Starting phenix.real_space_refine on Tue Mar 3 17:52:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej6_31153/03_2026/7ej6_31153_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej6_31153/03_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_31153/03_2026/7ej6_31153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej6_31153/03_2026/7ej6_31153.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej6_31153/03_2026/7ej6_31153_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej6_31153/03_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-5986/lib/python3.9/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: 1.81, 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: 0.96 Conformation dependent library (CDL) restraints added in 292.4 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: 0.32 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: 1.31 Time building geometry restraints manager: 1.17 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: 1002 0.066 - 0.131: 164 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: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.200 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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= 0.468 Angle : 1.028 18.994 10415 Z= 0.749 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 covalent geometry : bond 0.00777 ( 7697) covalent geometry : angle 1.02792 (10415) hydrogen bonds : bond 0.20898 ( 340) hydrogen bonds : angle 7.59755 ( 966) Misc. bond : bond 0.03288 ( 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 : 0.210 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: 0.0683 time to fit residues: 8.5880 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 : 0.238 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 132 HIS C 182 ASN C 194 GLN C 236 GLN C 242 HIS C 264 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.075913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.059649 restraints weight = 20033.944| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.95 r_work: 0.2787 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7703 Z= 0.141 Angle : 0.706 8.258 10415 Z= 0.369 Chirality : 0.046 0.166 1182 Planarity : 0.005 0.033 1314 Dihedral : 15.241 86.982 1229 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.75 % Favored : 91.61 % Rotamer: Outliers : 1.75 % Allowed : 10.90 % Favored : 87.34 % 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: -2.66 (0.25), residues: 942 helix: -1.07 (0.23), residues: 450 sheet: 0.84 (0.44), residues: 147 loop : -3.94 (0.26), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 52 TYR 0.014 0.001 TYR C 94 PHE 0.005 0.001 PHE C 80 HIS 0.003 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7697) covalent geometry : angle 0.70604 (10415) hydrogen bonds : bond 0.03942 ( 340) hydrogen bonds : angle 4.97713 ( 966) Misc. bond : bond 0.00875 ( 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 87 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.244 Fit side-chains REVERT: C 28 ASN cc_start: 0.8405 (p0) cc_final: 0.8074 (p0) outliers start: 14 outliers final: 2 residues processed: 87 average time/residue: 0.0654 time to fit residues: 8.5796 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 : 0.307 ------------------------------------------------------------------------------- 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: 0.4980 chunk 68 optimal weight: 0.4980 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.059503 restraints weight = 19870.584| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.96 r_work: 0.2788 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2855 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= 0.131 Angle : 0.609 6.668 10415 Z= 0.321 Chirality : 0.044 0.157 1182 Planarity : 0.004 0.030 1314 Dihedral : 14.211 81.674 1219 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.52 % Favored : 93.84 % Rotamer: Outliers : 2.26 % Allowed : 13.16 % 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: -1.65 (0.27), residues: 942 helix: 0.11 (0.26), residues: 450 sheet: 0.53 (0.42), residues: 153 loop : -3.67 (0.26), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 187 TYR 0.011 0.001 TYR B 226 PHE 0.007 0.001 PHE A 123 HIS 0.002 0.000 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7697) covalent geometry : angle 0.60932 (10415) hydrogen bonds : bond 0.03509 ( 340) hydrogen bonds : angle 4.45826 ( 966) Misc. bond : bond 0.00791 ( 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: 18 poor density : 62 time to evaluate : 0.273 Fit side-chains REVERT: C 28 ASN cc_start: 0.8378 (p0) cc_final: 0.8122 (p0) outliers start: 18 outliers final: 5 residues processed: 78 average time/residue: 0.0515 time to fit residues: 6.5548 Evaluate side-chains 57 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3257 r_free = 0.3257 target = 0.074400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.058054 restraints weight = 20074.549| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.94 r_work: 0.2742 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7703 Z= 0.168 Angle : 0.620 6.411 10415 Z= 0.323 Chirality : 0.045 0.193 1182 Planarity : 0.004 0.035 1314 Dihedral : 14.004 75.026 1218 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.11 % Favored : 92.25 % Rotamer: Outliers : 2.88 % Allowed : 12.66 % Favored : 84.46 % 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: -1.35 (0.27), residues: 942 helix: 0.27 (0.25), residues: 456 sheet: 0.90 (0.44), residues: 147 loop : -3.48 (0.26), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 187 TYR 0.009 0.001 TYR C 94 PHE 0.008 0.001 PHE A 123 HIS 0.002 0.000 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7697) covalent geometry : angle 0.61982 (10415) hydrogen bonds : bond 0.03807 ( 340) hydrogen bonds : angle 4.43563 ( 966) Misc. bond : bond 0.00832 ( 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 76 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8158 (t80) cc_final: 0.7928 (t80) outliers start: 23 outliers final: 12 residues processed: 73 average time/residue: 0.0537 time to fit residues: 6.4130 Evaluate side-chains 62 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 197 LEU 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 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 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3244 r_free = 0.3244 target = 0.073881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.057417 restraints weight = 20222.060| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.98 r_work: 0.2721 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7703 Z= 0.175 Angle : 0.611 6.732 10415 Z= 0.321 Chirality : 0.044 0.201 1182 Planarity : 0.004 0.036 1314 Dihedral : 14.054 76.274 1218 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.05 % Favored : 93.31 % Rotamer: Outliers : 3.38 % Allowed : 13.03 % 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: -1.21 (0.28), residues: 942 helix: 0.36 (0.25), residues: 459 sheet: 0.71 (0.44), residues: 153 loop : -3.33 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.009 0.001 TYR B 94 PHE 0.007 0.001 PHE A 123 HIS 0.002 0.000 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 7697) covalent geometry : angle 0.61098 (10415) hydrogen bonds : bond 0.03801 ( 340) hydrogen bonds : angle 4.38332 ( 966) Misc. bond : bond 0.00860 ( 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 83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.9082 (mmm) cc_final: 0.8756 (mtp) outliers start: 27 outliers final: 16 residues processed: 81 average time/residue: 0.0557 time to fit residues: 7.1845 Evaluate side-chains 67 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 113 THR Chi-restraints excluded: chain C residue 125 CYS 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 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: 4.9990 chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055880 restraints weight = 20319.261| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.98 r_work: 0.2690 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7703 Z= 0.234 Angle : 0.663 7.099 10415 Z= 0.347 Chirality : 0.046 0.232 1182 Planarity : 0.005 0.053 1314 Dihedral : 14.720 78.742 1218 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Rotamer: Outliers : 2.76 % Allowed : 13.28 % 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: -1.32 (0.27), residues: 942 helix: 0.25 (0.25), residues: 456 sheet: 0.45 (0.44), residues: 159 loop : -3.27 (0.29), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.013 0.001 TYR A 94 PHE 0.008 0.001 PHE A 123 HIS 0.002 0.000 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 7697) covalent geometry : angle 0.66251 (10415) hydrogen bonds : bond 0.04299 ( 340) hydrogen bonds : angle 4.53887 ( 966) Misc. bond : bond 0.00903 ( 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 77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.7890 (mmm160) REVERT: A 144 MET cc_start: 0.9031 (mmm) cc_final: 0.8736 (mtp) outliers start: 22 outliers final: 14 residues processed: 73 average time/residue: 0.0581 time to fit residues: 6.7197 Evaluate side-chains 64 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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 113 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.057170 restraints weight = 20243.192| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.93 r_work: 0.2710 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7703 Z= 0.187 Angle : 0.628 7.438 10415 Z= 0.329 Chirality : 0.045 0.206 1182 Planarity : 0.004 0.036 1314 Dihedral : 14.627 81.012 1218 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.37 % Favored : 92.99 % Rotamer: Outliers : 3.38 % Allowed : 13.03 % 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: -1.13 (0.27), residues: 942 helix: 0.37 (0.25), residues: 456 sheet: 0.93 (0.44), residues: 147 loop : -3.20 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.012 0.001 TYR A 94 PHE 0.006 0.001 PHE A 123 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7697) covalent geometry : angle 0.62831 (10415) hydrogen bonds : bond 0.03863 ( 340) hydrogen bonds : angle 4.38845 ( 966) Misc. bond : bond 0.00863 ( 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 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7950 (mmm160) REVERT: B 317 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: A 144 MET cc_start: 0.9036 (mmm) cc_final: 0.8789 (mtp) REVERT: A 164 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8658 (tpt170) outliers start: 27 outliers final: 22 residues processed: 79 average time/residue: 0.0699 time to fit residues: 8.2509 Evaluate side-chains 74 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 317 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 106 ILE 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 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 Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.057984 restraints weight = 20197.880| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.00 r_work: 0.2740 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3406 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= 0.146 Angle : 0.615 7.989 10415 Z= 0.318 Chirality : 0.044 0.186 1182 Planarity : 0.004 0.030 1314 Dihedral : 14.317 77.449 1218 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.16 % Favored : 93.21 % Rotamer: Outliers : 3.01 % Allowed : 13.28 % Favored : 83.71 % 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 (0.27), residues: 942 helix: 0.44 (0.25), residues: 456 sheet: 0.89 (0.45), residues: 147 loop : -3.15 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.010 0.001 TYR A 94 PHE 0.008 0.001 PHE A 253 HIS 0.002 0.000 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7697) covalent geometry : angle 0.61458 (10415) hydrogen bonds : bond 0.03536 ( 340) hydrogen bonds : angle 4.28761 ( 966) Misc. bond : bond 0.00828 ( 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 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8014 (mmm160) REVERT: B 317 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: A 144 MET cc_start: 0.9017 (mmm) cc_final: 0.8763 (mtp) REVERT: A 164 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8681 (tpt170) outliers start: 24 outliers final: 20 residues processed: 75 average time/residue: 0.0648 time to fit residues: 7.3841 Evaluate side-chains 74 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 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 179 CYS 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 317 GLU Chi-restraints excluded: chain C residue 106 ILE 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 317 GLU 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 Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.057768 restraints weight = 20172.817| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.01 r_work: 0.2728 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3441 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= 0.162 Angle : 0.625 8.371 10415 Z= 0.324 Chirality : 0.044 0.197 1182 Planarity : 0.004 0.033 1314 Dihedral : 14.349 79.514 1218 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.37 % Favored : 92.99 % Rotamer: Outliers : 3.51 % Allowed : 13.41 % Favored : 83.08 % 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: -1.04 (0.27), residues: 942 helix: 0.49 (0.25), residues: 456 sheet: 0.90 (0.45), residues: 147 loop : -3.19 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.011 0.001 TYR A 94 PHE 0.007 0.001 PHE A 253 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7697) covalent geometry : angle 0.62470 (10415) hydrogen bonds : bond 0.03713 ( 340) hydrogen bonds : angle 4.29640 ( 966) Misc. bond : bond 0.00834 ( 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 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7968 (mmm160) REVERT: B 317 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: A 94 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7358 (t80) REVERT: A 144 MET cc_start: 0.9056 (mmm) cc_final: 0.8787 (mtp) REVERT: A 164 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8662 (tpt170) outliers start: 28 outliers final: 24 residues processed: 73 average time/residue: 0.0656 time to fit residues: 7.2338 Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 179 CYS 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 317 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 94 TYR 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 Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 272 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: chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.075926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.059435 restraints weight = 20163.280| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.02 r_work: 0.2768 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3650 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= 0.129 Angle : 0.594 8.726 10415 Z= 0.307 Chirality : 0.043 0.174 1182 Planarity : 0.004 0.037 1314 Dihedral : 13.766 74.841 1218 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.94 % Favored : 93.42 % Rotamer: Outliers : 3.26 % Allowed : 13.78 % 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: -0.93 (0.28), residues: 942 helix: 0.65 (0.25), residues: 456 sheet: 0.87 (0.45), residues: 147 loop : -3.21 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.008 0.001 TYR A 94 PHE 0.007 0.001 PHE A 253 HIS 0.002 0.000 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7697) covalent geometry : angle 0.59380 (10415) hydrogen bonds : bond 0.03263 ( 340) hydrogen bonds : angle 4.16687 ( 966) Misc. bond : bond 0.00786 ( 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 83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8532 (tpt170) REVERT: A 144 MET cc_start: 0.9036 (mmm) cc_final: 0.8753 (mtp) REVERT: A 164 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8722 (tpt170) outliers start: 26 outliers final: 20 residues processed: 78 average time/residue: 0.0715 time to fit residues: 8.0875 Evaluate side-chains 73 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 179 CYS 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 113 THR Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 317 GLU 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 Chi-restraints excluded: chain A residue 272 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: chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.060547 restraints weight = 19921.529| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.02 r_work: 0.2794 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7703 Z= 0.120 Angle : 0.593 8.789 10415 Z= 0.305 Chirality : 0.043 0.156 1182 Planarity : 0.004 0.043 1314 Dihedral : 13.428 73.930 1218 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.26 % Favored : 93.21 % Rotamer: Outliers : 2.88 % Allowed : 13.91 % 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: -0.89 (0.28), residues: 942 helix: 0.62 (0.25), residues: 465 sheet: 0.81 (0.45), residues: 147 loop : -3.15 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 124 TYR 0.008 0.001 TYR A 94 PHE 0.007 0.001 PHE A 253 HIS 0.002 0.000 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7697) covalent geometry : angle 0.59294 (10415) hydrogen bonds : bond 0.03126 ( 340) hydrogen bonds : angle 4.12214 ( 966) Misc. bond : bond 0.00799 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1520.91 seconds wall clock time: 26 minutes 51.59 seconds (1611.59 seconds total)