Starting phenix.real_space_refine on Wed Feb 4 07:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pm6_71728/02_2026/9pm6_71728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pm6_71728/02_2026/9pm6_71728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pm6_71728/02_2026/9pm6_71728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pm6_71728/02_2026/9pm6_71728.map" model { file = "/net/cci-nas-00/data/ceres_data/9pm6_71728/02_2026/9pm6_71728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pm6_71728/02_2026/9pm6_71728.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5740 2.51 5 N 1576 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9162 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2906 Classifications: {'peptide': 378} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 361} Chain breaks: 4 Chain: "B" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2906 Classifications: {'peptide': 378} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 361} Chain breaks: 4 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 904 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 771 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 904 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "D" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 771 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 1.89, per 1000 atoms: 0.21 Number of scatterers: 9162 At special positions: 0 Unit cell: (111.125, 170.688, 66.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1786 8.00 N 1576 7.00 C 5740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS B 264 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 224.7 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 19 sheets defined 5.8% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.020A pdb=" N SER A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.620A pdb=" N HIS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.519A pdb=" N ALA A 241 " --> pdb=" O ASN A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.770A pdb=" N GLY B 104 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 238 through 241 removed outlier: 3.597A pdb=" N ALA B 241 " --> pdb=" O ASN B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.536A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.519A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.955A pdb=" N LYS C 64 " --> pdb=" O PRO C 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.176A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 50 current: chain 'A' and resid 109 through 129 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 109 through 129 current: chain 'A' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 164 through 169 current: chain 'A' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 209 through 213 current: chain 'A' and resid 281 through 284 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 26 removed outlier: 4.064A pdb=" N VAL A 21 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 186 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA A 178 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 188 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 176 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 249 removed outlier: 4.147A pdb=" N ALA A 248 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ARG A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 312 through 314 current: chain 'A' and resid 326 through 332 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 326 through 332 current: chain 'A' and resid 372 through 379 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.381A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N MET B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 12 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA B 35 " --> pdb=" O PRO B 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 50 current: chain 'B' and resid 109 through 129 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 109 through 129 current: chain 'B' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 164 through 169 current: chain 'B' and resid 209 through 212 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 209 through 212 current: chain 'B' and resid 281 through 284 Processing sheet with id=AA7, first strand: chain 'B' and resid 21 through 26 removed outlier: 4.743A pdb=" N LYS B 290 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'B' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 312 through 314 current: chain 'B' and resid 326 through 332 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 326 through 332 current: chain 'B' and resid 372 through 379 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.862A pdb=" N CYS B 339 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB3, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.775A pdb=" N LEU H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.472A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 58 current: chain 'H' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'L' and resid 33 through 38 removed outlier: 6.413A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'C' and resid 34 through 39 removed outlier: 4.197A pdb=" N TRP C 36 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 58 " --> pdb=" O TYR C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 58 current: chain 'C' and resid 100 through 102 Processing sheet with id=AB9, first strand: chain 'D' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 12 current: chain 'D' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 96 through 98 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 18 through 24 143 hydrogen bonds defined for protein. 372 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: 1.45 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2978 1.34 - 1.46: 2247 1.46 - 1.58: 4049 1.58 - 1.71: 0 1.71 - 1.83: 86 Bond restraints: 9360 Sorted by residual: bond pdb=" N MET B 295 " pdb=" CA MET B 295 " ideal model delta sigma weight residual 1.458 1.492 -0.034 9.00e-03 1.23e+04 1.42e+01 bond pdb=" N GLN H 105 " pdb=" CA GLN H 105 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 bond pdb=" CB GLN H 3 " pdb=" CG GLN H 3 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.72e+00 bond pdb=" CA THR B 233 " pdb=" C THR B 233 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.10e-02 2.27e+03 2.58e+00 bond pdb=" CA THR A 233 " pdb=" C THR A 233 " ideal model delta sigma weight residual 1.525 1.556 -0.031 2.10e-02 2.27e+03 2.17e+00 ... (remaining 9355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 12396 2.18 - 4.35: 234 4.35 - 6.53: 42 6.53 - 8.71: 9 8.71 - 10.88: 7 Bond angle restraints: 12688 Sorted by residual: angle pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " pdb=" CG GLU D 83 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" C PRO C 14 " pdb=" N SER C 15 " pdb=" CA SER C 15 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" N THR A 315 " pdb=" CA THR A 315 " pdb=" C THR A 315 " ideal model delta sigma weight residual 113.43 108.70 4.73 1.26e+00 6.30e-01 1.41e+01 angle pdb=" CA GLN H 3 " pdb=" CB GLN H 3 " pdb=" CG GLN H 3 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET A 349 " pdb=" CG MET A 349 " pdb=" SD MET A 349 " ideal model delta sigma weight residual 112.70 123.58 -10.88 3.00e+00 1.11e-01 1.32e+01 ... (remaining 12683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 4823 17.10 - 34.20: 567 34.20 - 51.31: 144 51.31 - 68.41: 31 68.41 - 85.51: 8 Dihedral angle restraints: 5573 sinusoidal: 2165 harmonic: 3408 Sorted by residual: dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 133.40 -40.40 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CA CYS A 105 " pdb=" C CYS A 105 " pdb=" N GLY A 106 " pdb=" CA GLY A 106 " ideal model delta harmonic sigma weight residual 180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 127.07 -34.07 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 5570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 892 0.037 - 0.074: 351 0.074 - 0.111: 119 0.111 - 0.149: 44 0.149 - 0.186: 10 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CB ILE H 29 " pdb=" CA ILE H 29 " pdb=" CG1 ILE H 29 " pdb=" CG2 ILE H 29 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA THR B 233 " pdb=" N THR B 233 " pdb=" C THR B 233 " pdb=" CB THR B 233 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CB ILE A 396 " pdb=" CA ILE A 396 " pdb=" CG1 ILE A 396 " pdb=" CG2 ILE A 396 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1413 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 14 " -0.040 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO L 15 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO H 14 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 67 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C ASP A 67 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP A 67 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 68 " 0.012 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2246 2.80 - 3.32: 7396 3.32 - 3.85: 14231 3.85 - 4.37: 15444 4.37 - 4.90: 28121 Nonbonded interactions: 67438 Sorted by model distance: nonbonded pdb=" OH TYR A 332 " pdb=" OD1 ASP A 336 " model vdw 2.269 3.040 nonbonded pdb=" O ASN A 52 " pdb=" ND2 ASN A 134 " model vdw 2.289 3.120 nonbonded pdb=" OG1 THR C 17 " pdb=" O LEU C 82 " model vdw 2.307 3.040 nonbonded pdb=" OG1 THR B 170 " pdb=" OD1 ASN B 172 " model vdw 2.309 3.040 nonbonded pdb=" O ALA A 178 " pdb=" OG SER A 185 " model vdw 2.321 3.040 ... (remaining 67433 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'L' } 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.290 Find NCS groups from input model: 0.130 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9377 Z= 0.173 Angle : 0.796 10.882 12722 Z= 0.423 Chirality : 0.048 0.186 1416 Planarity : 0.005 0.060 1616 Dihedral : 15.703 85.511 3350 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.30 % Allowed : 23.27 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.24), residues: 1176 helix: -2.10 (0.91), residues: 30 sheet: 0.59 (0.25), residues: 458 loop : -1.32 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.023 0.002 TYR A 386 PHE 0.025 0.002 PHE A 314 TRP 0.021 0.001 TRP A 20 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9360) covalent geometry : angle 0.79458 (12688) SS BOND : bond 0.00367 ( 17) SS BOND : angle 1.16841 ( 34) hydrogen bonds : bond 0.14286 ( 143) hydrogen bonds : angle 7.34120 ( 372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 88 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8368 (p) REVERT: H 29 ILE cc_start: 0.8265 (mm) cc_final: 0.8061 (mm) REVERT: C 81 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8037 (mmmt) outliers start: 3 outliers final: 1 residues processed: 148 average time/residue: 0.0774 time to fit residues: 16.4952 Evaluate side-chains 136 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain B residue 88 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS B 226 HIS C 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.138430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.108754 restraints weight = 16103.781| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.04 r_work: 0.3520 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9377 Z= 0.127 Angle : 0.549 6.567 12722 Z= 0.282 Chirality : 0.042 0.138 1416 Planarity : 0.004 0.046 1616 Dihedral : 4.386 22.193 1282 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.56 % Allowed : 20.10 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1176 helix: -1.55 (1.12), residues: 24 sheet: 0.60 (0.25), residues: 458 loop : -1.19 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 54 TYR 0.012 0.002 TYR C 91 PHE 0.012 0.002 PHE A 314 TRP 0.006 0.001 TRP B 400 HIS 0.003 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9360) covalent geometry : angle 0.54747 (12688) SS BOND : bond 0.00260 ( 17) SS BOND : angle 0.99327 ( 34) hydrogen bonds : bond 0.03031 ( 143) hydrogen bonds : angle 5.94611 ( 372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 373 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8037 (pptt) REVERT: C 81 LYS cc_start: 0.8463 (mmtm) cc_final: 0.8011 (mmmt) REVERT: D 83 GLU cc_start: 0.8537 (pt0) cc_final: 0.8153 (pm20) outliers start: 36 outliers final: 21 residues processed: 158 average time/residue: 0.0761 time to fit residues: 17.3680 Evaluate side-chains 155 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN H 105 GLN C 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.130503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101808 restraints weight = 16540.071| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.68 r_work: 0.3439 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 9377 Z= 0.328 Angle : 0.741 9.200 12722 Z= 0.386 Chirality : 0.046 0.202 1416 Planarity : 0.005 0.049 1616 Dihedral : 5.358 32.127 1281 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 6.93 % Allowed : 18.42 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.23), residues: 1176 helix: -1.51 (0.98), residues: 32 sheet: 0.21 (0.26), residues: 438 loop : -1.55 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 292 TYR 0.022 0.003 TYR D 36 PHE 0.023 0.003 PHE A 312 TRP 0.013 0.002 TRP B 400 HIS 0.008 0.002 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00759 ( 9360) covalent geometry : angle 0.73698 (12688) SS BOND : bond 0.00360 ( 17) SS BOND : angle 1.59111 ( 34) hydrogen bonds : bond 0.04230 ( 143) hydrogen bonds : angle 6.19426 ( 372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 141 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 294 LYS cc_start: 0.8095 (pttp) cc_final: 0.7831 (ttpp) REVERT: B 373 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7943 (pptt) REVERT: C 51 ILE cc_start: 0.9186 (tp) cc_final: 0.8777 (pt) REVERT: C 77 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: D 83 GLU cc_start: 0.8500 (pt0) cc_final: 0.8125 (pm20) outliers start: 70 outliers final: 52 residues processed: 185 average time/residue: 0.0662 time to fit residues: 18.0321 Evaluate side-chains 186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 32 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.134839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.106229 restraints weight = 16392.826| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.70 r_work: 0.3509 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9377 Z= 0.111 Angle : 0.556 6.808 12722 Z= 0.285 Chirality : 0.043 0.168 1416 Planarity : 0.004 0.050 1616 Dihedral : 4.600 25.798 1281 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.55 % Allowed : 22.08 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.24), residues: 1176 helix: -1.14 (1.13), residues: 24 sheet: 0.36 (0.26), residues: 444 loop : -1.37 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 94 TYR 0.022 0.001 TYR D 91 PHE 0.014 0.001 PHE C 100A TRP 0.009 0.001 TRP B 400 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9360) covalent geometry : angle 0.55424 (12688) SS BOND : bond 0.00225 ( 17) SS BOND : angle 0.98967 ( 34) hydrogen bonds : bond 0.02855 ( 143) hydrogen bonds : angle 5.85183 ( 372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 373 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7957 (pptt) REVERT: L 79 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.7000 (pt0) REVERT: C 51 ILE cc_start: 0.9139 (tp) cc_final: 0.8791 (pt) REVERT: D 83 GLU cc_start: 0.8475 (pt0) cc_final: 0.8064 (pm20) outliers start: 46 outliers final: 34 residues processed: 179 average time/residue: 0.0713 time to fit residues: 18.8915 Evaluate side-chains 169 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 90 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 106 optimal weight: 0.0040 chunk 66 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 0.0370 chunk 108 optimal weight: 4.9990 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN C 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.136548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107968 restraints weight = 16231.950| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.74 r_work: 0.3535 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9377 Z= 0.096 Angle : 0.549 9.754 12722 Z= 0.277 Chirality : 0.042 0.192 1416 Planarity : 0.004 0.050 1616 Dihedral : 4.256 20.395 1281 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.26 % Allowed : 23.47 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.24), residues: 1176 helix: -1.02 (1.12), residues: 24 sheet: 0.45 (0.26), residues: 442 loop : -1.25 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 292 TYR 0.022 0.001 TYR D 91 PHE 0.015 0.001 PHE B 314 TRP 0.008 0.001 TRP B 20 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9360) covalent geometry : angle 0.54801 (12688) SS BOND : bond 0.00411 ( 17) SS BOND : angle 0.94449 ( 34) hydrogen bonds : bond 0.02665 ( 143) hydrogen bonds : angle 5.62232 ( 372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 GLU cc_start: 0.7933 (tp30) cc_final: 0.7559 (tp30) REVERT: B 366 THR cc_start: 0.8343 (p) cc_final: 0.8084 (t) REVERT: B 373 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7955 (pptt) REVERT: C 51 ILE cc_start: 0.9111 (tp) cc_final: 0.8752 (pt) REVERT: D 83 GLU cc_start: 0.8440 (pt0) cc_final: 0.8052 (pm20) outliers start: 43 outliers final: 34 residues processed: 172 average time/residue: 0.0691 time to fit residues: 17.3677 Evaluate side-chains 170 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 21 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN C 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.133205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104893 restraints weight = 16388.067| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.61 r_work: 0.3487 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9377 Z= 0.179 Angle : 0.594 7.389 12722 Z= 0.302 Chirality : 0.043 0.184 1416 Planarity : 0.004 0.049 1616 Dihedral : 4.506 24.336 1281 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.54 % Allowed : 22.38 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.24), residues: 1176 helix: -0.86 (1.14), residues: 24 sheet: 0.28 (0.26), residues: 442 loop : -1.30 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.031 0.002 TYR H 32 PHE 0.015 0.002 PHE A 312 TRP 0.009 0.001 TRP B 400 HIS 0.004 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9360) covalent geometry : angle 0.59157 (12688) SS BOND : bond 0.00299 ( 17) SS BOND : angle 1.16557 ( 34) hydrogen bonds : bond 0.03088 ( 143) hydrogen bonds : angle 5.61645 ( 372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 62 GLU cc_start: 0.8068 (tp30) cc_final: 0.7551 (tp30) REVERT: B 295 MET cc_start: 0.7236 (ppp) cc_final: 0.6883 (ppp) REVERT: B 366 THR cc_start: 0.8379 (p) cc_final: 0.8091 (t) REVERT: B 373 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7942 (pptt) REVERT: L 79 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: C 51 ILE cc_start: 0.9154 (tp) cc_final: 0.8760 (pt) outliers start: 56 outliers final: 47 residues processed: 180 average time/residue: 0.0733 time to fit residues: 19.4178 Evaluate side-chains 183 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.6980 chunk 115 optimal weight: 0.0670 chunk 113 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN C 39 GLN D 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.136049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.107850 restraints weight = 16353.562| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.64 r_work: 0.3529 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9377 Z= 0.097 Angle : 0.540 7.207 12722 Z= 0.273 Chirality : 0.042 0.182 1416 Planarity : 0.004 0.048 1616 Dihedral : 4.188 20.626 1281 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.65 % Allowed : 23.56 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.24), residues: 1176 helix: -0.79 (1.14), residues: 24 sheet: 0.47 (0.26), residues: 430 loop : -1.23 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 61 TYR 0.022 0.001 TYR H 32 PHE 0.013 0.001 PHE B 314 TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9360) covalent geometry : angle 0.53884 (12688) SS BOND : bond 0.00202 ( 17) SS BOND : angle 0.76662 ( 34) hydrogen bonds : bond 0.02483 ( 143) hydrogen bonds : angle 5.34159 ( 372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 GLU cc_start: 0.8027 (tp30) cc_final: 0.7553 (tp30) REVERT: B 295 MET cc_start: 0.7210 (ppp) cc_final: 0.6799 (ppp) REVERT: B 366 THR cc_start: 0.8340 (p) cc_final: 0.8075 (t) REVERT: B 373 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7941 (pptt) REVERT: L 79 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7161 (pt0) REVERT: C 51 ILE cc_start: 0.9103 (tp) cc_final: 0.8742 (pt) REVERT: C 64 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8164 (mmmm) outliers start: 47 outliers final: 42 residues processed: 175 average time/residue: 0.0766 time to fit residues: 19.4759 Evaluate side-chains 179 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 90 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.135697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.107377 restraints weight = 16314.229| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.67 r_work: 0.3530 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9377 Z= 0.105 Angle : 0.547 8.019 12722 Z= 0.274 Chirality : 0.042 0.211 1416 Planarity : 0.004 0.048 1616 Dihedral : 4.080 19.959 1281 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.85 % Allowed : 23.76 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.24), residues: 1176 helix: -0.65 (1.16), residues: 24 sheet: 0.48 (0.26), residues: 430 loop : -1.20 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 61 TYR 0.022 0.001 TYR H 32 PHE 0.014 0.001 PHE B 183 TRP 0.006 0.001 TRP B 400 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9360) covalent geometry : angle 0.54601 (12688) SS BOND : bond 0.00207 ( 17) SS BOND : angle 0.81600 ( 34) hydrogen bonds : bond 0.02494 ( 143) hydrogen bonds : angle 5.24317 ( 372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8416 (t70) cc_final: 0.7968 (t0) REVERT: B 62 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: B 183 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.6192 (t80) REVERT: B 295 MET cc_start: 0.7228 (ppp) cc_final: 0.6818 (ppp) REVERT: B 366 THR cc_start: 0.8298 (p) cc_final: 0.8027 (t) REVERT: B 373 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7942 (pptt) REVERT: C 51 ILE cc_start: 0.9070 (tp) cc_final: 0.8701 (pt) REVERT: C 64 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8235 (mmmm) outliers start: 49 outliers final: 42 residues processed: 175 average time/residue: 0.0652 time to fit residues: 16.9240 Evaluate side-chains 185 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 2 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.136339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.108227 restraints weight = 16318.696| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.63 r_work: 0.3538 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9377 Z= 0.098 Angle : 0.543 7.838 12722 Z= 0.273 Chirality : 0.042 0.188 1416 Planarity : 0.004 0.048 1616 Dihedral : 3.995 19.576 1281 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.05 % Allowed : 23.66 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.24), residues: 1176 helix: -0.68 (1.15), residues: 24 sheet: 0.56 (0.26), residues: 430 loop : -1.16 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 61 TYR 0.018 0.001 TYR H 32 PHE 0.014 0.001 PHE B 314 TRP 0.006 0.001 TRP B 400 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9360) covalent geometry : angle 0.54231 (12688) SS BOND : bond 0.00201 ( 17) SS BOND : angle 0.73849 ( 34) hydrogen bonds : bond 0.02408 ( 143) hydrogen bonds : angle 5.17268 ( 372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 202 TYR cc_start: 0.7904 (m-80) cc_final: 0.7655 (m-80) REVERT: A 220 ASP cc_start: 0.8397 (t70) cc_final: 0.7971 (t0) REVERT: B 62 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: B 183 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.5903 (t80) REVERT: B 295 MET cc_start: 0.7253 (ppp) cc_final: 0.6795 (ppp) REVERT: B 366 THR cc_start: 0.8308 (p) cc_final: 0.8037 (t) REVERT: B 373 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7948 (pptt) REVERT: C 51 ILE cc_start: 0.9060 (tp) cc_final: 0.8701 (pt) REVERT: C 64 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8215 (mmmm) outliers start: 51 outliers final: 44 residues processed: 184 average time/residue: 0.0682 time to fit residues: 18.4552 Evaluate side-chains 185 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 90 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.0030 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN L 79 GLN C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.135983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107837 restraints weight = 16263.639| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.61 r_work: 0.3537 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9377 Z= 0.109 Angle : 0.559 8.709 12722 Z= 0.282 Chirality : 0.042 0.225 1416 Planarity : 0.004 0.048 1616 Dihedral : 4.013 19.456 1281 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.95 % Allowed : 23.86 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.24), residues: 1176 helix: -1.06 (1.05), residues: 24 sheet: 0.55 (0.26), residues: 430 loop : -1.21 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 61 TYR 0.025 0.001 TYR H 32 PHE 0.011 0.001 PHE A 312 TRP 0.006 0.001 TRP B 400 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9360) covalent geometry : angle 0.55700 (12688) SS BOND : bond 0.00196 ( 17) SS BOND : angle 0.97285 ( 34) hydrogen bonds : bond 0.02515 ( 143) hydrogen bonds : angle 5.27886 ( 372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 202 TYR cc_start: 0.7903 (m-80) cc_final: 0.7651 (m-80) REVERT: A 220 ASP cc_start: 0.8398 (t70) cc_final: 0.7970 (t0) REVERT: B 62 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: B 67 ASP cc_start: 0.7503 (t0) cc_final: 0.6977 (t0) REVERT: B 183 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6006 (t80) REVERT: B 295 MET cc_start: 0.7238 (ppp) cc_final: 0.6707 (ppp) REVERT: B 373 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7925 (pptt) REVERT: L 61 ARG cc_start: 0.7534 (mpp80) cc_final: 0.6793 (mtm180) REVERT: C 51 ILE cc_start: 0.9062 (tp) cc_final: 0.8706 (pt) REVERT: C 64 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8216 (mmmm) REVERT: C 81 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8226 (tppt) outliers start: 50 outliers final: 47 residues processed: 177 average time/residue: 0.0815 time to fit residues: 21.0648 Evaluate side-chains 187 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 90 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 70 optimal weight: 0.0970 chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS L 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.136204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.107093 restraints weight = 16327.887| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.82 r_work: 0.3508 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9377 Z= 0.136 Angle : 0.571 8.504 12722 Z= 0.288 Chirality : 0.042 0.223 1416 Planarity : 0.004 0.048 1616 Dihedral : 4.078 20.182 1281 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 5.35 % Allowed : 23.27 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1176 helix: -1.08 (1.05), residues: 24 sheet: 0.50 (0.26), residues: 432 loop : -1.22 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.028 0.001 TYR H 32 PHE 0.017 0.002 PHE B 314 TRP 0.007 0.001 TRP B 400 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9360) covalent geometry : angle 0.56854 (12688) SS BOND : bond 0.00259 ( 17) SS BOND : angle 1.11176 ( 34) hydrogen bonds : bond 0.02616 ( 143) hydrogen bonds : angle 5.26135 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.98 seconds wall clock time: 31 minutes 6.44 seconds (1866.44 seconds total)