.11018 ( 738) hydrogen bonds : angle 4.99587 ( 1629) metal coordination : bond 0.00157 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 GLN cc_start: 0.9283 (tp-100) cc_final: 0.8754 (tp-100) REVERT: B 171 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7832 (tt) REVERT: C 36 ASP cc_start: 0.8576 (m-30) cc_final: 0.7811 (m-30) REVERT: C 183 ASP cc_start: 0.8701 (t0) cc_final: 0.8335 (t0) REVERT: I 88 MET cc_start: 0.9159 (ttm) cc_final: 0.8720 (mmt) REVERT: J 46 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8291 (mmtp) REVERT: J 91 ASP cc_start: 0.8485 (p0) cc_final: 0.8253 (p0) REVERT: J 97 ASP cc_start: 0.8945 (t70) cc_final: 0.8479 (p0) REVERT: J 99 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8467 (mm110) REVERT: M 20 THR cc_start: 0.9384 (m) cc_final: 0.8921 (p) REVERT: M 75 MET cc_start: 0.9154 (ptp) cc_final: 0.8945 (ptp) REVERT: M 81 MET cc_start: 0.9150 (mtp) cc_final: 0.8691 (ttm) REVERT: M 95 LEU cc_start: 0.9385 (mt) cc_final: 0.9028 (mp) REVERT: N 62 ASN cc_start: 0.8834 (m-40) cc_final: 0.8244 (t0) REVERT: N 67 THR cc_start: 0.9153 (p) cc_final: 0.8487 (t) REVERT: N 86 GLU cc_start: 0.9254 (mp0) cc_final: 0.8895 (mp0) REVERT: N 93 ILE cc_start: 0.9526 (mm) cc_final: 0.9275 (mp) REVERT: S 66 MET cc_start: 0.8908 (mtp) cc_final: 0.8564 (mtp) outliers start: 23 outliers final: 11 residues processed: 195 average time/residue: 0.1530 time to fit residues: 44.5403 Evaluate side-chains 150 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 119 optimal weight: 0.0980 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 10.9990 chunk 142 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 140 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 122 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.037467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.026783 restraints weight = 166428.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.027373 restraints weight = 80355.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.027715 restraints weight = 54581.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027873 restraints weight = 44891.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.028009 restraints weight = 41374.582| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19763 Z= 0.262 Angle : 0.675 12.935 28897 Z= 0.342 Chirality : 0.039 0.263 3604 Planarity : 0.005 0.059 1988 Dihedral : 23.569 179.302 8369 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.59 % Allowed : 18.08 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.24), residues: 1087 helix: -0.20 (0.22), residues: 502 sheet: -1.27 (0.37), residues: 167 loop : -1.21 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 113 TYR 0.024 0.002 TYR C 168 PHE 0.014 0.002 PHE S 74 TRP 0.017 0.002 TRP G 103 HIS 0.007 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00506 (19762) covalent geometry : angle 0.67490 (28897) hydrogen bonds : bond 0.09924 ( 738) hydrogen bonds : angle 4.87955 ( 1629) metal coordination : bond 0.00261 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8872 (tp-100) REVERT: C 36 ASP cc_start: 0.8699 (m-30) cc_final: 0.7953 (m-30) REVERT: C 102 ASN cc_start: 0.9053 (m-40) cc_final: 0.8790 (m-40) REVERT: C 183 ASP cc_start: 0.8616 (t0) cc_final: 0.8257 (t0) REVERT: G 21 GLU cc_start: 0.8882 (pp20) cc_final: 0.8276 (tp30) REVERT: G 113 ASP cc_start: 0.8743 (t0) cc_final: 0.8506 (t0) REVERT: I 42 GLU cc_start: 0.8554 (tp30) cc_final: 0.8254 (tp30) REVERT: I 46 MET cc_start: 0.8987 (mtt) cc_final: 0.7894 (mtt) REVERT: I 88 MET cc_start: 0.9087 (ttm) cc_final: 0.8693 (mmt) REVERT: J 91 ASP cc_start: 0.8539 (p0) cc_final: 0.8324 (p0) REVERT: J 97 ASP cc_start: 0.8929 (t70) cc_final: 0.8674 (t0) REVERT: J 99 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8312 (mm110) REVERT: M 27 LYS cc_start: 0.9604 (tptm) cc_final: 0.9161 (tptt) REVERT: M 42 ASP cc_start: 0.7718 (m-30) cc_final: 0.7461 (t0) REVERT: M 81 MET cc_start: 0.9094 (mtp) cc_final: 0.8692 (ttm) REVERT: N 62 ASN cc_start: 0.8806 (m-40) cc_final: 0.8342 (t0) REVERT: N 67 THR cc_start: 0.9182 (p) cc_final: 0.8662 (t) REVERT: N 86 GLU cc_start: 0.9168 (mp0) cc_final: 0.8872 (mp0) REVERT: N 93 ILE cc_start: 0.9484 (mm) cc_final: 0.9278 (mp) REVERT: S 66 MET cc_start: 0.8842 (mtp) cc_final: 0.8639 (mtt) outliers start: 33 outliers final: 20 residues processed: 174 average time/residue: 0.1394 time to fit residues: 37.5393 Evaluate side-chains 154 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN C 8 ASN G 122 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.038124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.027299 restraints weight = 165160.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.027975 restraints weight = 78422.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.028350 restraints weight = 52614.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.028490 restraints weight = 42780.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028580 restraints weight = 39440.660| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19763 Z= 0.193 Angle : 0.628 11.854 28897 Z= 0.322 Chirality : 0.037 0.251 3604 Planarity : 0.004 0.051 1988 Dihedral : 23.487 179.625 8369 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.49 % Allowed : 21.02 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1087 helix: -0.01 (0.22), residues: 508 sheet: -1.06 (0.38), residues: 165 loop : -1.01 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 113 TYR 0.014 0.002 TYR I 6 PHE 0.013 0.001 PHE B 184 TRP 0.028 0.002 TRP G 103 HIS 0.008 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00371 (19762) covalent geometry : angle 0.62828 (28897) hydrogen bonds : bond 0.09620 ( 738) hydrogen bonds : angle 4.68551 ( 1629) metal coordination : bond 0.00383 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 GLN cc_start: 0.9105 (tp40) cc_final: 0.8819 (tp-100) REVERT: B 184 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6333 (m-10) REVERT: C 36 ASP cc_start: 0.8689 (m-30) cc_final: 0.7935 (m-30) REVERT: C 103 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8414 (mm) REVERT: C 183 ASP cc_start: 0.8654 (t0) cc_final: 0.8299 (t0) REVERT: G 113 ASP cc_start: 0.8855 (t0) cc_final: 0.8621 (t0) REVERT: I 42 GLU cc_start: 0.8595 (tp30) cc_final: 0.8173 (tp30) REVERT: I 46 MET cc_start: 0.9048 (mtt) cc_final: 0.8039 (mtt) REVERT: I 50 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8944 (mm-40) REVERT: I 88 MET cc_start: 0.9173 (ttm) cc_final: 0.8641 (mmm) REVERT: I 104 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8642 (t) REVERT: I 115 LYS cc_start: 0.9128 (mttt) cc_final: 0.8924 (mmtp) REVERT: J 63 ASP cc_start: 0.8231 (t70) cc_final: 0.7823 (t0) REVERT: J 91 ASP cc_start: 0.8540 (p0) cc_final: 0.8335 (p0) REVERT: J 97 ASP cc_start: 0.8953 (t70) cc_final: 0.8696 (t0) REVERT: J 99 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8326 (mm110) REVERT: M 27 LYS cc_start: 0.9593 (tptm) cc_final: 0.9111 (mmtt) REVERT: M 42 ASP cc_start: 0.7814 (m-30) cc_final: 0.7548 (t0) REVERT: M 81 MET cc_start: 0.9129 (mtp) cc_final: 0.8737 (ttm) REVERT: N 62 ASN cc_start: 0.8835 (m-40) cc_final: 0.8216 (t0) REVERT: N 67 THR cc_start: 0.9206 (p) cc_final: 0.8701 (t) REVERT: N 86 GLU cc_start: 0.9245 (mp0) cc_final: 0.8878 (mp0) REVERT: S 49 ILE cc_start: 0.9323 (mp) cc_final: 0.9021 (tp) REVERT: S 66 MET cc_start: 0.8893 (mtp) cc_final: 0.8633 (mtt) outliers start: 32 outliers final: 24 residues processed: 177 average time/residue: 0.1550 time to fit residues: 41.7001 Evaluate side-chains 159 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN C 8 ASN G 122 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.038814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.027997 restraints weight = 163731.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.028568 restraints weight = 79344.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.028947 restraints weight = 55168.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029133 restraints weight = 43452.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029257 restraints weight = 39556.683| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19763 Z= 0.148 Angle : 0.607 12.756 28897 Z= 0.309 Chirality : 0.036 0.243 3604 Planarity : 0.004 0.044 1988 Dihedral : 23.394 178.669 8369 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.36 % Allowed : 21.90 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.25), residues: 1087 helix: 0.20 (0.23), residues: 507 sheet: -0.97 (0.38), residues: 167 loop : -0.90 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 32 TYR 0.018 0.002 TYR I 6 PHE 0.013 0.001 PHE B 184 TRP 0.033 0.002 TRP G 103 HIS 0.004 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00290 (19762) covalent geometry : angle 0.60707 (28897) hydrogen bonds : bond 0.09451 ( 738) hydrogen bonds : angle 4.50870 ( 1629) metal coordination : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 GLN cc_start: 0.9114 (tp40) cc_final: 0.8857 (tp-100) REVERT: B 184 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6114 (m-10) REVERT: B 190 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7984 (m-40) REVERT: B 203 ASN cc_start: 0.5208 (p0) cc_final: 0.4966 (t0) REVERT: C 36 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: C 102 ASN cc_start: 0.9074 (m-40) cc_final: 0.8772 (m-40) REVERT: C 103 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8426 (mm) REVERT: C 183 ASP cc_start: 0.8656 (t0) cc_final: 0.8310 (t0) REVERT: I 42 GLU cc_start: 0.8587 (tp30) cc_final: 0.8123 (tp30) REVERT: I 46 MET cc_start: 0.9065 (mtt) cc_final: 0.7974 (mtt) REVERT: I 50 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8884 (mm-40) REVERT: I 88 MET cc_start: 0.9133 (ttm) cc_final: 0.8618 (mmm) REVERT: I 104 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8602 (t) REVERT: I 115 LYS cc_start: 0.9078 (mttt) cc_final: 0.8631 (mmtt) REVERT: J 19 ASP cc_start: 0.9254 (m-30) cc_final: 0.9045 (m-30) REVERT: J 63 ASP cc_start: 0.8205 (t70) cc_final: 0.7727 (t70) REVERT: J 91 ASP cc_start: 0.8564 (p0) cc_final: 0.8355 (p0) REVERT: J 97 ASP cc_start: 0.8918 (t70) cc_final: 0.7809 (p0) REVERT: J 99 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8540 (mp10) REVERT: M 27 LYS cc_start: 0.9570 (tptm) cc_final: 0.9151 (tptt) REVERT: M 42 ASP cc_start: 0.7813 (m-30) cc_final: 0.7562 (t0) REVERT: M 81 MET cc_start: 0.9160 (mtp) cc_final: 0.8900 (ttm) REVERT: N 62 ASN cc_start: 0.8804 (m-40) cc_final: 0.8513 (t0) REVERT: N 67 THR cc_start: 0.9174 (p) cc_final: 0.8607 (t) REVERT: N 86 GLU cc_start: 0.9252 (mp0) cc_final: 0.8858 (mp0) REVERT: S 32 ARG cc_start: 0.8519 (mtp-110) cc_final: 0.8297 (mtp-110) REVERT: S 66 MET cc_start: 0.8848 (mtp) cc_final: 0.8623 (mtt) outliers start: 40 outliers final: 23 residues processed: 190 average time/residue: 0.1464 time to fit residues: 42.1457 Evaluate side-chains 166 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain N residue 77 PHE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 92 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.026041 restraints weight = 172789.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.026616 restraints weight = 85109.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.026907 restraints weight = 57627.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.027074 restraints weight = 48320.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.027145 restraints weight = 44447.307| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 19763 Z= 0.464 Angle : 0.844 12.946 28897 Z= 0.423 Chirality : 0.045 0.264 3604 Planarity : 0.006 0.056 1988 Dihedral : 23.677 178.207 8369 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 27.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.12 % Allowed : 22.55 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1087 helix: -0.15 (0.22), residues: 500 sheet: -1.06 (0.38), residues: 164 loop : -1.00 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 3 TYR 0.016 0.002 TYR I 90 PHE 0.022 0.002 PHE B 198 TRP 0.030 0.003 TRP G 103 HIS 0.008 0.002 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00884 (19762) covalent geometry : angle 0.84369 (28897) hydrogen bonds : bond 0.10231 ( 738) hydrogen bonds : angle 4.92870 ( 1629) metal coordination : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 GLN cc_start: 0.8974 (tp40) cc_final: 0.8661 (tp-100) REVERT: B 184 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6347 (m-10) REVERT: B 190 ASN cc_start: 0.8143 (p0) cc_final: 0.7770 (m-40) REVERT: C 183 ASP cc_start: 0.8688 (t0) cc_final: 0.8399 (t0) REVERT: I 42 GLU cc_start: 0.8620 (tp30) cc_final: 0.8235 (tp30) REVERT: I 46 MET cc_start: 0.9004 (mtt) cc_final: 0.7858 (mtt) REVERT: I 53 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8752 (pp20) REVERT: I 88 MET cc_start: 0.9107 (ttm) cc_final: 0.8882 (ttm) REVERT: J 63 ASP cc_start: 0.8350 (t70) cc_final: 0.7726 (t70) REVERT: J 91 ASP cc_start: 0.8452 (p0) cc_final: 0.8218 (p0) REVERT: J 99 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8268 (mm110) REVERT: M 27 LYS cc_start: 0.9614 (tptm) cc_final: 0.9364 (tptt) REVERT: M 81 MET cc_start: 0.9172 (mtp) cc_final: 0.8856 (ttm) REVERT: N 62 ASN cc_start: 0.8808 (m-40) cc_final: 0.8478 (t0) REVERT: N 67 THR cc_start: 0.9297 (p) cc_final: 0.8824 (t) REVERT: N 86 GLU cc_start: 0.9227 (mp0) cc_final: 0.8876 (mp0) outliers start: 47 outliers final: 32 residues processed: 175 average time/residue: 0.1399 time to fit residues: 37.9577 Evaluate side-chains 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 101 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 190 ASN C 8 ASN C 102 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.027297 restraints weight = 163849.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.027916 restraints weight = 79791.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.028233 restraints weight = 56526.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.028417 restraints weight = 45057.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.028517 restraints weight = 40966.878| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19763 Z= 0.227 Angle : 0.681 12.764 28897 Z= 0.345 Chirality : 0.039 0.247 3604 Planarity : 0.005 0.056 1988 Dihedral : 23.614 179.337 8369 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.03 % Allowed : 24.18 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.25), residues: 1087 helix: -0.06 (0.22), residues: 501 sheet: -0.98 (0.39), residues: 165 loop : -0.87 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 3 TYR 0.014 0.002 TYR I 90 PHE 0.014 0.001 PHE B 198 TRP 0.034 0.002 TRP G 103 HIS 0.007 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00438 (19762) covalent geometry : angle 0.68068 (28897) hydrogen bonds : bond 0.09550 ( 738) hydrogen bonds : angle 4.68813 ( 1629) metal coordination : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.6058 (t0) cc_final: 0.5728 (p0) REVERT: B 120 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8737 (tp-100) REVERT: B 184 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.6262 (m-10) REVERT: B 190 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7684 (m-40) REVERT: C 36 ASP cc_start: 0.8873 (m-30) cc_final: 0.8202 (m-30) REVERT: C 102 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8688 (m-40) REVERT: C 183 ASP cc_start: 0.8621 (t0) cc_final: 0.8294 (t0) REVERT: G 53 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7386 (ptt-90) REVERT: I 42 GLU cc_start: 0.8563 (tp30) cc_final: 0.8087 (tp30) REVERT: I 46 MET cc_start: 0.8943 (mtt) cc_final: 0.7715 (mtt) REVERT: I 50 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8881 (mm-40) REVERT: I 88 MET cc_start: 0.9093 (ttm) cc_final: 0.8787 (mmm) REVERT: I 115 LYS cc_start: 0.9079 (mttt) cc_final: 0.8656 (mmtt) REVERT: J 63 ASP cc_start: 0.8264 (t70) cc_final: 0.7630 (t70) REVERT: J 91 ASP cc_start: 0.8410 (p0) cc_final: 0.8192 (p0) REVERT: J 97 ASP cc_start: 0.8443 (t0) cc_final: 0.7644 (p0) REVERT: J 99 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8412 (mp10) REVERT: M 27 LYS cc_start: 0.9586 (tptm) cc_final: 0.9105 (tptt) REVERT: M 42 ASP cc_start: 0.7594 (m-30) cc_final: 0.7260 (t0) REVERT: M 81 MET cc_start: 0.9148 (mtp) cc_final: 0.8814 (mtt) REVERT: N 62 ASN cc_start: 0.8748 (m-40) cc_final: 0.8410 (t0) REVERT: N 67 THR cc_start: 0.9314 (p) cc_final: 0.8757 (t) REVERT: N 86 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: S 66 MET cc_start: 0.8536 (mtt) cc_final: 0.8325 (mtt) outliers start: 37 outliers final: 26 residues processed: 169 average time/residue: 0.1429 time to fit residues: 37.4990 Evaluate side-chains 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 31 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN C 8 ASN C 102 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.027286 restraints weight = 165897.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.027864 restraints weight = 81494.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.028235 restraints weight = 55496.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.028382 restraints weight = 45189.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.028503 restraints weight = 41402.169| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19763 Z= 0.251 Angle : 0.688 11.890 28897 Z= 0.351 Chirality : 0.039 0.258 3604 Planarity : 0.005 0.060 1988 Dihedral : 23.613 179.438 8369 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.58 % Allowed : 24.29 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.25), residues: 1087 helix: -0.07 (0.22), residues: 500 sheet: -1.11 (0.39), residues: 170 loop : -0.92 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 3 TYR 0.020 0.002 TYR I 6 PHE 0.013 0.002 PHE B 184 TRP 0.038 0.002 TRP G 103 HIS 0.007 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00485 (19762) covalent geometry : angle 0.68816 (28897) hydrogen bonds : bond 0.09379 ( 738) hydrogen bonds : angle 4.72994 ( 1629) metal coordination : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.6021 (t0) cc_final: 0.5784 (p0) REVERT: B 120 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8656 (tp-100) REVERT: B 184 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6430 (m-10) REVERT: C 102 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8595 (m-40) REVERT: C 183 ASP cc_start: 0.8614 (t0) cc_final: 0.8307 (t0) REVERT: I 42 GLU cc_start: 0.8580 (tp30) cc_final: 0.8097 (tp30) REVERT: I 46 MET cc_start: 0.8940 (mtt) cc_final: 0.7745 (mtt) REVERT: I 50 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8468 (mm-40) REVERT: I 53 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8546 (pp20) REVERT: I 88 MET cc_start: 0.9044 (ttm) cc_final: 0.8807 (mmm) REVERT: I 115 LYS cc_start: 0.9077 (mttt) cc_final: 0.8617 (mmtt) REVERT: J 11 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8973 (mppt) REVERT: J 63 ASP cc_start: 0.8337 (t70) cc_final: 0.7738 (t70) REVERT: J 88 MET cc_start: 0.8727 (mmm) cc_final: 0.8481 (ptp) REVERT: J 91 ASP cc_start: 0.8437 (p0) cc_final: 0.8199 (p0) REVERT: J 97 ASP cc_start: 0.8339 (t0) cc_final: 0.7389 (t0) REVERT: M 27 LYS cc_start: 0.9576 (tptm) cc_final: 0.9107 (tptt) REVERT: M 81 MET cc_start: 0.9157 (mtp) cc_final: 0.8820 (mtt) REVERT: N 62 ASN cc_start: 0.8739 (m-40) cc_final: 0.8400 (t0) REVERT: N 67 THR cc_start: 0.9310 (p) cc_final: 0.8746 (t) REVERT: N 86 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8819 (mp0) outliers start: 42 outliers final: 32 residues processed: 171 average time/residue: 0.1458 time to fit residues: 38.2416 Evaluate side-chains 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 8 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.037051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.026861 restraints weight = 167473.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.027483 restraints weight = 82292.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.027732 restraints weight = 59194.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.027896 restraints weight = 47302.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.027951 restraints weight = 43135.938| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 19763 Z= 0.326 Angle : 0.740 11.168 28897 Z= 0.376 Chirality : 0.041 0.251 3604 Planarity : 0.005 0.088 1988 Dihedral : 23.680 179.753 8369 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.03 % Allowed : 26.25 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1087 helix: -0.29 (0.22), residues: 506 sheet: -1.00 (0.39), residues: 169 loop : -1.01 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 3 TYR 0.022 0.002 TYR I 6 PHE 0.016 0.002 PHE B 90 TRP 0.033 0.002 TRP G 103 HIS 0.012 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00626 (19762) covalent geometry : angle 0.74014 (28897) hydrogen bonds : bond 0.09544 ( 738) hydrogen bonds : angle 4.86013 ( 1629) metal coordination : bond 0.10597 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.6021 (t0) cc_final: 0.5776 (p0) REVERT: B 120 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8635 (tp-100) REVERT: B 203 ASN cc_start: 0.5079 (p0) cc_final: 0.4751 (t0) REVERT: C 102 ASN cc_start: 0.8853 (m-40) cc_final: 0.8630 (m-40) REVERT: C 183 ASP cc_start: 0.8616 (t0) cc_final: 0.8315 (t0) REVERT: I 42 GLU cc_start: 0.8609 (tp30) cc_final: 0.8141 (tp30) REVERT: I 46 MET cc_start: 0.9018 (mtt) cc_final: 0.7842 (mtt) REVERT: I 53 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8634 (pp20) REVERT: I 88 MET cc_start: 0.9097 (ttm) cc_final: 0.8827 (mmm) REVERT: I 115 LYS cc_start: 0.9086 (mttt) cc_final: 0.8623 (mmtt) REVERT: J 11 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8994 (mppt) REVERT: J 63 ASP cc_start: 0.8316 (t70) cc_final: 0.7693 (t70) REVERT: J 91 ASP cc_start: 0.8442 (p0) cc_final: 0.8198 (p0) REVERT: J 97 ASP cc_start: 0.8442 (t0) cc_final: 0.7388 (t0) REVERT: M 27 LYS cc_start: 0.9572 (tptm) cc_final: 0.9147 (tptt) REVERT: M 42 ASP cc_start: 0.7564 (m-30) cc_final: 0.7303 (t0) REVERT: M 81 MET cc_start: 0.9193 (mtp) cc_final: 0.8888 (ttm) REVERT: N 62 ASN cc_start: 0.8752 (m-40) cc_final: 0.8424 (t0) REVERT: N 67 THR cc_start: 0.9354 (p) cc_final: 0.8818 (t) REVERT: N 86 GLU cc_start: 0.9209 (mp0) cc_final: 0.8812 (mp0) outliers start: 37 outliers final: 33 residues processed: 165 average time/residue: 0.1420 time to fit residues: 36.2391 Evaluate side-chains 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 102 ASN G 28 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.037999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.027800 restraints weight = 164610.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.028455 restraints weight = 77997.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.028799 restraints weight = 51213.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.028984 restraints weight = 42447.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.029095 restraints weight = 38699.217| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19763 Z= 0.199 Angle : 0.678 12.155 28897 Z= 0.346 Chirality : 0.038 0.240 3604 Planarity : 0.005 0.086 1988 Dihedral : 23.629 178.587 8369 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.38 % Allowed : 26.69 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.25), residues: 1087 helix: -0.20 (0.22), residues: 505 sheet: -0.88 (0.40), residues: 170 loop : -0.89 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 138 TYR 0.015 0.002 TYR I 90 PHE 0.011 0.001 PHE B 90 TRP 0.053 0.002 TRP G 103 HIS 0.005 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00390 (19762) covalent geometry : angle 0.67787 (28897) hydrogen bonds : bond 0.09380 ( 738) hydrogen bonds : angle 4.77259 ( 1629) metal coordination : bond 0.00991 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.6065 (t0) cc_final: 0.5828 (p0) REVERT: B 120 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8698 (tp-100) REVERT: B 203 ASN cc_start: 0.5242 (p0) cc_final: 0.4951 (t0) REVERT: C 102 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8699 (m-40) REVERT: C 183 ASP cc_start: 0.8661 (t0) cc_final: 0.8280 (t0) REVERT: G 26 PHE cc_start: 0.9123 (t80) cc_final: 0.8913 (t80) REVERT: I 6 TYR cc_start: 0.7964 (m-10) cc_final: 0.7440 (m-10) REVERT: I 42 GLU cc_start: 0.8689 (tp30) cc_final: 0.8151 (tp30) REVERT: I 46 MET cc_start: 0.9031 (mtt) cc_final: 0.7887 (mtt) REVERT: I 50 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8462 (mm-40) REVERT: I 53 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8548 (pp20) REVERT: I 115 LYS cc_start: 0.8994 (mttt) cc_final: 0.8572 (mmtt) REVERT: J 11 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8893 (mppt) REVERT: J 63 ASP cc_start: 0.8304 (t70) cc_final: 0.7698 (t70) REVERT: J 91 ASP cc_start: 0.8572 (p0) cc_final: 0.8341 (p0) REVERT: J 97 ASP cc_start: 0.8543 (t0) cc_final: 0.7539 (t0) REVERT: M 27 LYS cc_start: 0.9597 (tptm) cc_final: 0.9164 (tptt) REVERT: M 42 ASP cc_start: 0.7783 (m-30) cc_final: 0.7552 (t0) REVERT: M 81 MET cc_start: 0.9252 (mtp) cc_final: 0.8933 (ttm) REVERT: N 62 ASN cc_start: 0.8746 (m-40) cc_final: 0.8328 (t0) REVERT: N 67 THR cc_start: 0.9348 (p) cc_final: 0.8784 (t) REVERT: N 86 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8993 (mt-10) outliers start: 31 outliers final: 23 residues processed: 164 average time/residue: 0.1478 time to fit residues: 36.8116 Evaluate side-chains 160 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 102 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.037360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.027217 restraints weight = 167651.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.027798 restraints weight = 80297.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.028188 restraints weight = 54646.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.028335 restraints weight = 45499.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.028401 restraints weight = 41338.600| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 19763 Z= 0.292 Angle : 0.733 12.633 28897 Z= 0.373 Chirality : 0.040 0.247 3604 Planarity : 0.005 0.081 1988 Dihedral : 23.653 179.637 8369 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.16 % Allowed : 27.34 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.25), residues: 1087 helix: -0.35 (0.22), residues: 505 sheet: -0.79 (0.40), residues: 169 loop : -1.01 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 32 TYR 0.019 0.002 TYR C 42 PHE 0.024 0.002 PHE B 198 TRP 0.035 0.002 TRP G 103 HIS 0.008 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00565 (19762) covalent geometry : angle 0.73325 (28897) hydrogen bonds : bond 0.09349 ( 738) hydrogen bonds : angle 4.85970 ( 1629) metal coordination : bond 0.00101 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.85 seconds wall clock time: 60 minutes 8.67 seconds (3608.67 seconds total)