Starting phenix.real_space_refine on Sat Jul 4 05:29:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afh_11765/07_2026/7afh_11765_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afh_11765/07_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_11765/07_2026/7afh_11765_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afh_11765/07_2026/7afh_11765_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7afh_11765/07_2026/7afh_11765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afh_11765/07_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-6108/lib/python3.11/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: 3.01, per 1000 atoms: 0.16 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: 1.68 Conformation dependent library (CDL) restraints added in 478.7 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: 2.12 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: 3.57 Time building geometry restraints manager: 2.19 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=" N9 A 11105 " pdb=" C4 A 11105 " ideal model delta sigma weight residual 1.374 1.346 0.028 6.00e-03 2.78e+04 2.16e+01 bond pdb=" N9 A 11227 " pdb=" C4 A 11227 " ideal model delta sigma weight residual 1.374 1.347 0.027 6.00e-03 2.78e+04 2.02e+01 bond pdb=" N9 A 11363 " pdb=" C4 A 11363 " ideal model delta sigma weight residual 1.374 1.348 0.026 6.00e-03 2.78e+04 1.92e+01 bond pdb=" N9 A 11110 " pdb=" C4 A 11110 " ideal model delta sigma weight residual 1.374 1.350 0.024 6.00e-03 2.78e+04 1.65e+01 bond pdb=" N9 A 11360 " pdb=" C4 A 11360 " ideal model delta sigma weight residual 1.374 1.350 0.024 6.00e-03 2.78e+04 1.61e+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=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sigma weight residual 117.70 124.72 -7.02 1.20e+00 6.94e-01 3.42e+01 angle pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C6 U 11008 " ideal model delta sigma weight residual 121.20 113.83 7.37 1.40e+00 5.10e-01 2.77e+01 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=" C6 A 11021 " pdb=" N1 A 11021 " pdb=" C2 A 11021 " ideal model delta sigma weight residual 118.60 121.38 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" C1' U 11168 " pdb=" N1 U 11168 " pdb=" C2 U 11168 " ideal model delta sigma weight residual 117.70 123.18 -5.48 1.20e+00 6.94e-01 2.08e+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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.460 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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= 0.799 Angle : 0.894 9.586 28897 Z= 0.758 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/Z covalent geometry : bond 0.00867 / 0.80 (19762) covalent geometry : angle 0.89368 / 0.76 (28897) hydrogen bonds : bond 0.26020 / 25.31 ( 738) hydrogen bonds : angle 9.01883 / 11.56 ( 1629) metal coordination : bond 0.15062 / 7.53 ( 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 : 0.461 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: 0.1553 time to fit residues: 54.8600 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 : 0.446 ------------------------------------------------------------------------------- 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: 20.0000 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... B 122 GLN B 146 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.027738 restraints weight = 165116.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.028310 restraints weight = 78726.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.028624 restraints weight = 54872.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028780 restraints weight = 44991.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028789 restraints weight = 41387.765| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19763 Z= 0.185 Angle : 0.649 13.024 28897 Z= 0.370 Chirality : 0.041 0.265 3604 Planarity : 0.006 0.058 1988 Dihedral : 23.899 177.453 8369 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.83 % Allowed : 17.97 % Favored : 79.19 % 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: -1.80 (0.24), residues: 1087 helix: -0.76 (0.21), residues: 499 sheet: -1.60 (0.36), residues: 157 loop : -1.36 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 113 TYR 0.017 0.002 TYR I 90 PHE 0.033 0.003 PHE B 198 TRP 0.014 0.001 TRP B 96 HIS 0.004 0.001 HIS M 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (19762) covalent geometry : angle 0.64850 / 0.37 (28897) hydrogen bonds : bond 0.13889 / 12.98 ( 738) hydrogen bonds : angle 5.32258 / 6.72 ( 1629) metal coordination : bond 0.01403 / 0.70 ( 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 199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.492 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 113 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.7055 (mtm180) REVERT: B 120 GLN cc_start: 0.9347 (tp-100) cc_final: 0.8748 (tp-100) REVERT: C 36 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: C 183 ASP cc_start: 0.8684 (t0) cc_final: 0.8388 (t0) REVERT: G 21 GLU cc_start: 0.8758 (pp20) cc_final: 0.8038 (tp30) REVERT: G 42 ILE cc_start: 0.7299 (mt) cc_final: 0.7076 (tp) REVERT: I 88 MET cc_start: 0.9007 (ttm) cc_final: 0.8748 (ttm) REVERT: J 46 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8471 (mmtp) REVERT: J 91 ASP cc_start: 0.8360 (p0) cc_final: 0.8005 (p0) REVERT: J 92 LEU cc_start: 0.8626 (mp) cc_final: 0.8355 (mt) REVERT: J 97 ASP cc_start: 0.8875 (t70) cc_final: 0.8519 (t0) REVERT: J 99 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8248 (mm110) REVERT: M 20 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.8853 (p) REVERT: M 75 MET cc_start: 0.9160 (ptp) cc_final: 0.8907 (ptp) REVERT: M 81 MET cc_start: 0.9092 (mtp) cc_final: 0.8665 (ttm) REVERT: M 95 LEU cc_start: 0.9426 (mt) cc_final: 0.9087 (mp) REVERT: N 62 ASN cc_start: 0.8710 (m-40) cc_final: 0.8020 (t0) REVERT: N 67 THR cc_start: 0.9055 (p) cc_final: 0.8402 (t) REVERT: N 86 GLU cc_start: 0.9185 (mp0) cc_final: 0.8958 (mp0) REVERT: N 93 ILE cc_start: 0.9502 (mm) cc_final: 0.9281 (mp) REVERT: S 66 MET cc_start: 0.8743 (mtp) cc_final: 0.8482 (mtp) outliers start: 26 outliers final: 8 residues processed: 184 average time/residue: 0.1440 time to fit residues: 40.3522 Evaluate side-chains 143 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 GLN 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 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.038118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.027649 restraints weight = 163788.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.028272 restraints weight = 78687.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028598 restraints weight = 52052.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.028745 restraints weight = 43289.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028830 restraints weight = 39772.070| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19763 Z= 0.186 Angle : 0.598 12.232 28897 Z= 0.341 Chirality : 0.040 0.260 3604 Planarity : 0.005 0.056 1988 Dihedral : 23.657 179.956 8369 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.47 % Allowed : 19.17 % Favored : 76.36 % 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: -1.47 (0.24), residues: 1087 helix: -0.53 (0.22), residues: 506 sheet: -1.17 (0.38), residues: 157 loop : -1.26 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 3 TYR 0.029 0.002 TYR C 42 PHE 0.020 0.002 PHE B 198 TRP 0.024 0.002 TRP G 103 HIS 0.005 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.19 (19762) covalent geometry : angle 0.59768 / 0.34 (28897) hydrogen bonds : bond 0.11772 / 10.73 ( 738) hydrogen bonds : angle 5.02721 / 6.35 ( 1629) metal coordination : bond 0.00506 / 0.25 ( 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 204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.453 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 100 MET cc_start: 0.8795 (ttt) cc_final: 0.8536 (mtp) REVERT: B 120 GLN cc_start: 0.9213 (tp-100) cc_final: 0.8963 (tp-100) REVERT: C 36 ASP cc_start: 0.8705 (m-30) cc_final: 0.7904 (m-30) REVERT: C 183 ASP cc_start: 0.8630 (t0) cc_final: 0.8271 (t0) REVERT: G 113 ASP cc_start: 0.8783 (t0) cc_final: 0.8553 (t0) REVERT: I 46 MET cc_start: 0.9090 (mtt) cc_final: 0.8795 (mtt) REVERT: I 88 MET cc_start: 0.9233 (ttm) cc_final: 0.8752 (mmt) REVERT: I 90 TYR cc_start: 0.8730 (t80) cc_final: 0.8509 (t80) REVERT: I 115 LYS cc_start: 0.9141 (mttt) cc_final: 0.8813 (mttm) REVERT: J 46 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8421 (mmmm) REVERT: J 59 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6356 (tttt) REVERT: J 91 ASP cc_start: 0.8410 (p0) cc_final: 0.8096 (p0) REVERT: J 92 LEU cc_start: 0.8610 (mp) cc_final: 0.8332 (mt) REVERT: J 97 ASP cc_start: 0.8911 (t70) cc_final: 0.8634 (t0) REVERT: J 99 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8350 (mm110) REVERT: M 81 MET cc_start: 0.9149 (mtp) cc_final: 0.8734 (ttm) REVERT: M 103 LYS cc_start: 0.9422 (tttt) cc_final: 0.9103 (tptp) REVERT: N 62 ASN cc_start: 0.8816 (m-40) cc_final: 0.8200 (t0) REVERT: N 67 THR cc_start: 0.9124 (p) cc_final: 0.8494 (t) REVERT: N 86 GLU cc_start: 0.9259 (mp0) cc_final: 0.8943 (mp0) REVERT: S 66 MET cc_start: 0.8941 (mtp) cc_final: 0.8603 (mtt) outliers start: 41 outliers final: 23 residues processed: 190 average time/residue: 0.1378 time to fit residues: 40.1024 Evaluate side-chains 158 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 SER 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 J residue 47 GLU Chi-restraints excluded: chain J residue 59 LYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 20.0000 chunk 146 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.038637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.028078 restraints weight = 161925.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028716 restraints weight = 77345.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.029051 restraints weight = 51136.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.029254 restraints weight = 42317.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.029394 restraints weight = 39089.986| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19763 Z= 0.148 Angle : 0.569 11.896 28897 Z= 0.326 Chirality : 0.038 0.255 3604 Planarity : 0.004 0.055 1988 Dihedral : 23.577 179.072 8369 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.92 % Allowed : 20.70 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.29 (0.24), residues: 1087 helix: -0.35 (0.22), residues: 507 sheet: -1.21 (0.38), residues: 162 loop : -1.14 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 222 TYR 0.021 0.001 TYR C 42 PHE 0.010 0.001 PHE B 126 TRP 0.028 0.002 TRP G 103 HIS 0.005 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (19762) covalent geometry : angle 0.56910 / 0.33 (28897) hydrogen bonds : bond 0.11273 / 10.21 ( 738) hydrogen bonds : angle 4.83973 / 6.08 ( 1629) metal coordination : bond 0.00115 / 0.06 ( 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 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.391 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: C 36 ASP cc_start: 0.8657 (m-30) cc_final: 0.7860 (m-30) REVERT: C 102 ASN cc_start: 0.9126 (m-40) cc_final: 0.8820 (m-40) REVERT: C 103 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8372 (mm) REVERT: C 183 ASP cc_start: 0.8655 (t0) cc_final: 0.8309 (t0) REVERT: G 113 ASP cc_start: 0.8798 (t0) cc_final: 0.8497 (t0) REVERT: I 42 GLU cc_start: 0.8671 (tp30) cc_final: 0.8215 (tp30) REVERT: I 46 MET cc_start: 0.8982 (mtt) cc_final: 0.8004 (mtt) REVERT: I 88 MET cc_start: 0.9148 (ttm) cc_final: 0.8643 (mmt) REVERT: I 115 LYS cc_start: 0.9151 (mttt) cc_final: 0.8808 (mttm) REVERT: J 19 ASP cc_start: 0.9255 (m-30) cc_final: 0.9051 (m-30) REVERT: J 97 ASP cc_start: 0.8941 (t70) cc_final: 0.8678 (t0) REVERT: J 99 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8320 (mm110) REVERT: M 42 ASP cc_start: 0.7536 (m-30) cc_final: 0.7278 (t0) REVERT: M 81 MET cc_start: 0.9129 (mtp) cc_final: 0.8695 (ttm) REVERT: M 95 LEU cc_start: 0.9509 (mm) cc_final: 0.9236 (mp) REVERT: M 103 LYS cc_start: 0.9345 (tttt) cc_final: 0.8950 (tptm) REVERT: N 62 ASN cc_start: 0.8791 (m-40) cc_final: 0.8174 (t0) REVERT: N 67 THR cc_start: 0.9100 (p) cc_final: 0.8487 (t) REVERT: S 49 ILE cc_start: 0.9247 (mp) cc_final: 0.8951 (tp) REVERT: S 66 MET cc_start: 0.8932 (mtp) cc_final: 0.8598 (mtt) outliers start: 36 outliers final: 26 residues processed: 187 average time/residue: 0.1216 time to fit residues: 35.0862 Evaluate side-chains 171 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 114 LEU 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 103 ILE Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 59 LEU 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 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 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: 20.0000 chunk 91 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** N 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.027563 restraints weight = 164346.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.028160 restraints weight = 78243.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.028468 restraints weight = 52276.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.028676 restraints weight = 43538.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.028740 restraints weight = 39167.835| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19763 Z= 0.167 Angle : 0.572 10.612 28897 Z= 0.327 Chirality : 0.039 0.253 3604 Planarity : 0.004 0.052 1988 Dihedral : 23.508 178.702 8369 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.49 % Allowed : 23.97 % Favored : 72.55 % 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: -1.20 (0.24), residues: 1087 helix: -0.25 (0.22), residues: 496 sheet: -1.22 (0.38), residues: 162 loop : -1.11 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 222 TYR 0.021 0.002 TYR C 42 PHE 0.011 0.001 PHE B 184 TRP 0.028 0.002 TRP G 103 HIS 0.011 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 (19762) covalent geometry : angle 0.57199 / 0.33 (28897) hydrogen bonds : bond 0.10903 / 9.88 ( 738) hydrogen bonds : angle 4.83249 / 6.10 ( 1629) metal coordination : bond 0.00166 / 0.08 ( 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 189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.460 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: B 120 GLN cc_start: 0.8602 (tp40) cc_final: 0.8385 (tp-100) REVERT: B 184 PHE cc_start: 0.6697 (m-80) cc_final: 0.6437 (m-80) REVERT: C 36 ASP cc_start: 0.8678 (m-30) cc_final: 0.7917 (m-30) REVERT: C 103 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8383 (mm) REVERT: C 183 ASP cc_start: 0.8660 (t0) cc_final: 0.8326 (t0) REVERT: G 113 ASP cc_start: 0.8721 (t0) cc_final: 0.8446 (t0) REVERT: I 42 GLU cc_start: 0.8694 (tp30) cc_final: 0.8432 (tp30) REVERT: I 46 MET cc_start: 0.9000 (mtt) cc_final: 0.8187 (mtt) REVERT: I 53 GLU cc_start: 0.8900 (pp20) cc_final: 0.8549 (pp20) REVERT: I 88 MET cc_start: 0.9185 (ttm) cc_final: 0.8929 (mmm) REVERT: I 104 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8600 (t) REVERT: I 115 LYS cc_start: 0.9206 (mttt) cc_final: 0.8696 (mmtt) REVERT: J 19 ASP cc_start: 0.9260 (m-30) cc_final: 0.9056 (m-30) REVERT: J 59 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6638 (tttt) REVERT: J 63 ASP cc_start: 0.8100 (t70) cc_final: 0.7654 (t0) REVERT: J 97 ASP cc_start: 0.8858 (t70) cc_final: 0.7687 (p0) REVERT: J 99 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8535 (mp10) REVERT: M 27 LYS cc_start: 0.9587 (tptm) cc_final: 0.9281 (tptt) REVERT: M 42 ASP cc_start: 0.7865 (m-30) cc_final: 0.7625 (t0) REVERT: M 81 MET cc_start: 0.9117 (mtp) cc_final: 0.8723 (ttm) REVERT: M 95 LEU cc_start: 0.9499 (mm) cc_final: 0.9167 (mp) REVERT: M 103 LYS cc_start: 0.9233 (tttt) cc_final: 0.8770 (tptm) REVERT: N 62 ASN cc_start: 0.8806 (m-40) cc_final: 0.8201 (t0) REVERT: N 67 THR cc_start: 0.9097 (p) cc_final: 0.8502 (t) REVERT: N 86 GLU cc_start: 0.9201 (mp0) cc_final: 0.8854 (mp0) REVERT: S 49 ILE cc_start: 0.9227 (mp) cc_final: 0.8940 (tp) REVERT: S 66 MET cc_start: 0.8943 (mtp) cc_final: 0.8656 (mtt) outliers start: 32 outliers final: 24 residues processed: 181 average time/residue: 0.1230 time to fit residues: 34.4064 Evaluate side-chains 169 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 56 GLU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 21 THR 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 59 LEU 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 79 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 15 LEU 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: 6.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.026867 restraints weight = 168812.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.027470 restraints weight = 82551.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.027773 restraints weight = 56267.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027946 restraints weight = 47434.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027946 restraints weight = 43935.259| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19763 Z= 0.319 Angle : 0.662 9.819 28897 Z= 0.375 Chirality : 0.043 0.263 3604 Planarity : 0.005 0.049 1988 Dihedral : 23.538 179.881 8369 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.58 % Allowed : 23.75 % Favored : 71.68 % 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: -1.30 (0.24), residues: 1087 helix: -0.33 (0.22), residues: 501 sheet: -1.12 (0.38), residues: 167 loop : -1.23 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 3 TYR 0.018 0.002 TYR C 42 PHE 0.016 0.002 PHE S 74 TRP 0.022 0.002 TRP B 96 HIS 0.008 0.002 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.32 (19762) covalent geometry : angle 0.66203 / 0.38 (28897) hydrogen bonds : bond 0.10994 / 10.29 ( 738) hydrogen bonds : angle 4.98064 / 6.34 ( 1629) metal coordination : bond 0.00296 / 0.15 ( 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 179 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.318 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 184 PHE cc_start: 0.6869 (m-80) cc_final: 0.6474 (m-80) REVERT: C 36 ASP cc_start: 0.8806 (m-30) cc_final: 0.8017 (m-30) REVERT: C 182 ILE cc_start: 0.9150 (mp) cc_final: 0.8831 (mm) REVERT: C 183 ASP cc_start: 0.8651 (t0) cc_final: 0.8418 (t0) REVERT: G 21 GLU cc_start: 0.8809 (pp20) cc_final: 0.8092 (tp30) REVERT: G 113 ASP cc_start: 0.8822 (t0) cc_final: 0.8613 (t0) REVERT: I 6 TYR cc_start: 0.8331 (m-80) cc_final: 0.7816 (m-10) REVERT: I 42 GLU cc_start: 0.8702 (tp30) cc_final: 0.8468 (tp30) REVERT: I 46 MET cc_start: 0.8992 (mtt) cc_final: 0.8202 (mtt) REVERT: I 53 GLU cc_start: 0.8936 (pp20) cc_final: 0.8653 (pp20) REVERT: I 115 LYS cc_start: 0.9231 (mttt) cc_final: 0.8973 (mmtp) REVERT: J 63 ASP cc_start: 0.8133 (t70) cc_final: 0.7598 (t70) REVERT: J 97 ASP cc_start: 0.8763 (t70) cc_final: 0.7795 (p0) REVERT: J 99 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8426 (mp10) REVERT: M 27 LYS cc_start: 0.9606 (tptm) cc_final: 0.9271 (tptt) REVERT: M 42 ASP cc_start: 0.7579 (m-30) cc_final: 0.7292 (t0) REVERT: M 81 MET cc_start: 0.9119 (mtp) cc_final: 0.8742 (ttm) REVERT: M 103 LYS cc_start: 0.9213 (tttt) cc_final: 0.8791 (tptm) REVERT: N 62 ASN cc_start: 0.8843 (m-40) cc_final: 0.8599 (m-40) REVERT: N 67 THR cc_start: 0.9237 (p) cc_final: 0.8755 (t) REVERT: N 86 GLU cc_start: 0.9197 (mp0) cc_final: 0.8826 (mp0) REVERT: S 49 ILE cc_start: 0.9232 (mp) cc_final: 0.8992 (tp) REVERT: S 66 MET cc_start: 0.8802 (mtp) cc_final: 0.8554 (mtt) outliers start: 42 outliers final: 33 residues processed: 169 average time/residue: 0.1221 time to fit residues: 32.2742 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 : 0.443 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 52 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 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 126 ASP 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 79 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 25 ILE 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 58 ASP Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 15 LEU 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: 5.9990 chunk 55 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.027395 restraints weight = 163624.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.028013 restraints weight = 78072.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.028390 restraints weight = 51940.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028580 restraints weight = 43586.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.028647 restraints weight = 39267.875| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19763 Z= 0.154 Angle : 0.585 12.619 28897 Z= 0.331 Chirality : 0.039 0.258 3604 Planarity : 0.004 0.052 1988 Dihedral : 23.553 178.340 8369 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.03 % Allowed : 23.64 % 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: -1.10 (0.24), residues: 1087 helix: -0.17 (0.22), residues: 499 sheet: -1.02 (0.39), residues: 165 loop : -1.10 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 222 TYR 0.019 0.002 TYR I 90 PHE 0.014 0.001 PHE B 184 TRP 0.015 0.001 TRP G 103 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (19762) covalent geometry : angle 0.58546 / 0.33 (28897) hydrogen bonds : bond 0.10711 / 9.77 ( 738) hydrogen bonds : angle 4.80394 / 6.19 ( 1629) metal coordination : bond 0.00147 / 0.07 ( 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 187 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.274 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 184 PHE cc_start: 0.7057 (m-80) cc_final: 0.6781 (m-80) REVERT: C 36 ASP cc_start: 0.8659 (m-30) cc_final: 0.7891 (m-30) REVERT: C 183 ASP cc_start: 0.8668 (t0) cc_final: 0.8324 (t0) REVERT: G 113 ASP cc_start: 0.8904 (t0) cc_final: 0.8661 (t0) REVERT: I 6 TYR cc_start: 0.8345 (m-80) cc_final: 0.7931 (m-10) REVERT: I 42 GLU cc_start: 0.8625 (tp30) cc_final: 0.8247 (tp30) REVERT: I 46 MET cc_start: 0.9046 (mtt) cc_final: 0.8150 (mtt) REVERT: I 53 GLU cc_start: 0.8932 (pp20) cc_final: 0.8598 (pp20) REVERT: I 88 MET cc_start: 0.9095 (ttm) cc_final: 0.8863 (mmm) REVERT: I 115 LYS cc_start: 0.9187 (mttt) cc_final: 0.8836 (mttm) REVERT: J 63 ASP cc_start: 0.8183 (t70) cc_final: 0.7679 (t70) REVERT: J 97 ASP cc_start: 0.8724 (t70) cc_final: 0.7558 (p0) REVERT: J 99 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8540 (mp10) REVERT: M 27 LYS cc_start: 0.9605 (tptm) cc_final: 0.9101 (mmtt) REVERT: M 42 ASP cc_start: 0.7775 (m-30) cc_final: 0.7477 (t0) REVERT: M 81 MET cc_start: 0.9212 (mtp) cc_final: 0.8937 (ttm) REVERT: M 103 LYS cc_start: 0.9194 (tttt) cc_final: 0.8926 (tptt) REVERT: N 62 ASN cc_start: 0.8815 (m-40) cc_final: 0.8543 (t0) REVERT: N 67 THR cc_start: 0.9204 (p) cc_final: 0.8661 (t) REVERT: N 86 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8863 (mp0) REVERT: S 49 ILE cc_start: 0.9294 (mp) cc_final: 0.8983 (tp) outliers start: 37 outliers final: 29 residues processed: 180 average time/residue: 0.1225 time to fit residues: 33.9402 Evaluate side-chains 166 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 52 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 59 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 51 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: 8.9990 chunk 53 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 105 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.027607 restraints weight = 163277.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.028203 restraints weight = 78338.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.028526 restraints weight = 52102.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.028742 restraints weight = 43763.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.028805 restraints weight = 39661.687| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19763 Z= 0.155 Angle : 0.591 11.975 28897 Z= 0.330 Chirality : 0.038 0.245 3604 Planarity : 0.005 0.051 1988 Dihedral : 23.477 177.802 8369 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.59 % Allowed : 25.60 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.25), residues: 1087 helix: -0.11 (0.22), residues: 500 sheet: -0.91 (0.39), residues: 165 loop : -1.06 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 222 TYR 0.019 0.001 TYR I 90 PHE 0.012 0.001 PHE B 184 TRP 0.015 0.001 TRP G 103 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (19762) covalent geometry : angle 0.59116 / 0.33 (28897) hydrogen bonds : bond 0.10456 / 9.50 ( 738) hydrogen bonds : angle 4.79463 / 6.16 ( 1629) metal coordination : bond 0.00049 / 0.02 ( 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 173 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.390 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: B 184 PHE cc_start: 0.7113 (m-80) cc_final: 0.6738 (m-80) REVERT: C 36 ASP cc_start: 0.8610 (m-30) cc_final: 0.7862 (m-30) REVERT: C 183 ASP cc_start: 0.8675 (t0) cc_final: 0.8336 (t0) REVERT: C 211 MET cc_start: 0.7039 (mmm) cc_final: 0.6698 (mmm) REVERT: G 113 ASP cc_start: 0.8914 (t0) cc_final: 0.8687 (t0) REVERT: I 6 TYR cc_start: 0.8352 (m-80) cc_final: 0.8122 (m-80) REVERT: I 42 GLU cc_start: 0.8657 (tp30) cc_final: 0.8237 (tp30) REVERT: I 46 MET cc_start: 0.9073 (mtt) cc_final: 0.8163 (mtt) REVERT: I 53 GLU cc_start: 0.8943 (pp20) cc_final: 0.8605 (pp20) REVERT: I 88 MET cc_start: 0.9095 (ttm) cc_final: 0.8851 (mmm) REVERT: I 115 LYS cc_start: 0.9176 (mttt) cc_final: 0.8974 (mmtp) REVERT: J 63 ASP cc_start: 0.8166 (t70) cc_final: 0.7647 (t70) REVERT: J 97 ASP cc_start: 0.8723 (t70) cc_final: 0.7527 (p0) REVERT: J 99 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8468 (mp10) REVERT: M 27 LYS cc_start: 0.9595 (tptm) cc_final: 0.9351 (tptt) REVERT: M 42 ASP cc_start: 0.7760 (m-30) cc_final: 0.7446 (t0) REVERT: M 81 MET cc_start: 0.9193 (mtp) cc_final: 0.8915 (ttm) REVERT: M 103 LYS cc_start: 0.9163 (tttt) cc_final: 0.8917 (tptt) REVERT: N 62 ASN cc_start: 0.8833 (m-40) cc_final: 0.8570 (t0) REVERT: N 67 THR cc_start: 0.9192 (p) cc_final: 0.8671 (t) REVERT: S 49 ILE cc_start: 0.9297 (mp) cc_final: 0.8998 (tp) REVERT: S 66 MET cc_start: 0.8656 (mtt) cc_final: 0.8267 (ptp) outliers start: 33 outliers final: 25 residues processed: 164 average time/residue: 0.1340 time to fit residues: 33.8071 Evaluate side-chains 161 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 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 114 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 21 THR 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 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 15 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 60 optimal weight: 0.0870 chunk 44 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.038724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.028057 restraints weight = 163643.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.028704 restraints weight = 76741.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.029059 restraints weight = 50683.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.029296 restraints weight = 42220.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029339 restraints weight = 38406.796| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19763 Z= 0.140 Angle : 0.593 12.770 28897 Z= 0.328 Chirality : 0.038 0.243 3604 Planarity : 0.004 0.047 1988 Dihedral : 23.431 177.295 8369 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.49 % Allowed : 25.93 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.25), residues: 1087 helix: -0.14 (0.22), residues: 499 sheet: -0.79 (0.39), residues: 167 loop : -1.00 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 222 TYR 0.019 0.001 TYR I 90 PHE 0.011 0.001 PHE B 184 TRP 0.020 0.001 TRP G 103 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (19762) covalent geometry : angle 0.59282 / 0.33 (28897) hydrogen bonds : bond 0.10348 / 9.39 ( 738) hydrogen bonds : angle 4.77194 / 6.11 ( 1629) metal coordination : bond 0.00068 / 0.03 ( 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 179 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.490 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: 0.6032 (t0) cc_final: 0.5691 (p0) REVERT: B 184 PHE cc_start: 0.6877 (m-80) cc_final: 0.6448 (m-80) REVERT: B 190 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7911 (m-40) REVERT: B 203 ASN cc_start: 0.5346 (p0) cc_final: 0.4983 (t0) REVERT: C 4 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9214 (mmtt) REVERT: C 36 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: C 102 ASN cc_start: 0.9027 (m-40) cc_final: 0.8767 (m-40) REVERT: C 183 ASP cc_start: 0.8698 (t0) cc_final: 0.8361 (t0) REVERT: C 211 MET cc_start: 0.7057 (mmm) cc_final: 0.6762 (mmm) REVERT: G 113 ASP cc_start: 0.8911 (t0) cc_final: 0.8670 (t0) REVERT: I 42 GLU cc_start: 0.8618 (tp30) cc_final: 0.8187 (tp30) REVERT: I 46 MET cc_start: 0.9051 (mtt) cc_final: 0.8151 (mtt) REVERT: I 50 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8870 (mm-40) REVERT: I 88 MET cc_start: 0.9060 (ttm) cc_final: 0.8806 (mmm) REVERT: I 115 LYS cc_start: 0.9146 (mttt) cc_final: 0.8613 (mmtt) REVERT: J 63 ASP cc_start: 0.8152 (t70) cc_final: 0.7620 (t70) REVERT: J 97 ASP cc_start: 0.8696 (t70) cc_final: 0.7517 (p0) REVERT: M 27 LYS cc_start: 0.9580 (tptm) cc_final: 0.9147 (tptt) REVERT: M 42 ASP cc_start: 0.7858 (m-30) cc_final: 0.7588 (t0) REVERT: M 81 MET cc_start: 0.9192 (mtp) cc_final: 0.8921 (ttm) REVERT: N 62 ASN cc_start: 0.8786 (m-40) cc_final: 0.8524 (t0) REVERT: N 67 THR cc_start: 0.9155 (p) cc_final: 0.8654 (t) REVERT: N 86 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8777 (pt0) REVERT: S 49 ILE cc_start: 0.9276 (mp) cc_final: 0.8986 (tp) REVERT: S 66 MET cc_start: 0.8587 (mtt) cc_final: 0.8113 (ptp) outliers start: 32 outliers final: 27 residues processed: 172 average time/residue: 0.1304 time to fit residues: 34.8057 Evaluate side-chains 169 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 36 ASP 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 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 15 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 143 optimal weight: 0.0370 chunk 125 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.038817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.028129 restraints weight = 163762.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.028792 restraints weight = 76937.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.029151 restraints weight = 50623.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.029366 restraints weight = 42206.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.029506 restraints weight = 38490.699| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.246 19763 Z= 0.203 Angle : 0.764 59.199 28897 Z= 0.449 Chirality : 0.039 0.356 3604 Planarity : 0.005 0.048 1988 Dihedral : 23.431 177.308 8369 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.49 % Allowed : 26.36 % Favored : 70.15 % Cbeta Deviations : 0.10 % 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: -0.98 (0.24), residues: 1087 helix: -0.16 (0.22), residues: 499 sheet: -0.77 (0.40), residues: 167 loop : -1.02 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG I 124 TYR 0.018 0.002 TYR I 90 PHE 0.012 0.001 PHE B 184 TRP 0.018 0.001 TRP G 103 HIS 0.026 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (19762) covalent geometry : angle 0.76367 / 0.45 (28897) hydrogen bonds : bond 0.10348 / 9.38 ( 738) hydrogen bonds : angle 4.78228 / 6.14 ( 1629) metal coordination : bond 0.00081 / 0.04 ( 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 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.451 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 184 PHE cc_start: 0.6860 (m-80) cc_final: 0.6428 (m-80) REVERT: C 4 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.9205 (mmtt) REVERT: C 36 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: C 102 ASN cc_start: 0.9059 (m-40) cc_final: 0.8794 (m-40) REVERT: C 183 ASP cc_start: 0.8711 (t0) cc_final: 0.8356 (t0) REVERT: C 211 MET cc_start: 0.7068 (mmm) cc_final: 0.6773 (mmm) REVERT: G 113 ASP cc_start: 0.8890 (t0) cc_final: 0.8672 (t0) REVERT: I 42 GLU cc_start: 0.8654 (tp30) cc_final: 0.8224 (tp30) REVERT: I 46 MET cc_start: 0.9084 (mtt) cc_final: 0.8221 (mtt) REVERT: I 50 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8855 (mm-40) REVERT: I 88 MET cc_start: 0.9094 (ttm) cc_final: 0.8819 (mmm) REVERT: I 115 LYS cc_start: 0.9139 (mttt) cc_final: 0.8615 (mmtt) REVERT: J 63 ASP cc_start: 0.8136 (t70) cc_final: 0.7611 (t70) REVERT: M 27 LYS cc_start: 0.9581 (tptm) cc_final: 0.9146 (tptt) REVERT: M 42 ASP cc_start: 0.7887 (m-30) cc_final: 0.7613 (t0) REVERT: M 81 MET cc_start: 0.9207 (mtp) cc_final: 0.8935 (ttm) REVERT: N 62 ASN cc_start: 0.8796 (m-40) cc_final: 0.8531 (m-40) REVERT: N 67 THR cc_start: 0.9161 (p) cc_final: 0.8657 (t) REVERT: N 86 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8781 (pt0) REVERT: S 49 ILE cc_start: 0.9293 (mp) cc_final: 0.8988 (tp) REVERT: S 66 MET cc_start: 0.8605 (mtt) cc_final: 0.8109 (ptp) outliers start: 32 outliers final: 27 residues processed: 158 average time/residue: 0.1393 time to fit residues: 33.7458 Evaluate side-chains 159 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 36 ASP 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 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 15 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 20.0000 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: 1.9990 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.038813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.028005 restraints weight = 164896.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028726 restraints weight = 77674.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.029105 restraints weight = 52112.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.029336 restraints weight = 42543.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.029421 restraints weight = 38292.665| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.246 19763 Z= 0.203 Angle : 0.764 59.199 28897 Z= 0.449 Chirality : 0.039 0.356 3604 Planarity : 0.005 0.048 1988 Dihedral : 23.431 177.308 8369 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.16 % Allowed : 26.58 % Favored : 70.26 % Cbeta Deviations : 0.10 % 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: -0.98 (0.24), residues: 1087 helix: -0.16 (0.22), residues: 499 sheet: -0.77 (0.40), residues: 167 loop : -1.02 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG I 124 TYR 0.018 0.002 TYR I 90 PHE 0.012 0.001 PHE B 184 TRP 0.018 0.001 TRP G 103 HIS 0.026 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (19762) covalent geometry : angle 0.76368 / 0.45 (28897) hydrogen bonds : bond 0.10348 / 9.38 ( 738) hydrogen bonds : angle 4.78228 / 6.14 ( 1629) metal coordination : bond 0.00081 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.26 seconds wall clock time: 56 minutes 38.23 seconds (3398.23 seconds total)