Starting phenix.real_space_refine on Sat Sep 12 21:52:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afh_11765/09_2026/7afh_11765_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afh_11765/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7afh_11765/09_2026/7afh_11765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afh_11765/09_2026/7afh_11765.map" model { file = "/net/cci-nas-00/data/ceres_data/7afh_11765/09_2026/7afh_11765_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afh_11765/09_2026/7afh_11765_neut.cif" } 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-2.2.1-6174/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: 3.96, per 1000 atoms: 0.21 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: 1.73 Conformation dependent library (CDL) restraints added in 541.6 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: 3.20 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: 4.47 Time building geometry restraints manager: 2.30 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: 26694 1.92 - 3.83: 2068 3.83 - 5.75: 107 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=" O5' C 11320 " pdb=" C5' C 11320 " pdb=" C4' C 11320 " ideal model delta sigma weight residual 109.40 113.22 -3.82 8.00e-01 1.56e+00 2.28e+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 ... (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: 2656 0.066 - 0.131: 789 0.131 - 0.197: 140 0.197 - 0.263: 16 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: 5.330 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 23.120 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- 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= 0.836 Angle : 1.012 9.586 28897 Z= 0.834 Chirality : 0.064 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 0.00887 / 0.83 (19762) covalent geometry : angle 1.01227 / 0.83 (28897) hydrogen bonds : bond 0.26020 / 27.94 ( 738) hydrogen bonds : angle 9.01883 / 11.84 ( 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 : 0.512 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 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: 0.8406 (t0) REVERT: J 46 LYS cc_start: 0.8842 (mptt) cc_final: 0.8552 (mmmm) REVERT: J 91 ASP cc_start: 0.8061 (p0) cc_final: 0.7779 (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: 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: 0.1599 time to fit residues: 56.6703 Evaluate side-chains 136 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 2.9990 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: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN B 146 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** 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 = 0.3072 r_free = 0.3072 target = 0.038104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.027713 restraints weight = 165054.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.028282 restraints weight = 79861.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028602 restraints weight = 53510.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.028747 restraints weight = 44859.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.028817 restraints weight = 41422.548| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19763 Z= 0.182 Angle : 0.697 13.190 28897 Z= 0.382 Chirality : 0.044 0.306 3604 Planarity : 0.006 0.065 1988 Dihedral : 23.767 177.755 8369 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.16 % Allowed : 17.43 % Favored : 79.41 % 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: -1.82 (0.24), residues: 1087 helix: -0.77 (0.21), residues: 500 sheet: -1.57 (0.37), residues: 157 loop : -1.39 (0.29), residues: 430 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 0.031 0.002 PHE B 198 TRP 0.014 0.001 TRP B 96 HIS 0.010 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (19762) covalent geometry : angle 0.69681 / 0.38 (28897) hydrogen bonds : bond 0.13958 / 14.38 ( 738) hydrogen bonds : angle 5.32409 / 6.97 ( 1629) metal coordination : bond 0.01212 / 0.61 ( 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 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.441 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: C 36 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: C 183 ASP cc_start: 0.8709 (t0) cc_final: 0.8397 (t0) REVERT: G 21 GLU cc_start: 0.8779 (pp20) cc_final: 0.8052 (tp30) REVERT: I 88 MET cc_start: 0.9025 (ttm) cc_final: 0.8788 (ttm) REVERT: J 91 ASP cc_start: 0.8354 (p0) cc_final: 0.8000 (p0) REVERT: J 92 LEU cc_start: 0.8628 (mp) cc_final: 0.8355 (mt) REVERT: J 97 ASP cc_start: 0.8887 (t70) cc_final: 0.8530 (t0) REVERT: J 99 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8263 (mm110) REVERT: M 20 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.8873 (p) REVERT: M 75 MET cc_start: 0.9149 (ptp) cc_final: 0.8939 (ptp) REVERT: M 81 MET cc_start: 0.9107 (mtp) cc_final: 0.8675 (ttm) REVERT: M 95 LEU cc_start: 0.9426 (mt) cc_final: 0.9081 (mp) REVERT: N 62 ASN cc_start: 0.8727 (m-40) cc_final: 0.8036 (t0) REVERT: N 86 GLU cc_start: 0.9185 (mp0) cc_final: 0.8899 (mp0) REVERT: N 93 ILE cc_start: 0.9507 (mm) cc_final: 0.9282 (mp) REVERT: S 66 MET cc_start: 0.8714 (mtp) cc_final: 0.8457 (mtp) outliers start: 29 outliers final: 12 residues processed: 189 average time/residue: 0.1331 time to fit residues: 38.4716 Evaluate side-chains 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 G residue 80 VAL 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 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 15 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: 0.9980 chunk 39 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 76 optimal weight: 0.0170 chunk 141 optimal weight: 8.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.027842 restraints weight = 162228.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.028519 restraints weight = 76755.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.028810 restraints weight = 51078.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028973 restraints weight = 42095.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.029085 restraints weight = 38825.202| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19763 Z= 0.168 Angle : 0.616 12.265 28897 Z= 0.341 Chirality : 0.041 0.298 3604 Planarity : 0.005 0.054 1988 Dihedral : 23.517 179.506 8369 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.14 % Allowed : 19.17 % Favored : 76.69 % 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: -1.41 (0.24), residues: 1087 helix: -0.44 (0.22), residues: 506 sheet: -1.17 (0.39), residues: 157 loop : -1.27 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 45 TYR 0.029 0.002 TYR C 42 PHE 0.019 0.002 PHE B 198 TRP 0.021 0.002 TRP G 103 HIS 0.010 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 (19762) covalent geometry : angle 0.61555 / 0.34 (28897) hydrogen bonds : bond 0.11950 / 12.06 ( 738) hydrogen bonds : angle 5.01678 / 6.59 ( 1629) metal coordination : bond 0.00498 / 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 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.8781 (ttt) cc_final: 0.8468 (mtt) REVERT: B 120 GLN cc_start: 0.9061 (tt0) cc_final: 0.8853 (tt0) REVERT: C 36 ASP cc_start: 0.8698 (m-30) cc_final: 0.7895 (m-30) REVERT: C 183 ASP cc_start: 0.8627 (t0) cc_final: 0.8286 (t0) REVERT: G 113 ASP cc_start: 0.8694 (t0) cc_final: 0.8445 (t0) REVERT: I 42 GLU cc_start: 0.8739 (tp30) cc_final: 0.8141 (tp30) REVERT: I 46 MET cc_start: 0.9080 (mtt) cc_final: 0.8034 (mtt) REVERT: I 88 MET cc_start: 0.9202 (ttm) cc_final: 0.8662 (mmt) REVERT: I 90 TYR cc_start: 0.8722 (t80) cc_final: 0.8510 (t80) REVERT: J 91 ASP cc_start: 0.8409 (p0) cc_final: 0.8096 (p0) REVERT: J 92 LEU cc_start: 0.8606 (mp) cc_final: 0.8330 (mt) REVERT: J 97 ASP cc_start: 0.8914 (t70) cc_final: 0.8629 (t0) REVERT: J 99 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8347 (mm110) REVERT: M 81 MET cc_start: 0.9148 (mtp) cc_final: 0.8737 (ttm) REVERT: M 103 LYS cc_start: 0.9381 (tptt) cc_final: 0.9055 (tptp) REVERT: N 62 ASN cc_start: 0.8837 (m-40) cc_final: 0.8212 (t0) REVERT: N 86 GLU cc_start: 0.9256 (mp0) cc_final: 0.8910 (mp0) REVERT: N 93 ILE cc_start: 0.9546 (mm) cc_final: 0.9345 (mp) REVERT: S 66 MET cc_start: 0.8933 (mtp) cc_final: 0.8639 (mtt) outliers start: 38 outliers final: 22 residues processed: 190 average time/residue: 0.1324 time to fit residues: 39.1252 Evaluate side-chains 156 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 113 ARG 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 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 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 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: 30.0000 chunk 146 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 HIS 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 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.038629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.027827 restraints weight = 163851.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.028335 restraints weight = 77329.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.028643 restraints weight = 50927.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.028794 restraints weight = 42850.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.028917 restraints weight = 39557.020| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19763 Z= 0.143 Angle : 0.589 11.691 28897 Z= 0.329 Chirality : 0.039 0.290 3604 Planarity : 0.005 0.053 1988 Dihedral : 23.416 179.054 8369 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.92 % Allowed : 20.92 % Favored : 75.16 % 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: -1.22 (0.24), residues: 1087 helix: -0.29 (0.22), residues: 508 sheet: -1.16 (0.38), residues: 162 loop : -1.12 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 45 TYR 0.023 0.002 TYR C 42 PHE 0.022 0.002 PHE B 69 TRP 0.029 0.002 TRP G 103 HIS 0.012 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (19762) covalent geometry : angle 0.58913 / 0.33 (28897) hydrogen bonds : bond 0.11269 / 11.32 ( 738) hydrogen bonds : angle 4.81647 / 6.29 ( 1629) metal coordination : bond 0.00910 / 0.46 ( 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 198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.449 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: C 36 ASP cc_start: 0.8634 (m-30) cc_final: 0.7852 (m-30) REVERT: C 102 ASN cc_start: 0.9118 (m-40) cc_final: 0.8820 (m-40) REVERT: C 103 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8382 (mm) REVERT: C 183 ASP cc_start: 0.8676 (t0) cc_final: 0.8333 (t0) REVERT: G 113 ASP cc_start: 0.8707 (t0) cc_final: 0.8397 (t0) REVERT: I 42 GLU cc_start: 0.8695 (tp30) cc_final: 0.8252 (tp30) REVERT: I 46 MET cc_start: 0.8981 (mtt) cc_final: 0.7980 (mtt) REVERT: I 88 MET cc_start: 0.9128 (ttm) cc_final: 0.8663 (mmt) REVERT: I 104 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8567 (t) REVERT: I 124 ARG cc_start: 0.9029 (ttm110) cc_final: 0.8733 (ttm110) REVERT: J 19 ASP cc_start: 0.9248 (m-30) cc_final: 0.9047 (m-30) REVERT: J 97 ASP cc_start: 0.8942 (t70) cc_final: 0.8668 (t0) REVERT: J 99 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8277 (mm110) REVERT: M 27 LYS cc_start: 0.9580 (tptm) cc_final: 0.9288 (tptt) REVERT: M 42 ASP cc_start: 0.7724 (m-30) cc_final: 0.7483 (t0) REVERT: M 81 MET cc_start: 0.9113 (mtp) cc_final: 0.8707 (ttm) REVERT: M 95 LEU cc_start: 0.9489 (mm) cc_final: 0.9253 (mp) REVERT: M 103 LYS cc_start: 0.9256 (tttt) cc_final: 0.8917 (tptm) REVERT: N 62 ASN cc_start: 0.8804 (m-40) cc_final: 0.8212 (t0) REVERT: N 89 MET cc_start: 0.8979 (mmm) cc_final: 0.8697 (mmm) REVERT: S 49 ILE cc_start: 0.9241 (mp) cc_final: 0.8955 (tp) REVERT: S 66 MET cc_start: 0.8931 (mtp) cc_final: 0.8620 (mtt) outliers start: 36 outliers final: 25 residues processed: 189 average time/residue: 0.1372 time to fit residues: 39.9645 Evaluate side-chains 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 113 ARG 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 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 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 104 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: 9.9990 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027988 restraints weight = 161747.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.028614 restraints weight = 77700.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.028921 restraints weight = 51793.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.029057 restraints weight = 43081.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.029151 restraints weight = 39289.899| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3251 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= 0.171 Angle : 0.585 10.464 28897 Z= 0.326 Chirality : 0.039 0.290 3604 Planarity : 0.005 0.053 1988 Dihedral : 23.363 178.949 8369 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.70 % Allowed : 22.55 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.24), residues: 1087 helix: -0.18 (0.22), residues: 503 sheet: -1.09 (0.38), residues: 167 loop : -1.14 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 222 TYR 0.020 0.002 TYR C 42 PHE 0.011 0.001 PHE S 10 TRP 0.033 0.002 TRP G 103 HIS 0.009 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.17 (19762) covalent geometry : angle 0.58466 / 0.33 (28897) hydrogen bonds : bond 0.10941 / 11.03 ( 738) hydrogen bonds : angle 4.77600 / 6.22 ( 1629) metal coordination : bond 0.00069 / 0.03 ( 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 190 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.5830 (t0) cc_final: 0.5555 (p0) REVERT: B 100 MET cc_start: 0.8849 (ttt) cc_final: 0.8648 (mtt) REVERT: C 36 ASP cc_start: 0.8721 (m-30) cc_final: 0.7944 (m-30) REVERT: C 103 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8392 (mm) REVERT: C 183 ASP cc_start: 0.8667 (t0) cc_final: 0.8343 (t0) REVERT: G 113 ASP cc_start: 0.8755 (t0) cc_final: 0.8466 (t0) REVERT: I 42 GLU cc_start: 0.8701 (tp30) cc_final: 0.8385 (tp30) REVERT: I 46 MET cc_start: 0.9003 (mtt) cc_final: 0.8164 (mtt) REVERT: I 53 GLU cc_start: 0.8904 (pp20) cc_final: 0.8666 (pp20) REVERT: I 88 MET cc_start: 0.9157 (ttm) cc_final: 0.8908 (mmm) REVERT: I 115 LYS cc_start: 0.9151 (mttt) cc_final: 0.8895 (mmtp) REVERT: I 124 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8756 (ttm110) REVERT: J 19 ASP cc_start: 0.9266 (m-30) cc_final: 0.9049 (m-30) REVERT: J 63 ASP cc_start: 0.7984 (t70) cc_final: 0.7553 (t0) REVERT: J 97 ASP cc_start: 0.8861 (t70) cc_final: 0.7704 (p0) REVERT: J 99 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8542 (mp10) REVERT: M 27 LYS cc_start: 0.9589 (tptm) cc_final: 0.9303 (tptt) REVERT: M 42 ASP cc_start: 0.7751 (m-30) cc_final: 0.7503 (t0) REVERT: M 81 MET cc_start: 0.9139 (mtp) cc_final: 0.8722 (ttm) REVERT: M 95 LEU cc_start: 0.9504 (mm) cc_final: 0.9193 (mp) REVERT: M 103 LYS cc_start: 0.9201 (tttt) cc_final: 0.8841 (tptm) REVERT: N 62 ASN cc_start: 0.8823 (m-40) cc_final: 0.8206 (t0) REVERT: N 86 GLU cc_start: 0.9247 (mp0) cc_final: 0.8939 (mp0) REVERT: S 49 ILE cc_start: 0.9225 (mp) cc_final: 0.8939 (tp) REVERT: S 66 MET cc_start: 0.8945 (mtp) cc_final: 0.8667 (mtt) outliers start: 34 outliers final: 28 residues processed: 183 average time/residue: 0.1282 time to fit residues: 36.9935 Evaluate side-chains 173 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 113 ARG 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 103 ILE Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 195 VAL 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 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 105 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 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 92 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 6.5790 ------------------------------------------------------------------------------- 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 = 0.3019 r_free = 0.3019 target = 0.037075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.026661 restraints weight = 166645.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.027286 restraints weight = 81873.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.027585 restraints weight = 55798.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.027758 restraints weight = 47108.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.027831 restraints weight = 42824.714| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19763 Z= 0.331 Angle : 0.734 9.589 28897 Z= 0.395 Chirality : 0.048 0.311 3604 Planarity : 0.006 0.053 1988 Dihedral : 23.451 179.466 8369 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.34 % Allowed : 23.86 % 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: -1.36 (0.24), residues: 1087 helix: -0.41 (0.22), residues: 513 sheet: -1.12 (0.38), residues: 165 loop : -1.24 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 3 TYR 0.020 0.002 TYR C 42 PHE 0.021 0.002 PHE B 198 TRP 0.041 0.003 TRP G 103 HIS 0.011 0.002 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.33 (19762) covalent geometry : angle 0.73422 / 0.40 (28897) hydrogen bonds : bond 0.11299 / 11.77 ( 738) hydrogen bonds : angle 5.04973 / 6.67 ( 1629) metal coordination : bond 0.00251 / 0.13 ( 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 185 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.5908 (t0) cc_final: 0.5561 (p0) REVERT: B 100 MET cc_start: 0.8739 (ttt) cc_final: 0.8528 (mtt) REVERT: B 120 GLN cc_start: 0.8966 (tt0) cc_final: 0.8514 (tp-100) REVERT: B 184 PHE cc_start: 0.6738 (m-80) cc_final: 0.6512 (m-80) REVERT: C 36 ASP cc_start: 0.8775 (m-30) cc_final: 0.8015 (m-30) REVERT: C 183 ASP cc_start: 0.8665 (t0) cc_final: 0.8421 (t0) REVERT: G 21 GLU cc_start: 0.8835 (pp20) cc_final: 0.8076 (tp30) REVERT: G 42 ILE cc_start: 0.7579 (tp) cc_final: 0.7363 (tp) REVERT: G 113 ASP cc_start: 0.8861 (t0) cc_final: 0.8640 (t0) REVERT: G 116 MET cc_start: 0.7686 (ttp) cc_final: 0.7209 (ttp) REVERT: I 6 TYR cc_start: 0.8324 (m-80) cc_final: 0.7883 (m-10) REVERT: I 42 GLU cc_start: 0.8725 (tp30) cc_final: 0.8489 (tp30) REVERT: I 46 MET cc_start: 0.9023 (mtt) cc_final: 0.8216 (mtt) REVERT: I 124 ARG cc_start: 0.9163 (ttm110) cc_final: 0.8903 (ttm110) REVERT: J 11 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8966 (mppt) REVERT: J 63 ASP cc_start: 0.8147 (t70) cc_final: 0.7590 (t70) REVERT: J 97 ASP cc_start: 0.8697 (t70) cc_final: 0.7543 (t0) REVERT: J 99 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8061 (mm110) REVERT: M 27 LYS cc_start: 0.9613 (tptm) cc_final: 0.9361 (tptt) REVERT: M 42 ASP cc_start: 0.7560 (m-30) cc_final: 0.7241 (t0) REVERT: M 81 MET cc_start: 0.9141 (mtp) cc_final: 0.8840 (mtt) REVERT: M 103 LYS cc_start: 0.9154 (tttt) cc_final: 0.8786 (tptm) REVERT: N 62 ASN cc_start: 0.8854 (m-40) cc_final: 0.8650 (m-40) REVERT: N 86 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8866 (mp0) REVERT: S 49 ILE cc_start: 0.9244 (mp) cc_final: 0.8984 (tp) REVERT: S 66 MET cc_start: 0.8809 (mtp) cc_final: 0.8606 (mtt) outliers start: 49 outliers final: 34 residues processed: 173 average time/residue: 0.1298 time to fit residues: 35.2417 Evaluate side-chains 166 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 113 ARG 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 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 115 SER 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 11 LYS Chi-restraints excluded: chain J residue 25 ILE 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 73 ILE 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 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: 9.9990 chunk 88 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 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 = 0.3071 r_free = 0.3071 target = 0.038209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.027538 restraints weight = 164994.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.028154 restraints weight = 77931.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.028493 restraints weight = 51568.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.028695 restraints weight = 43253.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.028818 restraints weight = 39491.973| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19763 Z= 0.138 Angle : 0.611 13.225 28897 Z= 0.336 Chirality : 0.039 0.297 3604 Planarity : 0.005 0.055 1988 Dihedral : 23.459 178.586 8369 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.27 % Allowed : 25.49 % Favored : 71.24 % 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: -1.04 (0.25), residues: 1087 helix: -0.13 (0.22), residues: 505 sheet: -0.98 (0.39), residues: 165 loop : -1.08 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 222 TYR 0.017 0.002 TYR C 42 PHE 0.020 0.001 PHE B 198 TRP 0.048 0.002 TRP G 103 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (19762) covalent geometry : angle 0.61090 / 0.34 (28897) hydrogen bonds : bond 0.10982 / 11.14 ( 738) hydrogen bonds : angle 4.76032 / 6.33 ( 1629) metal coordination : bond 0.00017 / 0.01 ( 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 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.5780 (t0) cc_final: 0.5492 (p0) REVERT: B 100 MET cc_start: 0.8840 (ttt) cc_final: 0.8605 (mtt) REVERT: B 184 PHE cc_start: 0.6947 (m-80) cc_final: 0.6635 (m-80) REVERT: B 203 ASN cc_start: 0.5329 (p0) cc_final: 0.4945 (t0) REVERT: C 36 ASP cc_start: 0.8635 (m-30) cc_final: 0.7874 (m-30) REVERT: C 183 ASP cc_start: 0.8687 (t0) cc_final: 0.8324 (t0) REVERT: G 113 ASP cc_start: 0.8924 (t0) cc_final: 0.8680 (t0) REVERT: I 6 TYR cc_start: 0.8294 (m-80) cc_final: 0.8047 (m-80) REVERT: I 42 GLU cc_start: 0.8612 (tp30) cc_final: 0.8201 (tp30) REVERT: I 46 MET cc_start: 0.9051 (mtt) cc_final: 0.8118 (mtt) REVERT: I 115 LYS cc_start: 0.9201 (mttt) cc_final: 0.8951 (mmtp) REVERT: I 124 ARG cc_start: 0.9078 (ttm110) cc_final: 0.8780 (ttm110) REVERT: J 63 ASP cc_start: 0.8198 (t70) cc_final: 0.7704 (t70) REVERT: J 88 MET cc_start: 0.9083 (mpp) cc_final: 0.8787 (pmm) REVERT: J 97 ASP cc_start: 0.8700 (t70) cc_final: 0.7601 (p0) REVERT: J 99 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8416 (mp10) REVERT: M 27 LYS cc_start: 0.9605 (tptm) cc_final: 0.9146 (tptt) REVERT: M 42 ASP cc_start: 0.7761 (m-30) cc_final: 0.7466 (t0) REVERT: M 81 MET cc_start: 0.9212 (mtp) cc_final: 0.8927 (ttm) REVERT: N 62 ASN cc_start: 0.8808 (m-40) cc_final: 0.8551 (m-40) REVERT: N 86 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8975 (mt-10) REVERT: S 49 ILE cc_start: 0.9279 (mp) cc_final: 0.8962 (tp) outliers start: 30 outliers final: 26 residues processed: 180 average time/residue: 0.1286 time to fit residues: 35.9527 Evaluate side-chains 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 113 ARG 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 52 VAL Chi-restraints excluded: chain C residue 56 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 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain M residue 47 GLU 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: 10.0000 chunk 53 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.037434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.027146 restraints weight = 165449.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.027734 restraints weight = 81516.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.028047 restraints weight = 58193.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.028201 restraints weight = 46778.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.028288 restraints weight = 42957.542| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19763 Z= 0.266 Angle : 0.675 11.926 28897 Z= 0.365 Chirality : 0.044 0.296 3604 Planarity : 0.005 0.068 1988 Dihedral : 23.387 179.235 8369 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.25 % Allowed : 26.58 % Favored : 69.17 % 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: -1.16 (0.24), residues: 1087 helix: -0.25 (0.22), residues: 512 sheet: -0.94 (0.39), residues: 165 loop : -1.18 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 132 TYR 0.018 0.002 TYR I 90 PHE 0.016 0.002 PHE B 198 TRP 0.039 0.002 TRP G 103 HIS 0.008 0.002 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.27 (19762) covalent geometry : angle 0.67535 / 0.37 (28897) hydrogen bonds : bond 0.10704 / 11.01 ( 738) hydrogen bonds : angle 4.92938 / 6.57 ( 1629) metal coordination : bond 0.00159 / 0.08 ( 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 176 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.5827 (t0) cc_final: 0.5528 (p0) REVERT: B 120 GLN cc_start: 0.9015 (tt0) cc_final: 0.8556 (tp-100) REVERT: B 184 PHE cc_start: 0.7096 (m-80) cc_final: 0.6769 (m-80) REVERT: C 36 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: C 142 MET cc_start: 0.8877 (mmp) cc_final: 0.8662 (mmm) REVERT: C 183 ASP cc_start: 0.8618 (t0) cc_final: 0.8354 (t0) REVERT: G 113 ASP cc_start: 0.8863 (t0) cc_final: 0.8596 (t0) REVERT: I 6 TYR cc_start: 0.8239 (m-80) cc_final: 0.8017 (m-80) REVERT: I 42 GLU cc_start: 0.8709 (tp30) cc_final: 0.8336 (tp30) REVERT: I 46 MET cc_start: 0.9020 (mtt) cc_final: 0.8157 (mtt) REVERT: I 88 MET cc_start: 0.8767 (mmm) cc_final: 0.8540 (mmm) REVERT: I 115 LYS cc_start: 0.9231 (mttt) cc_final: 0.8983 (mmtp) REVERT: I 124 ARG cc_start: 0.9146 (ttm110) cc_final: 0.8881 (ttm110) REVERT: I 129 LYS cc_start: 0.8683 (mmtm) cc_final: 0.7816 (mppt) REVERT: J 63 ASP cc_start: 0.8260 (t70) cc_final: 0.7703 (t70) REVERT: J 97 ASP cc_start: 0.8661 (t70) cc_final: 0.7734 (p0) REVERT: M 27 LYS cc_start: 0.9591 (tptm) cc_final: 0.9116 (tptt) REVERT: M 42 ASP cc_start: 0.7593 (m-30) cc_final: 0.7288 (t0) REVERT: M 81 MET cc_start: 0.9142 (mtp) cc_final: 0.8816 (mtt) REVERT: N 86 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8775 (mp0) outliers start: 39 outliers final: 34 residues processed: 165 average time/residue: 0.1306 time to fit residues: 33.9960 Evaluate side-chains 162 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 70 VAL Chi-restraints excluded: chain B residue 113 ARG 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 5 VAL Chi-restraints excluded: chain C residue 19 ASN 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 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 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 53 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain 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 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: 0.9990 chunk 37 optimal weight: 20.0000 chunk 60 optimal weight: 0.2980 chunk 44 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 = 0.3059 r_free = 0.3059 target = 0.038077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.027393 restraints weight = 164406.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.027992 restraints weight = 78351.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.028366 restraints weight = 53291.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028514 restraints weight = 43543.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.028645 restraints weight = 40119.885| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19763 Z= 0.156 Angle : 0.628 12.775 28897 Z= 0.343 Chirality : 0.040 0.286 3604 Planarity : 0.005 0.057 1988 Dihedral : 23.402 178.426 8369 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.14 % Allowed : 27.23 % Favored : 68.63 % 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: -1.05 (0.25), residues: 1087 helix: -0.23 (0.22), residues: 505 sheet: -0.72 (0.40), residues: 165 loop : -1.09 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 137 TYR 0.016 0.001 TYR I 90 PHE 0.020 0.001 PHE B 198 TRP 0.051 0.003 TRP G 103 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (19762) covalent geometry : angle 0.62774 / 0.34 (28897) hydrogen bonds : bond 0.10553 / 10.74 ( 738) hydrogen bonds : angle 4.82004 / 6.43 ( 1629) metal coordination : bond 0.00030 / 0.01 ( 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 171 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.463 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: B 184 PHE cc_start: 0.6960 (m-80) cc_final: 0.6602 (m-80) REVERT: C 36 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: C 102 ASN cc_start: 0.9017 (m-40) cc_final: 0.8766 (m-40) REVERT: C 183 ASP cc_start: 0.8662 (t0) cc_final: 0.8290 (t0) REVERT: G 113 ASP cc_start: 0.8959 (t0) cc_final: 0.8754 (t0) REVERT: I 6 TYR cc_start: 0.8374 (m-80) cc_final: 0.7952 (m-80) REVERT: I 42 GLU cc_start: 0.8683 (tp30) cc_final: 0.8261 (tp30) REVERT: I 46 MET cc_start: 0.9097 (mtt) cc_final: 0.8186 (mtt) REVERT: I 115 LYS cc_start: 0.9202 (mttt) cc_final: 0.8964 (mmtp) REVERT: I 124 ARG cc_start: 0.9091 (ttm110) cc_final: 0.8791 (ttm110) REVERT: J 63 ASP cc_start: 0.8221 (t70) cc_final: 0.7663 (t70) REVERT: J 74 VAL cc_start: 0.9564 (OUTLIER) cc_final: 0.9273 (m) REVERT: M 27 LYS cc_start: 0.9598 (tptm) cc_final: 0.9107 (mmtt) REVERT: M 42 ASP cc_start: 0.7861 (m-30) cc_final: 0.7545 (t0) REVERT: M 81 MET cc_start: 0.9214 (mtp) cc_final: 0.8929 (ttm) REVERT: M 103 LYS cc_start: 0.9311 (tptt) cc_final: 0.8958 (tptm) REVERT: N 86 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8935 (mt-10) REVERT: S 49 ILE cc_start: 0.9420 (mm) cc_final: 0.9023 (tp) REVERT: S 66 MET cc_start: 0.8363 (mpp) cc_final: 0.8040 (ptp) outliers start: 38 outliers final: 31 residues processed: 163 average time/residue: 0.1359 time to fit residues: 34.6100 Evaluate side-chains 163 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 113 ARG 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 5 VAL Chi-restraints excluded: chain C residue 19 ASN 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 62 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 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 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.037829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.027589 restraints weight = 163230.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.028167 restraints weight = 81029.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.028503 restraints weight = 59342.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.028697 restraints weight = 46663.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.028822 restraints weight = 42161.995| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19763 Z= 0.216 Angle : 0.657 13.563 28897 Z= 0.357 Chirality : 0.042 0.281 3604 Planarity : 0.005 0.070 1988 Dihedral : 23.370 178.696 8369 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.92 % Allowed : 28.00 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1087 helix: -0.30 (0.22), residues: 512 sheet: -0.64 (0.40), residues: 164 loop : -1.20 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 137 TYR 0.017 0.002 TYR I 90 PHE 0.018 0.002 PHE B 198 TRP 0.056 0.003 TRP G 103 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.22 (19762) covalent geometry : angle 0.65726 / 0.36 (28897) hydrogen bonds : bond 0.10412 / 10.65 ( 738) hydrogen bonds : angle 4.89509 / 6.52 ( 1629) metal coordination : bond 0.00105 / 0.05 ( 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 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 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: B 184 PHE cc_start: 0.6836 (m-80) cc_final: 0.6411 (m-80) REVERT: C 36 ASP cc_start: 0.8629 (m-30) cc_final: 0.7909 (m-30) REVERT: C 183 ASP cc_start: 0.8632 (t0) cc_final: 0.8296 (t0) REVERT: G 113 ASP cc_start: 0.9028 (t0) cc_final: 0.8825 (t0) REVERT: I 42 GLU cc_start: 0.8691 (tp30) cc_final: 0.8263 (tp30) REVERT: I 46 MET cc_start: 0.9006 (mtt) cc_final: 0.8035 (mtt) REVERT: I 88 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8444 (mmm) REVERT: I 115 LYS cc_start: 0.9205 (mttt) cc_final: 0.8974 (mmtp) REVERT: I 124 ARG cc_start: 0.9115 (ttm110) cc_final: 0.8834 (ttm110) REVERT: J 63 ASP cc_start: 0.8221 (t70) cc_final: 0.7679 (t70) REVERT: J 74 VAL cc_start: 0.9567 (OUTLIER) cc_final: 0.9270 (m) REVERT: M 27 LYS cc_start: 0.9590 (tptm) cc_final: 0.9103 (tptt) REVERT: M 42 ASP cc_start: 0.7716 (m-30) cc_final: 0.7409 (t0) REVERT: M 81 MET cc_start: 0.9177 (mtp) cc_final: 0.8842 (mtt) REVERT: S 49 ILE cc_start: 0.9372 (mm) cc_final: 0.9000 (tp) outliers start: 36 outliers final: 30 residues processed: 157 average time/residue: 0.1316 time to fit residues: 32.6408 Evaluate side-chains 157 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 113 ARG 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 5 VAL Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 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 I residue 88 MET Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 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 = 0.3006 r_free = 0.3006 target = 0.036688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.026159 restraints weight = 171399.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.026745 restraints weight = 84798.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.027069 restraints weight = 57651.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.027253 restraints weight = 48738.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.027325 restraints weight = 44022.280| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19763 Z= 0.355 Angle : 0.785 13.608 28897 Z= 0.418 Chirality : 0.049 0.290 3604 Planarity : 0.006 0.071 1988 Dihedral : 23.492 179.693 8369 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 28.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.25 % Allowed : 27.12 % Favored : 68.63 % 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: -1.43 (0.24), residues: 1087 helix: -0.52 (0.21), residues: 512 sheet: -0.72 (0.39), residues: 164 loop : -1.41 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 3 TYR 0.016 0.002 TYR C 42 PHE 0.019 0.002 PHE B 198 TRP 0.046 0.003 TRP G 103 HIS 0.009 0.002 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.36 (19762) covalent geometry : angle 0.78498 / 0.42 (28897) hydrogen bonds : bond 0.11103 / 11.58 ( 738) hydrogen bonds : angle 5.11507 / 6.82 ( 1629) metal coordination : bond 0.00106 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3267.24 seconds wall clock time: 57 minutes 40.95 seconds (3460.95 seconds total)