Starting phenix.real_space_refine on Fri Oct 23 01:44:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej6_31153/10_2026/7ej6_31153_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej6_31153/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ej6_31153/10_2026/7ej6_31153_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej6_31153/10_2026/7ej6_31153_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ej6_31153/10_2026/7ej6_31153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej6_31153/10_2026/7ej6_31153.map" } 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-2.3rc1-6221/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: 1.96, per 1000 atoms: 0.26 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: 0.75 Conformation dependent library (CDL) restraints added in 418.7 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: 0.24 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: 1.17 Time building geometry restraints manager: 0.92 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: 5.360 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: 8.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- 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 : 51.68 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 1.03717 / 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 : 0.269 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: 0.0714 time to fit residues: 9.0680 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 : 0.288 ------------------------------------------------------------------------------- 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: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] 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 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 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 = 0.3273 r_free = 0.3273 target = 0.075004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058683 restraints weight = 19996.144| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.94 r_work: 0.2770 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2078 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= 0.166 Angle : 0.740 7.115 10415 Z= 0.392 Chirality : 0.047 0.167 1182 Planarity : 0.005 0.044 1314 Dihedral : 15.747 88.473 1229 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Rotamer: Outliers : 1.75 % Allowed : 10.03 % Favored : 88.22 % 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: -2.68 (0.25), residues: 942 helix: -1.10 (0.23), residues: 450 sheet: 0.86 (0.43), residues: 147 loop : -3.96 (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 C 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 0.00331 / 0.16 ( 7697) covalent geometry : angle 0.74049 / 0.39 (10415) hydrogen bonds : bond 0.04575 / 3.09 ( 340) hydrogen bonds : angle 5.19447 / 3.65 ( 966) Misc. bond : bond 0.00831 / 0.42 ( 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 82 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.320 Fit side-chains REVERT: C 28 ASN cc_start: 0.8307 (p0) cc_final: 0.7842 (p0) REVERT: A 21 GLU cc_start: 0.7860 (mp0) cc_final: 0.7564 (mp0) REVERT: A 28 ASN cc_start: 0.8131 (p0) cc_final: 0.7905 (p0) REVERT: A 41 TYR cc_start: 0.7737 (m-80) cc_final: 0.7536 (m-80) REVERT: A 201 LEU cc_start: 0.9548 (tp) cc_final: 0.9267 (tp) outliers start: 14 outliers final: 2 residues processed: 82 average time/residue: 0.0637 time to fit residues: 7.9274 Evaluate side-chains 56 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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: [19, 68, 35, 6, 8, 57, 23, 63, 83, 38, 81] chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.075888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.059523 restraints weight = 19797.135| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.94 r_work: 0.2785 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2611 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= 0.132 Angle : 0.640 7.373 10415 Z= 0.335 Chirality : 0.045 0.162 1182 Planarity : 0.004 0.029 1314 Dihedral : 14.931 86.270 1219 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.94 % Favored : 93.42 % Rotamer: Outliers : 2.26 % Allowed : 11.03 % Favored : 86.72 % 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: -1.82 (0.27), residues: 942 helix: -0.02 (0.25), residues: 453 sheet: 0.64 (0.43), residues: 147 loop : -3.83 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.013 0.001 TYR B 226 PHE 0.005 0.001 PHE B 80 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 7697) covalent geometry : angle 0.63973 / 0.34 (10415) hydrogen bonds : bond 0.03770 / 2.56 ( 340) hydrogen bonds : angle 4.58515 / 3.21 ( 966) Misc. bond : bond 0.00822 / 0.43 ( 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 78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.321 Fit side-chains REVERT: C 28 ASN cc_start: 0.8358 (p0) cc_final: 0.8000 (p0) REVERT: A 21 GLU cc_start: 0.7915 (mp0) cc_final: 0.7596 (mp0) outliers start: 18 outliers final: 4 residues processed: 77 average time/residue: 0.0510 time to fit residues: 6.4155 Evaluate side-chains 55 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 95 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [23, 22, 10, 13, 6, 64, 34, 70, 24, 7, 37] chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.074651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.058278 restraints weight = 20087.520| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.98 r_work: 0.2747 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7703 Z= 0.156 Angle : 0.620 8.246 10415 Z= 0.324 Chirality : 0.044 0.159 1182 Planarity : 0.004 0.030 1314 Dihedral : 14.549 83.342 1218 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.22 % Favored : 92.14 % Rotamer: Outliers : 2.63 % Allowed : 11.40 % 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: -1.51 (0.27), residues: 942 helix: 0.22 (0.26), residues: 456 sheet: 0.72 (0.44), residues: 147 loop : -3.63 (0.27), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.011 0.001 TYR B 226 PHE 0.008 0.001 PHE A 123 HIS 0.001 0.000 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7697) covalent geometry : angle 0.61988 / 0.32 (10415) hydrogen bonds : bond 0.03802 / 2.57 ( 340) hydrogen bonds : angle 4.46972 / 3.13 ( 966) Misc. bond : bond 0.00832 / 0.43 ( 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 78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: C 28 ASN cc_start: 0.8404 (p0) cc_final: 0.8081 (p0) outliers start: 21 outliers final: 9 residues processed: 76 average time/residue: 0.0551 time to fit residues: 6.8407 Evaluate side-chains 61 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 255 VAL 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 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [69, 33, 22, 53, 27, 42, 36, 10, 8, 77, 74] chunk 69 optimal weight: 5.9990 chunk 33 optimal weight: 0.0370 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.076384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.060002 restraints weight = 19935.114| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.00 r_work: 0.2788 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7703 Z= 0.120 Angle : 0.588 8.072 10415 Z= 0.306 Chirality : 0.043 0.151 1182 Planarity : 0.004 0.029 1314 Dihedral : 14.189 79.299 1218 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.26 % Favored : 93.10 % 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: -1.24 (0.27), residues: 942 helix: 0.34 (0.25), residues: 459 sheet: 0.76 (0.44), residues: 147 loop : -3.32 (0.27), residues: 336 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 0.005 0.001 PHE A 123 HIS 0.002 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 7697) covalent geometry : angle 0.58827 / 0.31 (10415) hydrogen bonds : bond 0.03233 / 2.21 ( 340) hydrogen bonds : angle 4.30406 / 3.01 ( 966) Misc. bond : bond 0.00811 / 0.42 ( 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 88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7974 (mmm160) REVERT: A 164 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8653 (tpt170) outliers start: 32 outliers final: 13 residues processed: 84 average time/residue: 0.0677 time to fit residues: 8.6838 Evaluate side-chains 67 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain C residue 212 LEU 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 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: [38, 90, 43, 20, 4, 18, 41, 51, 67, 25, 64] chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.074882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.058281 restraints weight = 20188.471| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.00 r_work: 0.2748 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7703 Z= 0.156 Angle : 0.621 8.236 10415 Z= 0.321 Chirality : 0.044 0.197 1182 Planarity : 0.004 0.031 1314 Dihedral : 14.165 74.927 1218 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.48 % Favored : 92.89 % Rotamer: Outliers : 3.38 % Allowed : 11.53 % Favored : 85.09 % 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: -1.08 (0.28), residues: 942 helix: 0.36 (0.25), residues: 465 sheet: 0.92 (0.45), residues: 147 loop : -3.16 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.007 0.001 TYR A 94 PHE 0.007 0.001 PHE A 123 HIS 0.002 0.000 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7697) covalent geometry : angle 0.62100 / 0.32 (10415) hydrogen bonds : bond 0.03638 / 2.48 ( 340) hydrogen bonds : angle 4.32180 / 3.02 ( 966) Misc. bond : bond 0.00826 / 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 78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7943 (mmm160) REVERT: C 144 MET cc_start: 0.8809 (mtt) cc_final: 0.8583 (mtt) REVERT: A 164 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8642 (tpt170) outliers start: 27 outliers final: 15 residues processed: 75 average time/residue: 0.0662 time to fit residues: 7.5298 Evaluate side-chains 67 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 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 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 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 324 ILE Chi-restraints excluded: chain A residue 95 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [87, 82, 71, 31, 21, 48, 85, 76, 72, 30, 55] chunk 87 optimal weight: 0.0000 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.075432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.058914 restraints weight = 20108.162| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.00 r_work: 0.2761 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7703 Z= 0.136 Angle : 0.608 8.331 10415 Z= 0.311 Chirality : 0.043 0.164 1182 Planarity : 0.004 0.029 1314 Dihedral : 13.976 73.529 1218 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.37 % Favored : 92.99 % Rotamer: Outliers : 2.76 % Allowed : 11.90 % Favored : 85.34 % 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: -1.05 (0.28), residues: 942 helix: 0.40 (0.25), residues: 465 sheet: 0.90 (0.45), residues: 147 loop : -3.16 (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 0.006 0.001 PHE B 123 HIS 0.001 0.000 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7697) covalent geometry : angle 0.60816 / 0.31 (10415) hydrogen bonds : bond 0.03426 / 2.35 ( 340) hydrogen bonds : angle 4.24959 / 2.96 ( 966) Misc. bond : bond 0.00814 / 0.42 ( 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 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7966 (mmm160) REVERT: A 144 MET cc_start: 0.9028 (mmm) cc_final: 0.8695 (mtp) REVERT: A 164 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8665 (tpt170) outliers start: 22 outliers final: 18 residues processed: 76 average time/residue: 0.0677 time to fit residues: 7.5973 Evaluate side-chains 70 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 93 VAL 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 95 SER 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: [83, 89, 1, 0, 57, 70, 28, 47, 72, 27, 31] chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 28 optimal weight: 0.0270 chunk 47 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 overall best weight: 1.5442 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.075322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.058608 restraints weight = 20144.582| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.02 r_work: 0.2757 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7703 Z= 0.143 Angle : 0.615 9.282 10415 Z= 0.314 Chirality : 0.044 0.192 1182 Planarity : 0.004 0.031 1314 Dihedral : 13.908 74.341 1218 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.37 % Favored : 92.99 % Rotamer: Outliers : 3.13 % Allowed : 12.66 % Favored : 84.21 % 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: -1.02 (0.28), residues: 942 helix: 0.40 (0.25), residues: 465 sheet: 0.90 (0.45), residues: 147 loop : -3.09 (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 0.006 0.001 PHE B 123 HIS 0.001 0.000 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7697) covalent geometry : angle 0.61478 / 0.31 (10415) hydrogen bonds : bond 0.03525 / 2.42 ( 340) hydrogen bonds : angle 4.23026 / 2.95 ( 966) Misc. bond : bond 0.00811 / 0.42 ( 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 82 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7964 (mmm160) REVERT: A 144 MET cc_start: 0.9039 (mmm) cc_final: 0.8720 (mtp) REVERT: A 164 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8685 (tpt170) outliers start: 25 outliers final: 17 residues processed: 78 average time/residue: 0.0665 time to fit residues: 7.9168 Evaluate side-chains 71 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 95 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [76, 50, 23, 43, 30, 12, 67, 48, 69, 40, 37] chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.059468 restraints weight = 20260.993| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.03 r_work: 0.2772 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3401 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= 0.124 Angle : 0.617 11.150 10415 Z= 0.310 Chirality : 0.044 0.276 1182 Planarity : 0.004 0.028 1314 Dihedral : 13.716 73.940 1218 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.37 % Favored : 93.10 % Rotamer: Outliers : 2.88 % Allowed : 14.29 % Favored : 82.83 % 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: -0.98 (0.28), residues: 942 helix: 0.48 (0.25), residues: 465 sheet: 0.83 (0.45), residues: 147 loop : -3.10 (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 0.008 0.001 PHE C 253 HIS 0.001 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7697) covalent geometry : angle 0.61689 / 0.31 (10415) hydrogen bonds : bond 0.03299 / 2.28 ( 340) hydrogen bonds : angle 4.16998 / 2.92 ( 966) Misc. bond : bond 0.00798 / 0.42 ( 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 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8421 (tpt170) REVERT: C 200 GLN cc_start: 0.8554 (mt0) cc_final: 0.8196 (mm-40) REVERT: A 144 MET cc_start: 0.9058 (mmm) cc_final: 0.8740 (mtp) REVERT: A 164 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8691 (tpt170) REVERT: A 200 GLN cc_start: 0.8554 (mt0) cc_final: 0.8315 (mm110) outliers start: 23 outliers final: 17 residues processed: 77 average time/residue: 0.0620 time to fit residues: 7.2149 Evaluate side-chains 74 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 B residue 324 ILE Chi-restraints excluded: chain C residue 113 THR 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 95 SER 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 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [64, 20, 45, 60, 58, 87, 54, 67, 0, 92, 13] chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059888 restraints weight = 20106.834| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.02 r_work: 0.2778 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7703 Z= 0.126 Angle : 0.617 10.431 10415 Z= 0.310 Chirality : 0.044 0.248 1182 Planarity : 0.004 0.029 1314 Dihedral : 13.679 73.806 1218 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.58 % Favored : 92.89 % 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: -0.92 (0.28), residues: 942 helix: 0.54 (0.25), residues: 465 sheet: 0.82 (0.45), residues: 147 loop : -3.06 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.012 0.001 TYR C 41 PHE 0.007 0.001 PHE C 253 HIS 0.001 0.000 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7697) covalent geometry : angle 0.61674 / 0.31 (10415) hydrogen bonds : bond 0.03350 / 2.31 ( 340) hydrogen bonds : angle 4.13421 / 2.89 ( 966) Misc. bond : bond 0.00793 / 0.41 ( 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 78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8417 (tpt170) REVERT: C 200 GLN cc_start: 0.8535 (mt0) cc_final: 0.8293 (mm-40) REVERT: A 144 MET cc_start: 0.9045 (mmm) cc_final: 0.8713 (mtp) REVERT: A 164 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8702 (tpt170) REVERT: A 200 GLN cc_start: 0.8495 (mt0) cc_final: 0.8289 (mm110) outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.0667 time to fit residues: 7.7234 Evaluate side-chains 74 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 95 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: [92, 2, 77, 24, 22, 48, 14, 8, 52, 9, 72] chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.074936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.058305 restraints weight = 19901.777| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.02 r_work: 0.2742 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7703 Z= 0.165 Angle : 0.650 10.526 10415 Z= 0.328 Chirality : 0.045 0.248 1182 Planarity : 0.004 0.035 1314 Dihedral : 13.914 75.122 1218 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.79 % Favored : 92.57 % Rotamer: Outliers : 2.38 % Allowed : 14.66 % Favored : 82.96 % 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: -0.90 (0.28), residues: 942 helix: 0.52 (0.25), residues: 465 sheet: 0.89 (0.44), residues: 147 loop : -3.04 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 142 TYR 0.011 0.001 TYR C 41 PHE 0.007 0.001 PHE B 123 HIS 0.002 0.000 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 7697) covalent geometry : angle 0.64996 / 0.33 (10415) hydrogen bonds : bond 0.03755 / 2.55 ( 340) hydrogen bonds : angle 4.23769 / 2.97 ( 966) Misc. bond : bond 0.00828 / 0.43 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1534.94 seconds wall clock time: 27 minutes 10.97 seconds (1630.97 seconds total)