Starting phenix.real_space_refine on Wed Mar 4 03:26:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b6x_12057/03_2026/7b6x_12057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b6x_12057/03_2026/7b6x_12057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b6x_12057/03_2026/7b6x_12057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b6x_12057/03_2026/7b6x_12057.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b6x_12057/03_2026/7b6x_12057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b6x_12057/03_2026/7b6x_12057.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6713 2.51 5 N 1749 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10470 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "C" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1204 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1741 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "E" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1177 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "F" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1333 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1363 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1089 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Time building chain proxies: 2.49, per 1000 atoms: 0.24 Number of scatterers: 10470 At special positions: 0 Unit cell: (172.127, 148.255, 74.1276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1958 8.00 N 1749 7.00 C 6713 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: 0.73 Conformation dependent library (CDL) restraints added in 510.4 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 43.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.783A pdb=" N LEU A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 62 removed outlier: 4.250A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 126 through 140 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.318A pdb=" N PHE B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.699A pdb=" N ARG B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 removed outlier: 4.126A pdb=" N PHE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 104 through 121 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 166 through 182 Processing helix chain 'D' and resid 195 through 211 Processing helix chain 'E' and resid 26 through 55 removed outlier: 4.588A pdb=" N GLU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 110 removed outlier: 3.890A pdb=" N ASN E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 32 through 50 Processing helix chain 'F' and resid 52 through 78 removed outlier: 4.041A pdb=" N ARG F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.623A pdb=" N THR F 132 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 161 Processing helix chain 'F' and resid 181 through 191 Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.554A pdb=" N LEU G 18 " --> pdb=" O ASN G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 62 removed outlier: 3.552A pdb=" N MET G 52 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU G 56 " --> pdb=" O MET G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 85 removed outlier: 3.605A pdb=" N THR G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.705A pdb=" N THR G 121 " --> pdb=" O PRO G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 127 through 140 Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.712A pdb=" N GLY G 155 " --> pdb=" O GLN G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.884A pdb=" N VAL H 95 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.731A pdb=" N VAL A 163 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 103 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 161 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 160 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 164 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 145 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 166 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A 143 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.597A pdb=" N TYR B 86 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.908A pdb=" N ILE C 8 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR C 18 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 6 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 5 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 64 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR C 63 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU D 135 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 143 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 8 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32 removed outlier: 4.071A pdb=" N LYS D 30 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 96 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 65 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER D 99 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU D 63 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 71 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 40 through 43 Processing sheet with id=AA6, first strand: chain 'E' and resid 15 through 20 removed outlier: 3.583A pdb=" N TYR E 5 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 83 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS E 86 " --> pdb=" O PHE E 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 110 through 113 removed outlier: 3.509A pdb=" N ILE F 124 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 100 through 101 removed outlier: 3.505A pdb=" N PHE G 101 " --> pdb=" O VAL G 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 100 through 101 removed outlier: 3.505A pdb=" N PHE G 101 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU G 160 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU G 143 " --> pdb=" O VAL G 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.677A pdb=" N TYR H 61 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY H 70 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU H 59 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL H 72 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU H 57 " --> pdb=" O VAL H 72 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3376 1.34 - 1.46: 2294 1.46 - 1.58: 4932 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 10683 Sorted by residual: bond pdb=" C GLU F 127 " pdb=" N PRO F 128 " ideal model delta sigma weight residual 1.334 1.292 0.042 1.11e-02 8.12e+03 1.41e+01 bond pdb=" C HIS D 61 " pdb=" N VAL D 62 " ideal model delta sigma weight residual 1.334 1.292 0.041 1.24e-02 6.50e+03 1.11e+01 bond pdb=" C TRP C 115 " pdb=" N THR C 116 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.09e+01 bond pdb=" CB PHE A 17 " pdb=" CG PHE A 17 " ideal model delta sigma weight residual 1.502 1.448 0.054 2.30e-02 1.89e+03 5.53e+00 bond pdb=" CB ARG D 100 " pdb=" CG ARG D 100 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.24e+00 ... (remaining 10678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 14099 2.91 - 5.83: 308 5.83 - 8.74: 37 8.74 - 11.66: 5 11.66 - 14.57: 1 Bond angle restraints: 14450 Sorted by residual: angle pdb=" CB LEU D 197 " pdb=" CG LEU D 197 " pdb=" CD1 LEU D 197 " ideal model delta sigma weight residual 110.70 125.27 -14.57 3.00e+00 1.11e-01 2.36e+01 angle pdb=" C PRO A 65 " pdb=" N ARG A 66 " pdb=" CA ARG A 66 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C ASN B 16 " pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 122.19 116.63 5.56 1.41e+00 5.03e-01 1.56e+01 angle pdb=" CB MET A 70 " pdb=" CG MET A 70 " pdb=" SD MET A 70 " ideal model delta sigma weight residual 112.70 123.46 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C VAL A 114 " pdb=" N GLU A 115 " pdb=" CA GLU A 115 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 ... (remaining 14445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5726 17.41 - 34.82: 628 34.82 - 52.23: 75 52.23 - 69.64: 11 69.64 - 87.05: 11 Dihedral angle restraints: 6451 sinusoidal: 2653 harmonic: 3798 Sorted by residual: dihedral pdb=" CA ILE D 214 " pdb=" C ILE D 214 " pdb=" N SER D 215 " pdb=" CA SER D 215 " ideal model delta harmonic sigma weight residual 180.00 140.32 39.68 0 5.00e+00 4.00e-02 6.30e+01 dihedral pdb=" CA ILE F 134 " pdb=" C ILE F 134 " pdb=" N SER F 135 " pdb=" CA SER F 135 " ideal model delta harmonic sigma weight residual -180.00 -141.08 -38.92 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA SER A 15 " pdb=" C SER A 15 " pdb=" N GLU A 16 " pdb=" CA GLU A 16 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 6448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1414 0.083 - 0.166: 202 0.166 - 0.248: 9 0.248 - 0.331: 3 0.331 - 0.414: 3 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CB ILE F 134 " pdb=" CA ILE F 134 " pdb=" CG1 ILE F 134 " pdb=" CG2 ILE F 134 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CG LEU D 197 " pdb=" CB LEU D 197 " pdb=" CD1 LEU D 197 " pdb=" CD2 LEU D 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB ILE C 142 " pdb=" CA ILE C 142 " pdb=" CG1 ILE C 142 " pdb=" CG2 ILE C 142 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1628 not shown) Planarity restraints: 1849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 117 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO A 118 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 136 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO F 137 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO F 137 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 137 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 16 " -0.020 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR H 16 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR H 16 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 16 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR H 16 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 16 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 16 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 16 " -0.003 2.00e-02 2.50e+03 ... (remaining 1846 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 269 2.61 - 3.18: 11331 3.18 - 3.75: 18377 3.75 - 4.33: 25203 4.33 - 4.90: 37379 Nonbonded interactions: 92559 Sorted by model distance: nonbonded pdb=" O PHE B 61 " pdb=" OG1 THR B 64 " model vdw 2.035 3.040 nonbonded pdb=" OD1 ASN C 67 " pdb=" OG SER D 132 " model vdw 2.056 3.040 nonbonded pdb=" OG SER G 102 " pdb=" NH1 ARG G 162 " model vdw 2.079 3.120 nonbonded pdb=" OG1 THR C 30 " pdb=" OE1 GLU C 33 " model vdw 2.082 3.040 nonbonded pdb=" NH2 ARG B 51 " pdb=" O LEU H 44 " model vdw 2.085 3.120 ... (remaining 92554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'G' and resid 10 through 174) } 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: 6.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.008 0.088 10683 Z= 0.359 Angle : 1.062 14.570 14450 Z= 0.575 Chirality : 0.058 0.414 1631 Planarity : 0.006 0.076 1849 Dihedral : 14.167 87.051 3985 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 44.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.77 (0.22), residues: 1274 helix: -1.11 (0.21), residues: 520 sheet: -1.58 (0.38), residues: 180 loop : -2.59 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.002 ARG H 128 TYR 0.040 0.004 TYR H 16 PHE 0.037 0.004 PHE F 133 TRP 0.030 0.003 TRP A 147 HIS 0.017 0.003 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00777 (10683) covalent geometry : angle 1.06183 (14450) hydrogen bonds : bond 0.18238 ( 496) hydrogen bonds : angle 8.07276 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8539 (m-30) cc_final: 0.8142 (m-30) REVERT: B 59 MET cc_start: 0.8798 (pmm) cc_final: 0.8507 (pmm) REVERT: D 110 PHE cc_start: 0.8741 (t80) cc_final: 0.8416 (t80) REVERT: D 194 ARG cc_start: 0.7068 (mpp80) cc_final: 0.6656 (mpp80) REVERT: E 105 TYR cc_start: 0.8893 (t80) cc_final: 0.8421 (t80) REVERT: F 55 GLU cc_start: 0.8685 (pt0) cc_final: 0.8434 (tm-30) REVERT: F 177 MET cc_start: 0.7210 (tmm) cc_final: 0.6873 (tmm) REVERT: G 91 ILE cc_start: 0.3688 (mp) cc_final: 0.3207 (mt) REVERT: H 102 LEU cc_start: 0.8638 (tt) cc_final: 0.8157 (tp) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.0856 time to fit residues: 17.8721 Evaluate side-chains 104 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN A 145 GLN A 152 GLN B 25 HIS B 146 HIS ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.064467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.054795 restraints weight = 74207.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.056207 restraints weight = 50259.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.057233 restraints weight = 37341.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.057987 restraints weight = 29723.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.058508 restraints weight = 24797.006| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10683 Z= 0.173 Angle : 0.762 7.424 14450 Z= 0.402 Chirality : 0.048 0.236 1631 Planarity : 0.006 0.076 1849 Dihedral : 7.345 83.021 1408 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.03 % Allowed : 11.06 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.13 (0.23), residues: 1274 helix: -0.45 (0.22), residues: 532 sheet: -1.29 (0.38), residues: 189 loop : -2.42 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 59 TYR 0.027 0.002 TYR D 180 PHE 0.027 0.002 PHE B 35 TRP 0.013 0.002 TRP F 170 HIS 0.009 0.002 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00376 (10683) covalent geometry : angle 0.76224 (14450) hydrogen bonds : bond 0.05453 ( 496) hydrogen bonds : angle 6.09997 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8371 (t0) cc_final: 0.7890 (t0) REVERT: A 41 LYS cc_start: 0.8538 (mppt) cc_final: 0.8292 (tptt) REVERT: A 99 ASP cc_start: 0.8583 (m-30) cc_final: 0.8195 (m-30) REVERT: A 106 ASP cc_start: 0.7659 (t70) cc_final: 0.7325 (m-30) REVERT: A 113 PHE cc_start: 0.4617 (t80) cc_final: 0.4326 (t80) REVERT: A 145 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7917 (pp30) REVERT: D 110 PHE cc_start: 0.8703 (t80) cc_final: 0.8318 (t80) REVERT: E 5 TYR cc_start: 0.5988 (t80) cc_final: 0.5592 (t80) REVERT: E 105 TYR cc_start: 0.8543 (t80) cc_final: 0.8163 (t80) REVERT: E 110 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.7050 (mmp) REVERT: F 39 PHE cc_start: 0.7104 (t80) cc_final: 0.6894 (t80) REVERT: F 55 GLU cc_start: 0.8564 (pt0) cc_final: 0.8098 (tm-30) REVERT: G 91 ILE cc_start: 0.3630 (mp) cc_final: 0.3110 (mt) REVERT: H 102 LEU cc_start: 0.8601 (tt) cc_final: 0.8239 (tp) outliers start: 12 outliers final: 7 residues processed: 148 average time/residue: 0.0918 time to fit residues: 19.5557 Evaluate side-chains 118 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 94 optimal weight: 0.7980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN B 25 HIS B 83 HIS ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.063956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.054368 restraints weight = 73412.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.055743 restraints weight = 49490.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.056766 restraints weight = 36751.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.057493 restraints weight = 29115.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.058068 restraints weight = 24235.793| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10683 Z= 0.168 Angle : 0.730 8.510 14450 Z= 0.383 Chirality : 0.046 0.176 1631 Planarity : 0.005 0.074 1849 Dihedral : 7.038 83.949 1408 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.00 % Allowed : 15.87 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.92 (0.23), residues: 1274 helix: -0.15 (0.22), residues: 522 sheet: -1.28 (0.40), residues: 185 loop : -2.36 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 59 TYR 0.025 0.002 TYR C 69 PHE 0.023 0.002 PHE B 35 TRP 0.014 0.002 TRP F 170 HIS 0.010 0.002 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00373 (10683) covalent geometry : angle 0.73030 (14450) hydrogen bonds : bond 0.04934 ( 496) hydrogen bonds : angle 5.84625 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8368 (t0) cc_final: 0.7860 (t0) REVERT: A 113 PHE cc_start: 0.4605 (t80) cc_final: 0.4383 (t80) REVERT: C 95 GLU cc_start: 0.7077 (pm20) cc_final: 0.6702 (pm20) REVERT: D 110 PHE cc_start: 0.8730 (t80) cc_final: 0.8339 (t80) REVERT: E 5 TYR cc_start: 0.5995 (t80) cc_final: 0.5765 (t80) REVERT: E 94 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8215 (pt) REVERT: E 101 MET cc_start: 0.8119 (mmm) cc_final: 0.7880 (mmm) REVERT: E 105 TYR cc_start: 0.8576 (t80) cc_final: 0.8172 (t80) REVERT: F 55 GLU cc_start: 0.8597 (pt0) cc_final: 0.8139 (tm-30) REVERT: F 73 ASP cc_start: 0.7254 (t0) cc_final: 0.5504 (t0) REVERT: G 91 ILE cc_start: 0.3959 (mp) cc_final: 0.3495 (mt) REVERT: H 102 LEU cc_start: 0.8606 (tt) cc_final: 0.8300 (tp) outliers start: 35 outliers final: 20 residues processed: 154 average time/residue: 0.0894 time to fit residues: 20.1326 Evaluate side-chains 136 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 145 GLN B 25 HIS ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** 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 = 0.4117 r_free = 0.4117 target = 0.065227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.055378 restraints weight = 74843.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.056814 restraints weight = 50371.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.057834 restraints weight = 37316.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.058607 restraints weight = 29686.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.059162 restraints weight = 24830.712| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10683 Z= 0.140 Angle : 0.680 8.508 14450 Z= 0.356 Chirality : 0.045 0.209 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.711 83.098 1408 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.86 % Allowed : 17.24 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.63 (0.23), residues: 1274 helix: 0.11 (0.22), residues: 524 sheet: -1.20 (0.40), residues: 185 loop : -2.20 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.024 0.002 TYR D 180 PHE 0.028 0.002 PHE F 39 TRP 0.015 0.001 TRP G 94 HIS 0.005 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00307 (10683) covalent geometry : angle 0.67984 (14450) hydrogen bonds : bond 0.04549 ( 496) hydrogen bonds : angle 5.52159 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8290 (t0) cc_final: 0.7790 (t0) REVERT: A 106 ASP cc_start: 0.7611 (t70) cc_final: 0.7309 (m-30) REVERT: C 95 GLU cc_start: 0.6919 (pm20) cc_final: 0.6514 (pm20) REVERT: D 110 PHE cc_start: 0.8686 (t80) cc_final: 0.8286 (t80) REVERT: E 5 TYR cc_start: 0.5987 (t80) cc_final: 0.5676 (t80) REVERT: E 50 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8667 (pm20) REVERT: E 94 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8102 (pt) REVERT: E 105 TYR cc_start: 0.8557 (t80) cc_final: 0.8217 (t80) REVERT: F 55 GLU cc_start: 0.8549 (pt0) cc_final: 0.8148 (tm-30) REVERT: F 73 ASP cc_start: 0.7074 (t0) cc_final: 0.5365 (t0) REVERT: F 74 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7221 (mt) REVERT: F 107 GLU cc_start: 0.8050 (pm20) cc_final: 0.7849 (pm20) REVERT: F 177 MET cc_start: 0.6940 (tmm) cc_final: 0.6516 (tmm) REVERT: G 91 ILE cc_start: 0.3950 (mp) cc_final: 0.3437 (mt) REVERT: H 8 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7676 (mp) outliers start: 45 outliers final: 22 residues processed: 167 average time/residue: 0.0874 time to fit residues: 21.2432 Evaluate side-chains 144 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN A 122 ASN B 25 HIS C 22 ASN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** 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 = 0.4116 r_free = 0.4116 target = 0.065054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.055320 restraints weight = 73352.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.056761 restraints weight = 48875.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.057799 restraints weight = 36049.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.058565 restraints weight = 28460.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.059133 restraints weight = 23623.521| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10683 Z= 0.142 Angle : 0.683 8.777 14450 Z= 0.356 Chirality : 0.045 0.165 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.499 82.665 1405 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.77 % Allowed : 19.21 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.50 (0.23), residues: 1274 helix: 0.25 (0.22), residues: 524 sheet: -1.20 (0.39), residues: 188 loop : -2.14 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 76 TYR 0.026 0.002 TYR F 75 PHE 0.033 0.002 PHE F 133 TRP 0.012 0.001 TRP F 170 HIS 0.004 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00314 (10683) covalent geometry : angle 0.68284 (14450) hydrogen bonds : bond 0.04427 ( 496) hydrogen bonds : angle 5.38551 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8255 (t0) cc_final: 0.7705 (t0) REVERT: A 106 ASP cc_start: 0.7622 (t70) cc_final: 0.7332 (m-30) REVERT: D 110 PHE cc_start: 0.8716 (t80) cc_final: 0.8311 (t80) REVERT: E 5 TYR cc_start: 0.6003 (t80) cc_final: 0.5644 (t80) REVERT: E 94 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8098 (pt) REVERT: E 101 MET cc_start: 0.8303 (mmm) cc_final: 0.8087 (mmm) REVERT: E 105 TYR cc_start: 0.8611 (t80) cc_final: 0.8248 (t80) REVERT: F 55 GLU cc_start: 0.8615 (pt0) cc_final: 0.8189 (tm-30) REVERT: F 73 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.4938 (t0) REVERT: F 107 GLU cc_start: 0.8010 (pm20) cc_final: 0.7810 (pm20) REVERT: F 177 MET cc_start: 0.7006 (tmm) cc_final: 0.6426 (tmm) REVERT: F 191 MET cc_start: 0.7124 (mtt) cc_final: 0.6923 (mtm) REVERT: G 91 ILE cc_start: 0.3934 (mp) cc_final: 0.3451 (mt) outliers start: 44 outliers final: 28 residues processed: 163 average time/residue: 0.0820 time to fit residues: 19.7641 Evaluate side-chains 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 152 ASN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.065223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.055385 restraints weight = 73460.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.056831 restraints weight = 49063.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.057883 restraints weight = 36072.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.058616 restraints weight = 28579.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.059206 restraints weight = 23832.104| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10683 Z= 0.140 Angle : 0.675 9.368 14450 Z= 0.351 Chirality : 0.044 0.183 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.330 82.037 1405 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.95 % Allowed : 20.58 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.39 (0.23), residues: 1274 helix: 0.34 (0.22), residues: 524 sheet: -1.16 (0.39), residues: 192 loop : -2.08 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 76 TYR 0.024 0.002 TYR F 75 PHE 0.032 0.002 PHE F 133 TRP 0.010 0.001 TRP F 170 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (10683) covalent geometry : angle 0.67489 (14450) hydrogen bonds : bond 0.04369 ( 496) hydrogen bonds : angle 5.27546 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8345 (t0) cc_final: 0.7749 (t0) REVERT: A 106 ASP cc_start: 0.7641 (t70) cc_final: 0.7370 (m-30) REVERT: D 110 PHE cc_start: 0.8661 (t80) cc_final: 0.8267 (t80) REVERT: D 153 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8511 (mm) REVERT: E 5 TYR cc_start: 0.5920 (t80) cc_final: 0.5563 (t80) REVERT: E 50 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: E 94 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8055 (pt) REVERT: E 101 MET cc_start: 0.8195 (mmm) cc_final: 0.7984 (mmm) REVERT: F 55 GLU cc_start: 0.8610 (pt0) cc_final: 0.8181 (tm-30) REVERT: F 73 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6271 (p0) REVERT: F 177 MET cc_start: 0.6969 (tmm) cc_final: 0.6405 (tmm) REVERT: F 191 MET cc_start: 0.7003 (mtt) cc_final: 0.6797 (mtm) REVERT: G 91 ILE cc_start: 0.3951 (mp) cc_final: 0.3456 (mt) REVERT: H 110 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7571 (mm) outliers start: 46 outliers final: 30 residues processed: 168 average time/residue: 0.0795 time to fit residues: 19.9643 Evaluate side-chains 154 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 74 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.0270 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 77 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** 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 = 0.4118 r_free = 0.4118 target = 0.065587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.055772 restraints weight = 72291.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.057207 restraints weight = 48540.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.058251 restraints weight = 35910.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.059006 restraints weight = 28452.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.059546 restraints weight = 23694.448| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10683 Z= 0.135 Angle : 0.680 9.007 14450 Z= 0.351 Chirality : 0.045 0.289 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.234 80.063 1405 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.55 % Allowed : 21.01 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.24), residues: 1274 helix: 0.42 (0.22), residues: 524 sheet: -1.10 (0.39), residues: 192 loop : -2.02 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 151 TYR 0.024 0.002 TYR F 75 PHE 0.036 0.002 PHE F 133 TRP 0.009 0.001 TRP F 170 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00299 (10683) covalent geometry : angle 0.68015 (14450) hydrogen bonds : bond 0.04249 ( 496) hydrogen bonds : angle 5.17442 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7224 (mmt) cc_final: 0.7014 (mmt) REVERT: A 32 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7897 (t0) REVERT: A 35 ASN cc_start: 0.8339 (t0) cc_final: 0.7736 (t0) REVERT: A 82 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7327 (tpp80) REVERT: A 106 ASP cc_start: 0.7687 (t70) cc_final: 0.7396 (m-30) REVERT: B 86 TYR cc_start: 0.4991 (OUTLIER) cc_final: 0.4488 (p90) REVERT: D 110 PHE cc_start: 0.8695 (t80) cc_final: 0.8295 (t80) REVERT: D 153 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8525 (mm) REVERT: E 5 TYR cc_start: 0.5970 (t80) cc_final: 0.5624 (t80) REVERT: E 94 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8031 (pt) REVERT: E 110 MET cc_start: 0.7133 (mmp) cc_final: 0.5256 (mmm) REVERT: F 55 GLU cc_start: 0.8645 (pt0) cc_final: 0.8203 (tm-30) REVERT: G 91 ILE cc_start: 0.4054 (mp) cc_final: 0.3490 (mt) REVERT: H 110 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7567 (mm) outliers start: 53 outliers final: 35 residues processed: 173 average time/residue: 0.0856 time to fit residues: 21.7656 Evaluate side-chains 161 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 0.5980 chunk 100 optimal weight: 0.0050 chunk 12 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.0970 chunk 111 optimal weight: 8.9990 chunk 57 optimal weight: 0.0870 chunk 45 optimal weight: 0.2980 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 77 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** 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 = 0.4154 r_free = 0.4154 target = 0.066935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.057000 restraints weight = 74892.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.058459 restraints weight = 50282.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.059514 restraints weight = 37254.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.060287 restraints weight = 29613.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.060831 restraints weight = 24761.433| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10683 Z= 0.135 Angle : 0.712 14.000 14450 Z= 0.364 Chirality : 0.045 0.253 1631 Planarity : 0.004 0.072 1849 Dihedral : 6.040 77.383 1405 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.00 % Allowed : 22.81 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.23), residues: 1274 helix: 0.48 (0.22), residues: 524 sheet: -0.82 (0.40), residues: 178 loop : -2.06 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 119 TYR 0.035 0.002 TYR F 75 PHE 0.040 0.002 PHE F 133 TRP 0.009 0.001 TRP F 170 HIS 0.004 0.001 HIS E 86 Details of bonding type rmsd covalent geometry : bond 0.00287 (10683) covalent geometry : angle 0.71151 (14450) hydrogen bonds : bond 0.04246 ( 496) hydrogen bonds : angle 5.05947 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7214 (mmt) cc_final: 0.6998 (mmt) REVERT: A 35 ASN cc_start: 0.8293 (t0) cc_final: 0.7694 (t0) REVERT: A 82 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7411 (ttm-80) REVERT: A 106 ASP cc_start: 0.7563 (t70) cc_final: 0.7359 (m-30) REVERT: A 113 PHE cc_start: 0.4671 (t80) cc_final: 0.3811 (t80) REVERT: B 86 TYR cc_start: 0.4865 (OUTLIER) cc_final: 0.4303 (p90) REVERT: D 110 PHE cc_start: 0.8640 (t80) cc_final: 0.8242 (t80) REVERT: D 153 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8382 (mm) REVERT: E 5 TYR cc_start: 0.5803 (t80) cc_final: 0.5455 (t80) REVERT: E 89 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7904 (mmtt) REVERT: E 94 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.7955 (pt) REVERT: E 101 MET cc_start: 0.8048 (mmm) cc_final: 0.7698 (mmm) REVERT: E 110 MET cc_start: 0.6426 (mmp) cc_final: 0.6099 (mmp) REVERT: E 138 LEU cc_start: 0.3253 (mm) cc_final: 0.3040 (mm) REVERT: F 55 GLU cc_start: 0.8589 (pt0) cc_final: 0.8169 (tm-30) REVERT: G 91 ILE cc_start: 0.4049 (mp) cc_final: 0.3457 (mt) outliers start: 35 outliers final: 27 residues processed: 170 average time/residue: 0.0868 time to fit residues: 21.7202 Evaluate side-chains 155 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** 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 = 0.4103 r_free = 0.4103 target = 0.065146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.055337 restraints weight = 75010.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.056750 restraints weight = 50139.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.057762 restraints weight = 37221.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.058498 restraints weight = 29621.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.059043 restraints weight = 24785.326| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10683 Z= 0.165 Angle : 0.740 12.007 14450 Z= 0.380 Chirality : 0.046 0.239 1631 Planarity : 0.005 0.069 1849 Dihedral : 6.174 79.022 1405 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.86 % Allowed : 22.47 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1274 helix: 0.47 (0.22), residues: 520 sheet: -0.91 (0.39), residues: 190 loop : -2.02 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 128 TYR 0.030 0.002 TYR F 75 PHE 0.035 0.002 PHE F 133 TRP 0.009 0.001 TRP F 170 HIS 0.025 0.002 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00372 (10683) covalent geometry : angle 0.73985 (14450) hydrogen bonds : bond 0.04411 ( 496) hydrogen bonds : angle 5.19852 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7890 (t0) REVERT: A 35 ASN cc_start: 0.8318 (t0) cc_final: 0.7737 (t0) REVERT: A 82 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7329 (tpp80) REVERT: A 106 ASP cc_start: 0.7618 (t70) cc_final: 0.7348 (m-30) REVERT: A 113 PHE cc_start: 0.4740 (t80) cc_final: 0.3793 (t80) REVERT: B 86 TYR cc_start: 0.4670 (OUTLIER) cc_final: 0.4059 (p90) REVERT: D 110 PHE cc_start: 0.8648 (t80) cc_final: 0.8250 (t80) REVERT: F 55 GLU cc_start: 0.8629 (pt0) cc_final: 0.8176 (tm-30) REVERT: H 110 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7608 (mm) outliers start: 45 outliers final: 36 residues processed: 157 average time/residue: 0.0874 time to fit residues: 20.4166 Evaluate side-chains 154 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain G residue 14 ASN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** 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 = 0.4136 r_free = 0.4136 target = 0.066392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.056515 restraints weight = 74293.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.057945 restraints weight = 49906.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.058988 restraints weight = 36939.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.059747 restraints weight = 29211.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.060275 restraints weight = 24370.497| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10683 Z= 0.138 Angle : 0.731 12.509 14450 Z= 0.372 Chirality : 0.046 0.232 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.057 77.378 1405 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.77 % Allowed : 22.38 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.15 (0.24), residues: 1274 helix: 0.52 (0.22), residues: 520 sheet: -0.88 (0.39), residues: 186 loop : -1.97 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 194 TYR 0.027 0.001 TYR F 75 PHE 0.043 0.002 PHE F 39 TRP 0.007 0.001 TRP F 170 HIS 0.013 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00307 (10683) covalent geometry : angle 0.73076 (14450) hydrogen bonds : bond 0.04236 ( 496) hydrogen bonds : angle 5.09542 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7151 (mmt) cc_final: 0.6841 (mmt) REVERT: A 32 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7914 (t0) REVERT: A 35 ASN cc_start: 0.8268 (t0) cc_final: 0.7739 (t0) REVERT: A 82 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7291 (tpp80) REVERT: A 106 ASP cc_start: 0.7611 (t70) cc_final: 0.7367 (m-30) REVERT: A 113 PHE cc_start: 0.4565 (t80) cc_final: 0.4288 (t80) REVERT: B 86 TYR cc_start: 0.4686 (OUTLIER) cc_final: 0.4030 (p90) REVERT: D 110 PHE cc_start: 0.8635 (t80) cc_final: 0.8232 (t80) REVERT: D 153 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8419 (mm) REVERT: E 5 TYR cc_start: 0.5924 (t80) cc_final: 0.5240 (t80) REVERT: E 84 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8339 (mm) REVERT: E 89 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7892 (mmtt) REVERT: E 110 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6460 (mmp) REVERT: E 138 LEU cc_start: 0.3253 (mm) cc_final: 0.3032 (mm) REVERT: F 55 GLU cc_start: 0.8573 (pt0) cc_final: 0.8168 (tm-30) REVERT: F 145 CYS cc_start: 0.6184 (t) cc_final: 0.5605 (t) REVERT: H 3 PHE cc_start: 0.7179 (m-80) cc_final: 0.6889 (m-80) REVERT: H 110 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7640 (mm) REVERT: H 134 MET cc_start: 0.6926 (mmt) cc_final: 0.6495 (mmp) outliers start: 44 outliers final: 33 residues processed: 160 average time/residue: 0.0825 time to fit residues: 19.4293 Evaluate side-chains 156 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 85 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 24 optimal weight: 8.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** 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 = 0.4138 r_free = 0.4138 target = 0.066198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.056302 restraints weight = 73192.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.057742 restraints weight = 48935.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.058792 restraints weight = 36159.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.059546 restraints weight = 28710.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.060108 restraints weight = 23939.945| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10683 Z= 0.137 Angle : 0.721 11.613 14450 Z= 0.367 Chirality : 0.046 0.251 1631 Planarity : 0.004 0.059 1849 Dihedral : 5.991 76.748 1405 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.52 % Allowed : 22.30 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.11 (0.24), residues: 1274 helix: 0.56 (0.22), residues: 520 sheet: -0.91 (0.40), residues: 175 loop : -1.91 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 76 TYR 0.025 0.002 TYR F 75 PHE 0.035 0.002 PHE F 133 TRP 0.008 0.001 TRP F 170 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00306 (10683) covalent geometry : angle 0.72127 (14450) hydrogen bonds : bond 0.04188 ( 496) hydrogen bonds : angle 5.05948 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.82 seconds wall clock time: 37 minutes 33.08 seconds (2253.08 seconds total)