Starting phenix.real_space_refine on Thu Jul 2 08:03:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej6_31153/07_2026/7ej6_31153_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej6_31153/07_2026/7ej6_31153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ej6_31153/07_2026/7ej6_31153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej6_31153/07_2026/7ej6_31153.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej6_31153/07_2026/7ej6_31153_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej6_31153/07_2026/7ej6_31153_trim.cif" } resolution = 3.21 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= 0.001 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4674 2.51 5 N 1326 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7584 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "C" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.84, per 1000 atoms: 0.24 Number of scatterers: 7584 At special positions: 0 Unit cell: (84.96, 97.35, 111.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 18 15.00 Mg 3 11.99 O 1524 8.00 N 1326 7.00 C 4674 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 377.8 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 48.3% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.600A pdb=" N TYR B 25 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 removed outlier: 3.920A pdb=" N LYS B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 61 through 76 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.981A pdb=" N HIS B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 136 " --> pdb=" O HIS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 161 through 171 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 190 through 205 removed outlier: 3.594A pdb=" N VAL B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.727A pdb=" N VAL B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.693A pdb=" N ARG B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.579A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.601A pdb=" N TYR C 25 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 38 removed outlier: 3.920A pdb=" N LYS C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 61 through 76 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.668A pdb=" N VAL C 136 " --> pdb=" O HIS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 161 through 171 Processing helix chain 'C' and resid 175 through 181 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.594A pdb=" N VAL C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 226 removed outlier: 3.727A pdb=" N VAL C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.693A pdb=" N ARG C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 removed outlier: 3.579A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.599A pdb=" N TYR A 25 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 38 removed outlier: 3.919A pdb=" N LYS A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.667A pdb=" N VAL A 136 " --> pdb=" O HIS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.594A pdb=" N VAL A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.727A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.693A pdb=" N ARG A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.579A pdb=" N ALA A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 183 through 187 removed outlier: 5.748A pdb=" N LYS B 150 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 212 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER B 115 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU B 259 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR B 117 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASN B 261 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 119 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 294 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS B 318 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 264 removed outlier: 5.007A pdb=" N LYS B 280 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 183 through 187 removed outlier: 5.747A pdb=" N LYS C 150 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 212 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER C 115 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU C 259 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR C 117 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN C 261 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 119 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG C 294 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS C 318 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 263 through 264 removed outlier: 5.006A pdb=" N LYS C 280 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 187 removed outlier: 5.748A pdb=" N LYS A 150 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 212 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER A 115 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU A 259 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR A 117 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN A 261 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 119 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG A 294 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS A 318 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 264 removed outlier: 5.007A pdb=" N LYS A 280 " --> pdb=" O GLN A 264 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 966 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: 1.04 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2215 1.33 - 1.45: 1087 1.45 - 1.57: 4303 1.57 - 1.69: 32 1.69 - 1.81: 60 Bond restraints: 7697 Sorted by residual: bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C4 ATP C 402 " pdb=" C5 ATP C 402 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.67e+01 bond pdb=" C5 ATP C 402 " pdb=" C6 ATP C 402 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.29e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.28e+01 ... (remaining 7692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 10300 3.80 - 7.60: 98 7.60 - 11.40: 10 11.40 - 15.20: 1 15.20 - 18.99: 6 Bond angle restraints: 10415 Sorted by residual: angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 117.84 18.99 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 117.85 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 117.86 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP C 402 " pdb=" O3B ATP C 402 " pdb=" PG ATP C 402 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.17 18.70 1.00e+00 1.00e+00 3.50e+02 ... (remaining 10410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4134 17.88 - 35.76: 422 35.76 - 53.64: 132 53.64 - 71.53: 13 71.53 - 89.41: 24 Dihedral angle restraints: 4725 sinusoidal: 2037 harmonic: 2688 Sorted by residual: dihedral pdb=" CA PRO B 82 " pdb=" C PRO B 82 " pdb=" N ALA B 83 " pdb=" CA ALA B 83 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO A 82 " pdb=" C PRO A 82 " pdb=" N ALA A 83 " pdb=" CA ALA A 83 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO C 82 " pdb=" C PRO C 82 " pdb=" N ALA C 83 " pdb=" CA ALA C 83 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 996 0.066 - 0.131: 170 0.131 - 0.197: 9 0.197 - 0.263: 6 0.263 - 0.328: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA THR C 128 " pdb=" N THR C 128 " pdb=" C THR C 128 " pdb=" CB THR C 128 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA THR A 128 " pdb=" N THR A 128 " pdb=" C THR A 128 " pdb=" CB THR A 128 " both_signs ideal model delta sigma weight residual False 2.53 2.77 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1179 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 124 " 0.024 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C ARG C 124 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG C 124 " 0.034 2.00e-02 2.50e+03 pdb=" N CYS C 125 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 315 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C MET A 315 " -0.059 2.00e-02 2.50e+03 pdb=" O MET A 315 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 316 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 315 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C MET B 315 " 0.059 2.00e-02 2.50e+03 pdb=" O MET B 315 " -0.022 2.00e-02 2.50e+03 pdb=" N PRO B 316 " -0.020 2.00e-02 2.50e+03 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 217 2.60 - 3.17: 7583 3.17 - 3.75: 11248 3.75 - 4.32: 16575 4.32 - 4.90: 27290 Nonbonded interactions: 62913 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O3B ATP C 401 " model vdw 2.019 2.170 nonbonded pdb=" O3B ATP B 602 " pdb="MG MG A 601 " model vdw 2.020 2.170 nonbonded pdb=" O3B ATP C 402 " pdb="MG MG C 403 " model vdw 2.020 2.170 nonbonded pdb=" O TYR A 94 " pdb=" OG1 THR A 113 " model vdw 2.079 3.040 nonbonded pdb=" O TYR C 94 " pdb=" OG1 THR C 113 " model vdw 2.080 3.040 ... (remaining 62908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 334) selection = (chain 'B' and resid 16 through 334) selection = (chain 'C' and resid 16 through 334) } 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.700 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 7703 Z= 0.493 Angle : 1.037 18.994 10415 Z= 0.775 Chirality : 0.048 0.328 1182 Planarity : 0.004 0.050 1314 Dihedral : 16.919 89.407 3009 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 51.61 Ramachandran Plot: Outliers : 0.74 % Allowed : 12.10 % Favored : 87.15 % Rotamer: Outliers : 1.13 % Allowed : 6.02 % Favored : 92.86 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -4.78 (0.21), residues: 942 helix: -3.46 (0.16), residues: 435 sheet: 0.42 (0.43), residues: 153 loop : -4.39 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 294 TYR 0.010 0.001 TYR C 41 PHE 0.005 0.001 PHE A 123 HIS 0.002 0.000 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00775 / 0.48 ( 7697) covalent geometry : angle 1.03700 / 0.77 (10415) hydrogen bonds : bond 0.20898 / 13.83 ( 340) hydrogen bonds : angle 7.59755 / 5.34 ( 966) Misc. bond : bond 0.03288 / 1.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.295 Fit side-chains REVERT: B 178 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8743 (m) REVERT: C 178 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8834 (t) REVERT: A 127 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: A 178 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8669 (m) outliers start: 9 outliers final: 4 residues processed: 85 average time/residue: 0.0661 time to fit residues: 8.3513 Evaluate side-chains 61 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 178 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 132 HIS B 182 ASN B 194 GLN B 236 GLN B 242 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 132 HIS C 182 ASN C 194 GLN C 236 GLN C 242 HIS ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 194 GLN A 236 GLN A 242 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.058329 restraints weight = 19880.345| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.93 r_work: 0.2757 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7703 Z= 0.162 Angle : 0.736 7.042 10415 Z= 0.387 Chirality : 0.047 0.167 1182 Planarity : 0.005 0.045 1314 Dihedral : 15.859 88.438 1229 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.54 % Favored : 91.83 % Rotamer: Outliers : 1.50 % Allowed : 9.65 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -2.70 (0.25), residues: 942 helix: -1.12 (0.23), residues: 450 sheet: 0.86 (0.43), residues: 147 loop : -3.97 (0.25), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 52 TYR 0.016 0.002 TYR B 94 PHE 0.010 0.001 PHE A 123 HIS 0.004 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 7697) covalent geometry : angle 0.73633 / 0.39 (10415) hydrogen bonds : bond 0.04684 / 3.16 ( 340) hydrogen bonds : angle 5.22405 / 3.68 ( 966) Misc. bond : bond 0.00873 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.299 Fit side-chains REVERT: C 28 ASN cc_start: 0.8309 (p0) cc_final: 0.7851 (p0) REVERT: A 21 GLU cc_start: 0.7827 (mp0) cc_final: 0.7494 (mp0) REVERT: A 28 ASN cc_start: 0.8125 (p0) cc_final: 0.7907 (p0) REVERT: A 41 TYR cc_start: 0.7720 (m-80) cc_final: 0.7509 (m-80) outliers start: 12 outliers final: 2 residues processed: 81 average time/residue: 0.0659 time to fit residues: 8.1496 Evaluate side-chains 54 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain C residue 324 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 63 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.057967 restraints weight = 19812.312| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.92 r_work: 0.2737 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7703 Z= 0.157 Angle : 0.657 7.317 10415 Z= 0.344 Chirality : 0.045 0.162 1182 Planarity : 0.004 0.030 1314 Dihedral : 15.012 85.701 1219 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.48 % Favored : 92.89 % Rotamer: Outliers : 2.76 % Allowed : 11.28 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.27), residues: 942 helix: -0.13 (0.25), residues: 453 sheet: 0.77 (0.43), residues: 147 loop : -3.82 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.012 0.001 TYR B 226 PHE 0.007 0.001 PHE A 123 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 7697) covalent geometry : angle 0.65721 / 0.34 (10415) hydrogen bonds : bond 0.04058 / 2.71 ( 340) hydrogen bonds : angle 4.67334 / 3.28 ( 966) Misc. bond : bond 0.00855 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: C 28 ASN cc_start: 0.8437 (p0) cc_final: 0.8113 (p0) REVERT: C 112 MET cc_start: 0.9086 (mmm) cc_final: 0.8859 (mmp) REVERT: A 21 GLU cc_start: 0.7953 (mp0) cc_final: 0.7568 (mp0) outliers start: 22 outliers final: 8 residues processed: 79 average time/residue: 0.0576 time to fit residues: 7.3388 Evaluate side-chains 60 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.057215 restraints weight = 20041.716| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.96 r_work: 0.2721 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7703 Z= 0.176 Angle : 0.642 8.164 10415 Z= 0.336 Chirality : 0.045 0.160 1182 Planarity : 0.004 0.037 1314 Dihedral : 14.578 82.042 1218 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.54 % Favored : 91.83 % Rotamer: Outliers : 2.76 % Allowed : 11.78 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.27), residues: 942 helix: 0.17 (0.25), residues: 456 sheet: 0.84 (0.44), residues: 147 loop : -3.61 (0.27), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.010 0.001 TYR B 226 PHE 0.009 0.001 PHE A 123 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 7697) covalent geometry : angle 0.64189 / 0.34 (10415) hydrogen bonds : bond 0.03988 / 2.69 ( 340) hydrogen bonds : angle 4.51242 / 3.16 ( 966) Misc. bond : bond 0.00869 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7970 (mmm160) REVERT: C 28 ASN cc_start: 0.8407 (p0) cc_final: 0.8099 (p0) REVERT: C 112 MET cc_start: 0.9071 (mmm) cc_final: 0.8814 (mmp) REVERT: A 21 GLU cc_start: 0.7914 (mp0) cc_final: 0.7607 (mp0) outliers start: 22 outliers final: 12 residues processed: 78 average time/residue: 0.0665 time to fit residues: 7.9662 Evaluate side-chains 68 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.058260 restraints weight = 19942.215| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.96 r_work: 0.2741 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7703 Z= 0.136 Angle : 0.601 8.175 10415 Z= 0.315 Chirality : 0.044 0.159 1182 Planarity : 0.004 0.030 1314 Dihedral : 14.347 78.916 1218 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.79 % Favored : 92.57 % Rotamer: Outliers : 4.01 % Allowed : 10.78 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.28), residues: 942 helix: 0.29 (0.25), residues: 459 sheet: 0.89 (0.45), residues: 144 loop : -3.38 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.014 0.001 TYR A 94 PHE 0.007 0.001 PHE A 123 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7697) covalent geometry : angle 0.60102 / 0.31 (10415) hydrogen bonds : bond 0.03593 / 2.44 ( 340) hydrogen bonds : angle 4.37646 / 3.06 ( 966) Misc. bond : bond 0.00836 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7961 (mp0) cc_final: 0.7650 (mp0) REVERT: A 164 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8632 (tpt170) outliers start: 32 outliers final: 17 residues processed: 90 average time/residue: 0.0639 time to fit residues: 8.8953 Evaluate side-chains 72 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** A 23 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 = 0.3299 r_free = 0.3299 target = 0.076401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.059953 restraints weight = 20087.725| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.00 r_work: 0.2790 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7703 Z= 0.119 Angle : 0.613 9.459 10415 Z= 0.314 Chirality : 0.043 0.156 1182 Planarity : 0.004 0.029 1314 Dihedral : 14.000 73.161 1218 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.11 % Favored : 92.36 % Rotamer: Outliers : 2.51 % Allowed : 12.53 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.28), residues: 942 helix: 0.37 (0.25), residues: 465 sheet: 0.77 (0.45), residues: 147 loop : -3.28 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.009 0.001 TYR C 41 PHE 0.007 0.001 PHE A 253 HIS 0.002 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 7697) covalent geometry : angle 0.61346 / 0.31 (10415) hydrogen bonds : bond 0.03109 / 2.13 ( 340) hydrogen bonds : angle 4.21496 / 2.93 ( 966) Misc. bond : bond 0.00812 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.347 Fit side-chains REVERT: B 164 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8468 (tpt170) REVERT: A 21 GLU cc_start: 0.7955 (mp0) cc_final: 0.7697 (mp0) REVERT: A 144 MET cc_start: 0.9000 (mmm) cc_final: 0.8694 (mtp) REVERT: A 164 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8681 (tpt170) outliers start: 20 outliers final: 9 residues processed: 76 average time/residue: 0.0671 time to fit residues: 7.7492 Evaluate side-chains 65 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.059428 restraints weight = 20056.796| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.99 r_work: 0.2777 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7703 Z= 0.125 Angle : 0.600 8.612 10415 Z= 0.308 Chirality : 0.043 0.162 1182 Planarity : 0.004 0.029 1314 Dihedral : 13.905 72.107 1218 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.26 % Favored : 93.21 % Rotamer: Outliers : 2.63 % Allowed : 12.78 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.28), residues: 942 helix: 0.46 (0.25), residues: 465 sheet: 0.82 (0.45), residues: 147 loop : -3.22 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 124 TYR 0.006 0.001 TYR A 226 PHE 0.005 0.001 PHE A 253 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7697) covalent geometry : angle 0.59996 / 0.31 (10415) hydrogen bonds : bond 0.03296 / 2.26 ( 340) hydrogen bonds : angle 4.18601 / 2.90 ( 966) Misc. bond : bond 0.00798 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8440 (tpt170) REVERT: A 144 MET cc_start: 0.9011 (mmm) cc_final: 0.8724 (mtp) REVERT: A 164 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8649 (tpt170) outliers start: 21 outliers final: 16 residues processed: 75 average time/residue: 0.0686 time to fit residues: 7.8385 Evaluate side-chains 74 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.0000 chunk 89 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 28 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.9166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.076768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.060075 restraints weight = 20066.729| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.01 r_work: 0.2791 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7703 Z= 0.120 Angle : 0.585 9.243 10415 Z= 0.302 Chirality : 0.043 0.163 1182 Planarity : 0.003 0.029 1314 Dihedral : 13.719 72.559 1218 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.37 % Favored : 93.10 % Rotamer: Outliers : 2.38 % Allowed : 13.66 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.28), residues: 942 helix: 0.48 (0.25), residues: 465 sheet: 0.81 (0.45), residues: 147 loop : -3.14 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.008 0.001 TYR A 94 PHE 0.005 0.001 PHE A 253 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 7697) covalent geometry : angle 0.58485 / 0.30 (10415) hydrogen bonds : bond 0.03105 / 2.12 ( 340) hydrogen bonds : angle 4.11353 / 2.86 ( 966) Misc. bond : bond 0.00784 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.295 Fit side-chains REVERT: B 164 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8447 (tpt170) REVERT: B 200 GLN cc_start: 0.8570 (mt0) cc_final: 0.8362 (mm110) REVERT: A 74 LYS cc_start: 0.9174 (mmtp) cc_final: 0.8954 (mttt) REVERT: A 144 MET cc_start: 0.8996 (mmm) cc_final: 0.8713 (mtp) REVERT: A 164 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8642 (tpt170) REVERT: A 200 GLN cc_start: 0.8576 (mt0) cc_final: 0.8344 (mm110) outliers start: 19 outliers final: 16 residues processed: 77 average time/residue: 0.0707 time to fit residues: 8.1762 Evaluate side-chains 75 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 43 optimal weight: 0.0030 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.077945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061673 restraints weight = 19925.722| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.95 r_work: 0.2823 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7703 Z= 0.108 Angle : 0.586 10.941 10415 Z= 0.297 Chirality : 0.042 0.152 1182 Planarity : 0.003 0.027 1314 Dihedral : 13.445 71.634 1218 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.16 % Favored : 93.31 % Rotamer: Outliers : 2.38 % Allowed : 14.04 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.28), residues: 942 helix: 0.56 (0.25), residues: 465 sheet: 0.80 (0.46), residues: 147 loop : -3.10 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 124 TYR 0.006 0.001 TYR A 94 PHE 0.005 0.001 PHE A 253 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 7697) covalent geometry : angle 0.58597 / 0.30 (10415) hydrogen bonds : bond 0.02867 / 1.94 ( 340) hydrogen bonds : angle 4.01962 / 2.78 ( 966) Misc. bond : bond 0.00758 / 0.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8470 (tpt170) REVERT: B 315 MET cc_start: 0.7785 (mmm) cc_final: 0.7585 (mmm) REVERT: C 200 GLN cc_start: 0.8535 (mt0) cc_final: 0.8276 (mm-40) REVERT: A 144 MET cc_start: 0.8969 (mmm) cc_final: 0.8691 (mtp) REVERT: A 164 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8675 (tpt170) REVERT: A 200 GLN cc_start: 0.8531 (mt0) cc_final: 0.8282 (mm110) outliers start: 19 outliers final: 14 residues processed: 76 average time/residue: 0.0746 time to fit residues: 8.3888 Evaluate side-chains 73 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.060535 restraints weight = 19909.458| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.01 r_work: 0.2801 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7703 Z= 0.125 Angle : 0.594 9.175 10415 Z= 0.302 Chirality : 0.043 0.167 1182 Planarity : 0.003 0.029 1314 Dihedral : 13.485 71.887 1218 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.48 % Favored : 92.99 % Rotamer: Outliers : 2.26 % Allowed : 14.41 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.28), residues: 942 helix: 0.57 (0.25), residues: 465 sheet: 0.85 (0.45), residues: 147 loop : -3.01 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.007 0.001 TYR A 226 PHE 0.005 0.001 PHE B 123 HIS 0.002 0.000 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7697) covalent geometry : angle 0.59370 / 0.30 (10415) hydrogen bonds : bond 0.03120 / 2.11 ( 340) hydrogen bonds : angle 4.04093 / 2.80 ( 966) Misc. bond : bond 0.00774 / 0.40 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8447 (tpt170) REVERT: A 144 MET cc_start: 0.9030 (mmm) cc_final: 0.8766 (mtp) REVERT: A 164 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8642 (tpt170) REVERT: A 200 GLN cc_start: 0.8548 (mt0) cc_final: 0.8311 (mm110) outliers start: 18 outliers final: 16 residues processed: 79 average time/residue: 0.0736 time to fit residues: 8.7059 Evaluate side-chains 75 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.076893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.060439 restraints weight = 19792.732| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.00 r_work: 0.2793 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7703 Z= 0.126 Angle : 0.603 8.837 10415 Z= 0.307 Chirality : 0.043 0.164 1182 Planarity : 0.003 0.029 1314 Dihedral : 13.482 72.922 1218 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.26 % Favored : 93.21 % Rotamer: Outliers : 2.38 % Allowed : 14.41 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.28), residues: 942 helix: 0.62 (0.25), residues: 465 sheet: 0.84 (0.45), residues: 147 loop : -2.97 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.008 0.001 TYR A 94 PHE 0.005 0.001 PHE B 123 HIS 0.001 0.000 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7697) covalent geometry : angle 0.60315 / 0.31 (10415) hydrogen bonds : bond 0.03136 / 2.11 ( 340) hydrogen bonds : angle 4.04798 / 2.80 ( 966) Misc. bond : bond 0.00780 / 0.40 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.48 seconds wall clock time: 30 minutes 13.68 seconds (1813.68 seconds total)