Starting phenix.real_space_refine on Wed Aug 5 22:27:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x4g_66544/08_2026/9x4g_66544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x4g_66544/08_2026/9x4g_66544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x4g_66544/08_2026/9x4g_66544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x4g_66544/08_2026/9x4g_66544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x4g_66544/08_2026/9x4g_66544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x4g_66544/08_2026/9x4g_66544.map" } resolution = 3.1 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= -0.076 sd= 0.174 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 66 5.16 5 C 7436 2.51 5 N 2086 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11768 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2502 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1511 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 3, 'TRANS': 185} Chain breaks: 2 Chain: "C" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1270 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain breaks: 4 Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: E, F, G, H Time building chain proxies: 2.26, per 1000 atoms: 0.19 Number of scatterers: 11768 At special positions: 0 Unit cell: (182.82, 92.241, 110.523, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 66 16.00 O 2178 8.00 N 2086 7.00 C 7436 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: 0.65 Conformation dependent library (CDL) restraints added in 413.0 milliseconds 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 16 sheets defined 50.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 41 through 64 removed outlier: 4.528A pdb=" N GLY A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 157 through 170 removed outlier: 4.206A pdb=" N ASN A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 205 through 222 removed outlier: 4.067A pdb=" N ILE A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.542A pdb=" N GLU A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 255 removed outlier: 3.993A pdb=" N LEU A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.737A pdb=" N CYS A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 4.181A pdb=" N ALA A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 87 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.712A pdb=" N LYS B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.673A pdb=" N ILE B 209 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'C' and resid 32 through 42 Processing helix chain 'C' and resid 58 through 75 Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 95 through 105 removed outlier: 4.416A pdb=" N ILE C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.838A pdb=" N GLY C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Proline residue: C 144 - end of helix Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.784A pdb=" N SER C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 50 removed outlier: 5.260A pdb=" N VAL D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 104 Processing helix chain 'E' and resid 41 through 64 removed outlier: 4.528A pdb=" N GLY E 58 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 111 through 123 Processing helix chain 'E' and resid 157 through 170 removed outlier: 4.207A pdb=" N ASN E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'E' and resid 205 through 222 removed outlier: 4.066A pdb=" N ILE E 209 " --> pdb=" O SER E 205 " (cutoff:3.500A) Proline residue: E 218 - end of helix removed outlier: 3.542A pdb=" N GLU E 222 " --> pdb=" O PRO E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 255 removed outlier: 3.994A pdb=" N LEU E 231 " --> pdb=" O THR E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.738A pdb=" N CYS E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 311 removed outlier: 4.180A pdb=" N ALA E 302 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER E 311 " --> pdb=" O LEU E 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 87 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 122 through 124 No H-bonds generated for 'chain 'F' and resid 122 through 124' Processing helix chain 'F' and resid 125 through 146 removed outlier: 3.712A pdb=" N LYS F 129 " --> pdb=" O ASP F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 205 through 221 removed outlier: 3.673A pdb=" N ILE F 209 " --> pdb=" O CYS F 205 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 58 through 75 Processing helix chain 'G' and resid 83 through 91 Processing helix chain 'G' and resid 95 through 105 removed outlier: 4.415A pdb=" N ILE G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 removed outlier: 3.837A pdb=" N GLY G 142 " --> pdb=" O PRO G 138 " (cutoff:3.500A) Proline residue: G 144 - end of helix Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.784A pdb=" N SER G 183 " --> pdb=" O LYS G 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 50 removed outlier: 5.260A pdb=" N VAL H 46 " --> pdb=" O THR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.565A pdb=" N VAL A 23 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 20 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 18 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR A 78 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 7.472A pdb=" N LEU A 259 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200 removed outlier: 3.519A pdb=" N ASP A 203 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41 removed outlier: 7.369A pdb=" N GLN B 103 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 97 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 105 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 160 removed outlier: 4.528A pdb=" N THR B 170 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 7 through 8 removed outlier: 4.160A pdb=" N TYR C 7 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS C 22 " --> pdb=" O TYR C 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AA9, first strand: chain 'E' and resid 23 through 26 removed outlier: 3.565A pdb=" N VAL E 23 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG E 20 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 18 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR E 78 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 147 through 150 removed outlier: 7.472A pdb=" N LEU E 259 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 199 through 200 removed outlier: 3.519A pdb=" N ASP E 203 " --> pdb=" O LYS E 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 39 through 41 removed outlier: 7.368A pdb=" N GLN F 103 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE F 97 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE F 105 " --> pdb=" O TYR F 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 159 through 160 removed outlier: 4.529A pdb=" N THR F 170 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 7 through 8 removed outlier: 4.161A pdb=" N TYR G 7 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS G 22 " --> pdb=" O TYR G 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 26 through 28 Processing sheet with id=AB7, first strand: chain 'H' and resid 32 through 33 582 hydrogen bonds defined for protein. 1716 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: 1.10 Time building geometry restraints manager: 0.89 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: 3903 1.34 - 1.46: 1799 1.46 - 1.58: 6136 1.58 - 1.70: 0 1.70 - 1.81: 104 Bond restraints: 11942 Sorted by residual: bond pdb=" C LEU C 143 " pdb=" N PRO C 144 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.51e-02 4.39e+03 2.05e+00 bond pdb=" C LEU G 143 " pdb=" N PRO G 144 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.51e-02 4.39e+03 2.05e+00 bond pdb=" CA VAL H 70 " pdb=" CB VAL H 70 " ideal model delta sigma weight residual 1.532 1.548 -0.015 1.08e-02 8.57e+03 2.01e+00 bond pdb=" C VAL G 137 " pdb=" N PRO G 138 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.01e-02 9.80e+03 1.88e+00 bond pdb=" C VAL C 137 " pdb=" N PRO C 138 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.01e-02 9.80e+03 1.88e+00 ... (remaining 11937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 15256 1.62 - 3.23: 634 3.23 - 4.85: 142 4.85 - 6.46: 36 6.46 - 8.08: 10 Bond angle restraints: 16078 Sorted by residual: angle pdb=" C GLN B 223 " pdb=" N PHE B 224 " pdb=" CA PHE B 224 " ideal model delta sigma weight residual 120.38 127.07 -6.69 1.37e+00 5.33e-01 2.38e+01 angle pdb=" C GLN F 223 " pdb=" N PHE F 224 " pdb=" CA PHE F 224 " ideal model delta sigma weight residual 120.38 126.99 -6.61 1.37e+00 5.33e-01 2.33e+01 angle pdb=" N GLY A 75 " pdb=" CA GLY A 75 " pdb=" C GLY A 75 " ideal model delta sigma weight residual 110.38 116.70 -6.32 1.48e+00 4.57e-01 1.82e+01 angle pdb=" N GLY E 75 " pdb=" CA GLY E 75 " pdb=" C GLY E 75 " ideal model delta sigma weight residual 110.38 116.65 -6.27 1.48e+00 4.57e-01 1.80e+01 angle pdb=" N ASN E 65 " pdb=" CA ASN E 65 " pdb=" C ASN E 65 " ideal model delta sigma weight residual 111.37 117.19 -5.82 1.64e+00 3.72e-01 1.26e+01 ... (remaining 16073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 6523 16.87 - 33.73: 631 33.73 - 50.60: 134 50.60 - 67.47: 26 67.47 - 84.33: 10 Dihedral angle restraints: 7324 sinusoidal: 2984 harmonic: 4340 Sorted by residual: dihedral pdb=" CA LEU E 100 " pdb=" C LEU E 100 " pdb=" N THR E 101 " pdb=" CA THR E 101 " ideal model delta harmonic sigma weight residual 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU A 100 " pdb=" C LEU A 100 " pdb=" N THR A 101 " pdb=" CA THR A 101 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PRO D 78 " pdb=" C PRO D 78 " pdb=" N LYS D 79 " pdb=" CA LYS D 79 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1462 0.054 - 0.108: 313 0.108 - 0.162: 55 0.162 - 0.216: 10 0.216 - 0.270: 6 Chirality restraints: 1846 Sorted by residual: chirality pdb=" CB ILE F 159 " pdb=" CA ILE F 159 " pdb=" CG1 ILE F 159 " pdb=" CG2 ILE F 159 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE B 159 " pdb=" CA ILE B 159 " pdb=" CG1 ILE B 159 " pdb=" CG2 ILE B 159 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 7 " pdb=" CA ILE A 7 " pdb=" CG1 ILE A 7 " pdb=" CG2 ILE A 7 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1843 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 127 " 0.058 5.00e-02 4.00e+02 8.82e-02 1.25e+01 pdb=" N PRO E 128 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 127 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO A 128 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 62 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO F 63 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO F 63 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 63 " 0.031 5.00e-02 4.00e+02 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 2742 2.80 - 3.39: 14411 3.39 - 3.97: 22313 3.97 - 4.56: 30170 4.56 - 5.14: 44436 Nonbonded interactions: 114072 Sorted by model distance: nonbonded pdb=" NE2 GLN F 135 " pdb=" OE2 GLU F 214 " model vdw 2.216 3.120 nonbonded pdb=" NE2 GLN B 135 " pdb=" OE2 GLU B 214 " model vdw 2.216 3.120 nonbonded pdb=" O GLU D 74 " pdb=" OG SER D 75 " model vdw 2.301 3.040 nonbonded pdb=" O GLU H 74 " pdb=" OG SER H 75 " model vdw 2.301 3.040 nonbonded pdb=" NH1 ARG F 162 " pdb=" O LYS F 168 " model vdw 2.316 3.120 ... (remaining 114067 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.430 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 : 0.003 0.032 11942 Z= 0.164 Angle : 0.806 8.079 16078 Z= 0.433 Chirality : 0.049 0.270 1846 Planarity : 0.006 0.088 2066 Dihedral : 14.170 84.334 4512 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.62 % Favored : 86.70 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.22), residues: 1474 helix: 0.23 (0.20), residues: 712 sheet: -1.37 (0.57), residues: 102 loop : -3.56 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 165 TYR 0.020 0.002 TYR B 216 PHE 0.013 0.001 PHE B 224 TRP 0.011 0.001 TRP F 117 HIS 0.019 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (11942) covalent geometry : angle 0.80627 / 0.43 (16078) hydrogen bonds : bond 0.11457 / 8.04 ( 582) hydrogen bonds : angle 5.89799 / 4.12 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.6682 (mmp) cc_final: 0.6314 (mmp) REVERT: B 37 GLU cc_start: 0.7513 (tp30) cc_final: 0.7250 (mt-10) REVERT: F 37 GLU cc_start: 0.7663 (tp30) cc_final: 0.7223 (mt-10) REVERT: F 100 GLU cc_start: 0.7420 (pm20) cc_final: 0.7180 (pm20) REVERT: F 216 TYR cc_start: 0.6846 (m-10) cc_final: 0.6549 (m-80) REVERT: F 222 LYS cc_start: 0.8700 (tttp) cc_final: 0.8462 (ttpp) REVERT: G 151 MET cc_start: 0.3109 (tmm) cc_final: 0.2864 (tmm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1058 time to fit residues: 35.8435 Evaluate side-chains 185 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 89 GLN A 139 GLN B 103 GLN B 135 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN E 67 GLN E 89 GLN E 137 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN G 160 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.170886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.149428 restraints weight = 32378.688| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 3.21 r_work: 0.4041 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11942 Z= 0.248 Angle : 0.841 15.067 16078 Z= 0.440 Chirality : 0.051 0.218 1846 Planarity : 0.006 0.052 2066 Dihedral : 5.874 25.472 1620 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.68 % Allowed : 13.23 % Favored : 86.09 % Rotamer: Outliers : 2.91 % Allowed : 10.08 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.22), residues: 1474 helix: 0.07 (0.20), residues: 716 sheet: -1.08 (0.65), residues: 88 loop : -3.51 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 249 TYR 0.020 0.003 TYR C 156 PHE 0.025 0.002 PHE F 137 TRP 0.010 0.001 TRP B 117 HIS 0.014 0.002 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (11942) covalent geometry : angle 0.84121 / 0.44 (16078) hydrogen bonds : bond 0.05463 / 3.97 ( 582) hydrogen bonds : angle 5.66597 / 4.03 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7049 (mmp) cc_final: 0.6640 (mmp) REVERT: C 67 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7877 (ttp80) REVERT: C 127 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6764 (pttm) REVERT: E 139 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8515 (pt0) REVERT: G 140 MET cc_start: 0.5231 (pmm) cc_final: 0.4901 (ppp) outliers start: 37 outliers final: 19 residues processed: 224 average time/residue: 0.1231 time to fit residues: 37.1874 Evaluate side-chains 209 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 60 optimal weight: 0.0370 chunk 18 optimal weight: 0.0470 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.170662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.149179 restraints weight = 32969.056| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 3.28 r_work: 0.4056 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11942 Z= 0.176 Angle : 0.772 12.443 16078 Z= 0.396 Chirality : 0.048 0.210 1846 Planarity : 0.005 0.048 2066 Dihedral : 5.577 24.370 1620 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.68 % Allowed : 13.23 % Favored : 86.09 % Rotamer: Outliers : 3.86 % Allowed : 11.97 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.22), residues: 1474 helix: 0.21 (0.20), residues: 718 sheet: -1.03 (0.64), residues: 88 loop : -3.50 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 31 TYR 0.022 0.002 TYR C 156 PHE 0.010 0.001 PHE B 133 TRP 0.011 0.001 TRP A 102 HIS 0.011 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (11942) covalent geometry : angle 0.77159 / 0.40 (16078) hydrogen bonds : bond 0.04877 / 3.55 ( 582) hydrogen bonds : angle 5.39271 / 3.83 ( 1716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7040 (mmp) cc_final: 0.6621 (mmp) REVERT: A 330 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.6249 (pm20) REVERT: B 223 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7814 (pp30) REVERT: C 67 ARG cc_start: 0.8423 (ttp80) cc_final: 0.7963 (ttt-90) REVERT: C 127 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6648 (pttm) REVERT: C 151 MET cc_start: 0.1771 (tmm) cc_final: -0.0308 (mtt) REVERT: D 94 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6516 (tt) REVERT: F 141 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6398 (mm) REVERT: F 186 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7417 (mm-30) REVERT: F 223 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7760 (pp30) REVERT: G 67 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7875 (ttp80) REVERT: G 140 MET cc_start: 0.5157 (pmm) cc_final: 0.4803 (ppp) REVERT: H 70 VAL cc_start: 0.7308 (p) cc_final: 0.7050 (p) outliers start: 49 outliers final: 24 residues processed: 226 average time/residue: 0.1166 time to fit residues: 36.0268 Evaluate side-chains 224 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 142 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 223 GLN ** 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 = 0.4615 r_free = 0.4615 target = 0.171847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.150187 restraints weight = 32966.124| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 3.30 r_work: 0.4033 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11942 Z= 0.201 Angle : 0.787 13.697 16078 Z= 0.406 Chirality : 0.048 0.216 1846 Planarity : 0.006 0.072 2066 Dihedral : 5.697 24.948 1620 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.68 % Allowed : 13.91 % Favored : 85.41 % Rotamer: Outliers : 3.54 % Allowed : 15.28 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.22), residues: 1474 helix: 0.16 (0.20), residues: 714 sheet: -0.96 (0.65), residues: 88 loop : -3.54 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 31 TYR 0.021 0.002 TYR C 156 PHE 0.013 0.001 PHE F 224 TRP 0.009 0.001 TRP B 117 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (11942) covalent geometry : angle 0.78732 / 0.41 (16078) hydrogen bonds : bond 0.05026 / 3.66 ( 582) hydrogen bonds : angle 5.43541 / 3.86 ( 1716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7129 (mmp) cc_final: 0.6710 (mmp) REVERT: B 223 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7802 (pp30) REVERT: C 67 ARG cc_start: 0.8416 (ttp80) cc_final: 0.7982 (ttt-90) REVERT: C 127 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6688 (pttm) REVERT: C 143 LEU cc_start: 0.6256 (mt) cc_final: 0.5826 (mt) REVERT: C 151 MET cc_start: 0.1747 (tmm) cc_final: -0.0135 (mtt) REVERT: D 94 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6472 (tt) REVERT: F 186 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7643 (mm-30) REVERT: F 223 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7749 (pp30) REVERT: G 140 MET cc_start: 0.5478 (pmm) cc_final: 0.4976 (ppp) REVERT: H 95 SER cc_start: 0.6790 (m) cc_final: 0.6562 (m) outliers start: 45 outliers final: 31 residues processed: 228 average time/residue: 0.1166 time to fit residues: 36.3116 Evaluate side-chains 227 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 0.9980 chunk 135 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 137 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 chunk 136 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 103 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.171806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.149960 restraints weight = 33328.359| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.38 r_work: 0.4044 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11942 Z= 0.176 Angle : 0.760 12.620 16078 Z= 0.390 Chirality : 0.047 0.205 1846 Planarity : 0.005 0.046 2066 Dihedral : 5.526 25.066 1620 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.68 % Allowed : 14.11 % Favored : 85.21 % Rotamer: Outliers : 4.09 % Allowed : 17.09 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.22), residues: 1474 helix: 0.20 (0.20), residues: 716 sheet: -0.70 (0.72), residues: 78 loop : -3.56 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 31 TYR 0.023 0.002 TYR C 156 PHE 0.023 0.001 PHE F 137 TRP 0.011 0.001 TRP A 102 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (11942) covalent geometry : angle 0.76027 / 0.39 (16078) hydrogen bonds : bond 0.04802 / 3.49 ( 582) hydrogen bonds : angle 5.31704 / 3.79 ( 1716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7146 (mmp) cc_final: 0.6668 (mmp) REVERT: B 223 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7741 (pp30) REVERT: C 67 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8020 (ttt-90) REVERT: C 127 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6691 (pttm) REVERT: D 94 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6537 (tt) REVERT: F 77 GLU cc_start: 0.8230 (tp30) cc_final: 0.8029 (tp30) REVERT: F 141 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6407 (mm) REVERT: G 67 ARG cc_start: 0.8410 (ttp80) cc_final: 0.7974 (ttt-90) REVERT: G 76 ARG cc_start: 0.8223 (tpm170) cc_final: 0.8004 (tpm170) REVERT: G 140 MET cc_start: 0.5349 (pmm) cc_final: 0.4846 (ppp) REVERT: G 151 MET cc_start: 0.2332 (tmm) cc_final: 0.0217 (mtt) REVERT: H 80 SER cc_start: 0.3995 (OUTLIER) cc_final: 0.3637 (p) REVERT: H 95 SER cc_start: 0.6884 (m) cc_final: 0.6644 (m) outliers start: 52 outliers final: 32 residues processed: 235 average time/residue: 0.1024 time to fit residues: 33.7210 Evaluate side-chains 232 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 26 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 126 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 103 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** 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 = 0.4617 r_free = 0.4617 target = 0.172422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.150861 restraints weight = 32750.223| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.26 r_work: 0.4029 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11942 Z= 0.189 Angle : 0.771 13.298 16078 Z= 0.397 Chirality : 0.048 0.205 1846 Planarity : 0.005 0.046 2066 Dihedral : 5.597 24.763 1620 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.04 % Favored : 85.35 % Rotamer: Outliers : 4.02 % Allowed : 18.11 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.22), residues: 1474 helix: 0.15 (0.20), residues: 716 sheet: -0.76 (0.71), residues: 78 loop : -3.57 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 31 TYR 0.023 0.002 TYR B 192 PHE 0.019 0.001 PHE F 224 TRP 0.011 0.001 TRP A 102 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (11942) covalent geometry : angle 0.77075 / 0.40 (16078) hydrogen bonds : bond 0.04897 / 3.56 ( 582) hydrogen bonds : angle 5.36681 / 3.83 ( 1716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7164 (mmp) cc_final: 0.6687 (mmp) REVERT: B 137 PHE cc_start: 0.7646 (t80) cc_final: 0.7431 (t80) REVERT: B 223 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7797 (pp30) REVERT: C 67 ARG cc_start: 0.8387 (ttp80) cc_final: 0.7967 (ttt-90) REVERT: C 127 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6748 (pttm) REVERT: C 143 LEU cc_start: 0.6511 (mt) cc_final: 0.6049 (mt) REVERT: D 94 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6534 (tt) REVERT: D 99 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7062 (tp) REVERT: F 141 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6404 (mm) REVERT: F 223 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7753 (pp30) REVERT: G 67 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8017 (ttt-90) REVERT: G 140 MET cc_start: 0.5443 (pmm) cc_final: 0.4961 (ppp) REVERT: H 80 SER cc_start: 0.4062 (OUTLIER) cc_final: 0.3749 (p) REVERT: H 95 SER cc_start: 0.6827 (m) cc_final: 0.6591 (m) outliers start: 51 outliers final: 34 residues processed: 233 average time/residue: 0.1254 time to fit residues: 40.4964 Evaluate side-chains 231 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 83 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 123 optimal weight: 6.9990 chunk 97 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 0.0010 chunk 120 optimal weight: 1.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 103 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.164115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.142631 restraints weight = 33624.227| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 3.28 r_work: 0.4068 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11942 Z= 0.161 Angle : 0.761 11.461 16078 Z= 0.390 Chirality : 0.047 0.213 1846 Planarity : 0.005 0.046 2066 Dihedral : 5.446 24.640 1620 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.54 % Allowed : 13.84 % Favored : 85.62 % Rotamer: Outliers : 4.02 % Allowed : 20.24 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.22), residues: 1474 helix: 0.24 (0.20), residues: 712 sheet: -0.84 (0.71), residues: 78 loop : -3.58 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 31 TYR 0.023 0.002 TYR F 192 PHE 0.014 0.001 PHE F 224 TRP 0.011 0.001 TRP A 102 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11942) covalent geometry : angle 0.76057 / 0.39 (16078) hydrogen bonds : bond 0.04683 / 3.40 ( 582) hydrogen bonds : angle 5.22182 / 3.73 ( 1716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7223 (mmp) cc_final: 0.6749 (mmp) REVERT: B 223 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7811 (pp30) REVERT: C 38 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7130 (mp10) REVERT: C 67 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8108 (ttt-90) REVERT: C 127 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6733 (pttm) REVERT: C 143 LEU cc_start: 0.6483 (mt) cc_final: 0.6030 (mt) REVERT: D 99 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.7002 (tp) REVERT: F 141 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6364 (mm) REVERT: F 223 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: G 67 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8043 (ttt-90) REVERT: G 140 MET cc_start: 0.5617 (pmm) cc_final: 0.5064 (ppp) REVERT: H 80 SER cc_start: 0.4099 (OUTLIER) cc_final: 0.3755 (p) REVERT: H 92 ILE cc_start: 0.3669 (OUTLIER) cc_final: 0.3055 (mm) REVERT: H 95 SER cc_start: 0.6832 (m) cc_final: 0.6614 (m) outliers start: 51 outliers final: 33 residues processed: 229 average time/residue: 0.1055 time to fit residues: 33.9159 Evaluate side-chains 235 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 0.0060 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** 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 = 0.4607 r_free = 0.4607 target = 0.161413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.138424 restraints weight = 35220.024| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 3.45 r_work: 0.4042 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11942 Z= 0.193 Angle : 0.797 13.410 16078 Z= 0.409 Chirality : 0.048 0.245 1846 Planarity : 0.005 0.078 2066 Dihedral : 5.609 24.562 1620 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.25 % Favored : 85.21 % Rotamer: Outliers : 4.41 % Allowed : 20.94 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.21), residues: 1474 helix: 0.10 (0.19), residues: 714 sheet: -0.71 (0.71), residues: 76 loop : -3.59 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 31 TYR 0.027 0.002 TYR B 192 PHE 0.026 0.002 PHE F 137 TRP 0.009 0.001 TRP B 117 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (11942) covalent geometry : angle 0.79670 / 0.41 (16078) hydrogen bonds : bond 0.04937 / 3.58 ( 582) hydrogen bonds : angle 5.36220 / 3.82 ( 1716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7144 (mmp) cc_final: 0.6663 (mmp) REVERT: B 223 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7758 (pp30) REVERT: C 67 ARG cc_start: 0.8359 (ttp80) cc_final: 0.7641 (ttp80) REVERT: C 127 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6825 (pttm) REVERT: C 143 LEU cc_start: 0.6771 (mt) cc_final: 0.6224 (mt) REVERT: D 92 ILE cc_start: 0.3285 (OUTLIER) cc_final: 0.2718 (mm) REVERT: D 99 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6943 (tp) REVERT: D 100 LYS cc_start: 0.7073 (pttm) cc_final: 0.6853 (pttm) REVERT: E 269 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8610 (mm) REVERT: F 141 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6455 (mm) REVERT: F 223 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: G 67 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8069 (ttt-90) REVERT: G 140 MET cc_start: 0.5857 (pmm) cc_final: 0.5240 (ppp) REVERT: H 80 SER cc_start: 0.4254 (OUTLIER) cc_final: 0.3928 (p) REVERT: H 95 SER cc_start: 0.6788 (m) cc_final: 0.6556 (m) outliers start: 56 outliers final: 37 residues processed: 237 average time/residue: 0.1054 time to fit residues: 34.8821 Evaluate side-chains 235 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.0070 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** F 103 GLN ** 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 = 0.4620 r_free = 0.4620 target = 0.172018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.150709 restraints weight = 32385.202| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 3.24 r_work: 0.4040 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11942 Z= 0.188 Angle : 0.802 12.994 16078 Z= 0.411 Chirality : 0.048 0.212 1846 Planarity : 0.005 0.045 2066 Dihedral : 5.604 25.335 1620 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 13.91 % Favored : 85.55 % Rotamer: Outliers : 3.78 % Allowed : 21.89 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.21), residues: 1474 helix: 0.07 (0.19), residues: 712 sheet: -0.76 (0.72), residues: 76 loop : -3.61 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 31 TYR 0.029 0.002 TYR B 192 PHE 0.026 0.001 PHE F 137 TRP 0.009 0.001 TRP B 117 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (11942) covalent geometry : angle 0.80199 / 0.41 (16078) hydrogen bonds : bond 0.04891 / 3.54 ( 582) hydrogen bonds : angle 5.36151 / 3.83 ( 1716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7050 (mmp) cc_final: 0.6579 (mmp) REVERT: C 67 ARG cc_start: 0.8380 (ttp80) cc_final: 0.7724 (ttp80) REVERT: C 127 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6755 (pttm) REVERT: C 143 LEU cc_start: 0.6849 (mt) cc_final: 0.6218 (mt) REVERT: D 92 ILE cc_start: 0.3216 (OUTLIER) cc_final: 0.2621 (mm) REVERT: D 99 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6963 (tp) REVERT: E 269 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8635 (mm) REVERT: F 141 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6507 (mm) REVERT: G 67 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8075 (ttt-90) REVERT: G 140 MET cc_start: 0.5887 (pmm) cc_final: 0.5240 (ppp) REVERT: H 80 SER cc_start: 0.4258 (OUTLIER) cc_final: 0.3909 (p) REVERT: H 95 SER cc_start: 0.6872 (m) cc_final: 0.6636 (m) outliers start: 48 outliers final: 36 residues processed: 225 average time/residue: 0.1006 time to fit residues: 32.0799 Evaluate side-chains 236 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN C 38 GLN ** F 103 GLN ** 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 = 0.4594 r_free = 0.4594 target = 0.167235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.145838 restraints weight = 32858.262| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.15 r_work: 0.4016 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11942 Z= 0.235 Angle : 0.869 14.110 16078 Z= 0.448 Chirality : 0.050 0.236 1846 Planarity : 0.006 0.064 2066 Dihedral : 5.869 25.179 1620 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.93 % Favored : 84.53 % Rotamer: Outliers : 3.78 % Allowed : 22.20 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.21), residues: 1474 helix: -0.11 (0.19), residues: 710 sheet: -0.79 (0.72), residues: 76 loop : -3.62 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 31 TYR 0.034 0.002 TYR B 192 PHE 0.013 0.002 PHE F 224 TRP 0.009 0.001 TRP B 117 HIS 0.005 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (11942) covalent geometry : angle 0.86859 / 0.45 (16078) hydrogen bonds : bond 0.05234 / 3.79 ( 582) hydrogen bonds : angle 5.56034 / 3.95 ( 1716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7216 (mmp) cc_final: 0.6735 (mmp) REVERT: C 127 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6853 (pttm) REVERT: D 92 ILE cc_start: 0.3328 (OUTLIER) cc_final: 0.2703 (mm) REVERT: D 99 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.7023 (tp) REVERT: E 269 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8717 (mm) REVERT: F 141 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6526 (mm) REVERT: H 80 SER cc_start: 0.4338 (OUTLIER) cc_final: 0.4021 (p) REVERT: H 95 SER cc_start: 0.6795 (m) cc_final: 0.6559 (m) outliers start: 48 outliers final: 35 residues processed: 230 average time/residue: 0.1032 time to fit residues: 33.5692 Evaluate side-chains 234 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 0.0020 chunk 1 optimal weight: 0.0040 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 chunk 22 optimal weight: 0.0980 chunk 135 optimal weight: 0.8980 chunk 6 optimal weight: 0.0670 overall best weight: 0.0938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN C 38 GLN C 160 ASN ** F 103 GLN ** 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 = 0.4667 r_free = 0.4667 target = 0.175411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.154889 restraints weight = 32993.412| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 3.23 r_work: 0.4116 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11942 Z= 0.156 Angle : 0.817 10.458 16078 Z= 0.420 Chirality : 0.048 0.196 1846 Planarity : 0.005 0.047 2066 Dihedral : 5.377 24.071 1620 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.54 % Allowed : 13.09 % Favored : 86.36 % Rotamer: Outliers : 2.36 % Allowed : 23.86 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.22), residues: 1474 helix: 0.13 (0.20), residues: 712 sheet: -0.81 (0.71), residues: 76 loop : -3.61 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 31 TYR 0.028 0.002 TYR B 192 PHE 0.023 0.001 PHE B 137 TRP 0.013 0.001 TRP A 102 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (11942) covalent geometry : angle 0.81738 / 0.42 (16078) hydrogen bonds : bond 0.04685 / 3.37 ( 582) hydrogen bonds : angle 5.13165 / 3.67 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3030.07 seconds wall clock time: 52 minutes 46.34 seconds (3166.34 seconds total)