Starting phenix.real_space_refine on Wed Feb 4 12:10:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o9x_70265/02_2026/9o9x_70265.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o9x_70265/02_2026/9o9x_70265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o9x_70265/02_2026/9o9x_70265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o9x_70265/02_2026/9o9x_70265.map" model { file = "/net/cci-nas-00/data/ceres_data/9o9x_70265/02_2026/9o9x_70265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o9x_70265/02_2026/9o9x_70265.cif" } resolution = 3.4 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= 0.028 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 52 5.16 5 C 6584 2.51 5 N 1752 2.21 5 O 1982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 10370 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain: "C" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3392 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 9, 'TRANS': 426} Chain: "D" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3392 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 9, 'TRANS': 426} Chain: "B" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 8, 'TRANS': 222} Time building chain proxies: 2.59, per 1000 atoms: 0.25 Number of scatterers: 10370 At special positions: 0 Unit cell: (82.398, 95.688, 155.936, 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 52 16.00 O 1982 8.00 N 1752 7.00 C 6584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 524.8 milliseconds 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 14 sheets defined 53.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.962A pdb=" N GLU A 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 103 through 116 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 118 through 134 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.552A pdb=" N HIS A 138 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 139 " --> pdb=" O GLU A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 147 through 161 Processing helix chain 'A' and resid 177 through 195 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.634A pdb=" N LYS C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 57 removed outlier: 3.588A pdb=" N MET C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 4.036A pdb=" N ASP C 70 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 71 " --> pdb=" O GLU C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 71' Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 151 through 164 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 278 through 323 removed outlier: 4.269A pdb=" N GLY C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'C' and resid 336 through 382 Proline residue: C 375 - end of helix removed outlier: 3.805A pdb=" N SER C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.645A pdb=" N LEU C 389 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 425 removed outlier: 4.282A pdb=" N ASN C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 427 through 432 removed outlier: 3.679A pdb=" N ALA C 431 " --> pdb=" O ASN C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.707A pdb=" N LYS D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 57 removed outlier: 3.634A pdb=" N GLY D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 removed outlier: 4.183A pdb=" N LEU D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 74 through 80' Processing helix chain 'D' and resid 115 through 121 removed outlier: 3.661A pdb=" N GLU D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.675A pdb=" N ARG D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 4.231A pdb=" N LYS D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 240 Processing helix chain 'D' and resid 258 through 272 Processing helix chain 'D' and resid 278 through 324 removed outlier: 3.506A pdb=" N GLU D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 Processing helix chain 'D' and resid 336 through 379 Proline residue: D 375 - end of helix Processing helix chain 'D' and resid 399 through 425 removed outlier: 4.227A pdb=" N ASN D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) Proline residue: D 419 - end of helix Processing helix chain 'D' and resid 427 through 433 Processing helix chain 'B' and resid 47 through 57 Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 103 through 116 Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 118 through 134 removed outlier: 4.019A pdb=" N GLN B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 177 through 195 Processing helix chain 'B' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.124A pdb=" N GLN A 5 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 65 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE A 7 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS A 63 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.501A pdb=" N ALA A 38 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR A 203 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE A 40 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE A 216 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS A 39 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 218 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 41 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS A 215 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 226 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 removed outlier: 3.580A pdb=" N LEU C 149 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 113 through 114 Processing sheet with id=AA6, first strand: chain 'C' and resid 137 through 140 removed outlier: 7.514A pdb=" N VAL C 140 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 213 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 67 removed outlier: 6.508A pdb=" N TYR D 275 " --> pdb=" O MET D 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AA9, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AB1, first strand: chain 'D' and resid 137 through 140 removed outlier: 6.976A pdb=" N ILE D 138 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY D 212 " --> pdb=" O ILE D 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 187 through 188 Processing sheet with id=AB3, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.650A pdb=" N GLN B 5 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 65 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE B 7 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS B 63 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'B' and resid 202 through 203 removed outlier: 7.634A pdb=" N THR B 203 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 40 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS B 39 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU B 218 " --> pdb=" O CYS B 39 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B 41 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS B 215 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY B 226 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1527 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: 1.63 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3400 1.34 - 1.46: 2153 1.46 - 1.58: 4877 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 10524 Sorted by residual: bond pdb=" N LYS C 244 " pdb=" CA LYS C 244 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.74e+00 bond pdb=" N PHE C 243 " pdb=" CA PHE C 243 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.37e-02 5.33e+03 5.63e+00 bond pdb=" N ASP C 242 " pdb=" CA ASP C 242 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.25e+00 bond pdb=" N ASN C 247 " pdb=" CA ASN C 247 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.10e+00 bond pdb=" N LYS C 196 " pdb=" CA LYS C 196 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.91e+00 ... (remaining 10519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 13956 2.17 - 4.34: 184 4.34 - 6.51: 34 6.51 - 8.68: 7 8.68 - 10.85: 3 Bond angle restraints: 14184 Sorted by residual: angle pdb=" C LYS C 196 " pdb=" N THR C 197 " pdb=" CA THR C 197 " ideal model delta sigma weight residual 121.71 114.02 7.69 1.39e+00 5.18e-01 3.06e+01 angle pdb=" N ASN C 247 " pdb=" CA ASN C 247 " pdb=" C ASN C 247 " ideal model delta sigma weight residual 110.80 99.95 10.85 2.13e+00 2.20e-01 2.60e+01 angle pdb=" C ARG D 323 " pdb=" N THR D 324 " pdb=" CA THR D 324 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" N GLY C 198 " pdb=" CA GLY C 198 " pdb=" C GLY C 198 " ideal model delta sigma weight residual 113.18 123.18 -10.00 2.37e+00 1.78e-01 1.78e+01 angle pdb=" N GLY D 198 " pdb=" CA GLY D 198 " pdb=" C GLY D 198 " ideal model delta sigma weight residual 113.18 123.16 -9.98 2.37e+00 1.78e-01 1.77e+01 ... (remaining 14179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5493 17.72 - 35.43: 679 35.43 - 53.15: 191 53.15 - 70.86: 29 70.86 - 88.58: 10 Dihedral angle restraints: 6402 sinusoidal: 2584 harmonic: 3818 Sorted by residual: dihedral pdb=" CA LYS D 196 " pdb=" C LYS D 196 " pdb=" N THR D 197 " pdb=" CA THR D 197 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA TYR D 395 " pdb=" C TYR D 395 " pdb=" N ILE D 396 " pdb=" CA ILE D 396 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU C 188 " pdb=" C LEU C 188 " pdb=" N SER C 189 " pdb=" CA SER C 189 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 6399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1245 0.045 - 0.089: 313 0.089 - 0.134: 95 0.134 - 0.178: 6 0.178 - 0.223: 1 Chirality restraints: 1660 Sorted by residual: chirality pdb=" CA ASN C 247 " pdb=" N ASN C 247 " pdb=" C ASN C 247 " pdb=" CB ASN C 247 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU B 52 " pdb=" CB LEU B 52 " pdb=" CD1 LEU B 52 " pdb=" CD2 LEU B 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CB ILE B 211 " pdb=" CA ILE B 211 " pdb=" CG1 ILE B 211 " pdb=" CG2 ILE B 211 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 1657 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 195 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C SER C 195 " 0.055 2.00e-02 2.50e+03 pdb=" O SER C 195 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS C 196 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 324 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C THR D 324 " 0.040 2.00e-02 2.50e+03 pdb=" O THR D 324 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN D 325 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 246 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C GLY C 246 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY C 246 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN C 247 " -0.012 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2180 2.78 - 3.31: 11114 3.31 - 3.84: 17959 3.84 - 4.37: 20430 4.37 - 4.90: 34696 Nonbonded interactions: 86379 Sorted by model distance: nonbonded pdb=" C GLY C 246 " pdb=" N VAL C 248 " model vdw 2.253 3.350 nonbonded pdb=" OG1 THR A 104 " pdb=" O HIS A 141 " model vdw 2.331 3.040 nonbonded pdb=" O GLY C 246 " pdb=" N VAL C 248 " model vdw 2.331 3.120 nonbonded pdb=" N ASN C 247 " pdb=" N VAL C 248 " model vdw 2.393 2.560 nonbonded pdb=" O GLN B 124 " pdb=" OD1 ASP B 128 " model vdw 2.475 3.040 ... (remaining 86374 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 'D' } 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.620 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 0.041 10524 Z= 0.163 Angle : 0.657 10.853 14184 Z= 0.352 Chirality : 0.043 0.223 1660 Planarity : 0.004 0.045 1806 Dihedral : 16.825 88.578 3946 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.28 % Favored : 90.20 % Rotamer: Outliers : 0.61 % Allowed : 29.03 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1326 helix: 0.94 (0.19), residues: 678 sheet: -1.01 (0.55), residues: 112 loop : -2.39 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 342 TYR 0.022 0.001 TYR D 395 PHE 0.021 0.001 PHE A 96 TRP 0.005 0.001 TRP A 81 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00326 (10524) covalent geometry : angle 0.65690 (14184) hydrogen bonds : bond 0.10873 ( 528) hydrogen bonds : angle 5.88377 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8031 (m-30) cc_final: 0.7636 (t0) REVERT: A 65 ARG cc_start: 0.8049 (ptm-80) cc_final: 0.7633 (ptm-80) REVERT: C 65 MET cc_start: 0.6301 (tpt) cc_final: 0.5923 (tpt) REVERT: C 124 MET cc_start: 0.5760 (tmm) cc_final: 0.4644 (tpp) REVERT: C 133 LYS cc_start: 0.7676 (mttm) cc_final: 0.7188 (mmmt) REVERT: D 61 LYS cc_start: 0.8551 (tptp) cc_final: 0.7311 (pttt) REVERT: D 135 GLU cc_start: 0.4965 (mm-30) cc_final: 0.4741 (tp30) REVERT: D 233 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7724 (t80) REVERT: D 251 ASN cc_start: 0.8975 (m-40) cc_final: 0.8232 (p0) REVERT: D 376 MET cc_start: 0.7228 (ttm) cc_final: 0.6557 (mmm) REVERT: D 426 THR cc_start: 0.8620 (p) cc_final: 0.7871 (m) REVERT: B 27 ASP cc_start: 0.7313 (t0) cc_final: 0.7045 (t0) REVERT: B 43 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7794 (mtm110) REVERT: B 95 SER cc_start: 0.8659 (m) cc_final: 0.8051 (t) REVERT: B 106 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7206 (tp30) REVERT: B 181 GLU cc_start: 0.8962 (tt0) cc_final: 0.8675 (tt0) outliers start: 7 outliers final: 3 residues processed: 180 average time/residue: 0.1023 time to fit residues: 26.0686 Evaluate side-chains 165 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 233 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS B 141 HIS B 163 ASN B 192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.234482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146317 restraints weight = 12761.477| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.42 r_work: 0.3387 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10524 Z= 0.174 Angle : 0.598 9.625 14184 Z= 0.317 Chirality : 0.043 0.135 1660 Planarity : 0.004 0.047 1806 Dihedral : 5.156 50.445 1424 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.28 % Favored : 90.27 % Rotamer: Outliers : 4.68 % Allowed : 25.65 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1326 helix: 1.06 (0.19), residues: 669 sheet: -1.09 (0.55), residues: 108 loop : -2.34 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 342 TYR 0.018 0.001 TYR D 395 PHE 0.018 0.002 PHE C 344 TRP 0.007 0.001 TRP A 81 HIS 0.009 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00398 (10524) covalent geometry : angle 0.59765 (14184) hydrogen bonds : bond 0.04439 ( 528) hydrogen bonds : angle 4.96138 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8223 (m-30) cc_final: 0.7650 (t0) REVERT: A 65 ARG cc_start: 0.8153 (ptm-80) cc_final: 0.7497 (ptm-80) REVERT: A 81 TRP cc_start: 0.7732 (OUTLIER) cc_final: 0.7525 (t60) REVERT: C 124 MET cc_start: 0.5717 (tmm) cc_final: 0.5022 (tpp) REVERT: D 135 GLU cc_start: 0.5676 (mm-30) cc_final: 0.5445 (tp30) REVERT: D 233 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8113 (t80) REVERT: D 251 ASN cc_start: 0.8973 (m-40) cc_final: 0.8266 (p0) REVERT: D 376 MET cc_start: 0.7383 (ttm) cc_final: 0.6522 (mmm) REVERT: B 27 ASP cc_start: 0.8015 (t0) cc_final: 0.7783 (t0) REVERT: B 43 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7220 (ptp-170) REVERT: B 48 LYS cc_start: 0.8665 (ptmm) cc_final: 0.8453 (ptmt) REVERT: B 95 SER cc_start: 0.8753 (m) cc_final: 0.8079 (t) REVERT: B 106 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7082 (tp30) REVERT: B 181 GLU cc_start: 0.9063 (tt0) cc_final: 0.8749 (tt0) REVERT: B 219 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.7755 (t-90) outliers start: 54 outliers final: 21 residues processed: 205 average time/residue: 0.0912 time to fit residues: 26.9019 Evaluate side-chains 174 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 81 TRP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN C 92 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.233759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 145)---------------| | r_work = 0.3854 r_free = 0.3854 target = 0.153271 restraints weight = 12894.600| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.94 r_work: 0.3446 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10524 Z= 0.172 Angle : 0.601 9.564 14184 Z= 0.318 Chirality : 0.043 0.138 1660 Planarity : 0.004 0.047 1806 Dihedral : 5.134 50.567 1422 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.43 % Favored : 90.12 % Rotamer: Outliers : 4.25 % Allowed : 26.17 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.23), residues: 1326 helix: 1.03 (0.19), residues: 680 sheet: -1.19 (0.54), residues: 108 loop : -2.44 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 342 TYR 0.019 0.001 TYR D 395 PHE 0.018 0.001 PHE C 344 TRP 0.007 0.001 TRP A 81 HIS 0.009 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00389 (10524) covalent geometry : angle 0.60072 (14184) hydrogen bonds : bond 0.04359 ( 528) hydrogen bonds : angle 4.81677 ( 1527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8221 (m-30) cc_final: 0.7724 (t0) REVERT: A 65 ARG cc_start: 0.8136 (ptm-80) cc_final: 0.7527 (ptm-80) REVERT: A 110 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8197 (tpp) REVERT: A 177 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.6871 (p0) REVERT: C 89 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: C 116 MET cc_start: 0.7135 (mmp) cc_final: 0.6830 (mmp) REVERT: D 233 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7930 (t80) REVERT: D 251 ASN cc_start: 0.8997 (m-40) cc_final: 0.8240 (p0) REVERT: D 372 LEU cc_start: 0.8278 (mm) cc_final: 0.7979 (mm) REVERT: D 376 MET cc_start: 0.7467 (ttm) cc_final: 0.6620 (mmm) REVERT: D 396 ILE cc_start: 0.4545 (OUTLIER) cc_final: 0.3950 (mm) REVERT: B 27 ASP cc_start: 0.7740 (t0) cc_final: 0.7469 (t0) REVERT: B 43 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7693 (mtm110) REVERT: B 95 SER cc_start: 0.8747 (m) cc_final: 0.8091 (t) REVERT: B 106 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7113 (tp30) REVERT: B 181 GLU cc_start: 0.9078 (tt0) cc_final: 0.8791 (tt0) REVERT: B 219 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.7798 (t-90) outliers start: 49 outliers final: 26 residues processed: 207 average time/residue: 0.0874 time to fit residues: 26.2379 Evaluate side-chains 190 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 219 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 37 optimal weight: 30.0000 chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.230717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140712 restraints weight = 12863.346| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.84 r_work: 0.3302 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10524 Z= 0.256 Angle : 0.657 9.471 14184 Z= 0.348 Chirality : 0.045 0.174 1660 Planarity : 0.004 0.047 1806 Dihedral : 5.309 57.732 1422 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.65 % Favored : 89.89 % Rotamer: Outliers : 5.20 % Allowed : 26.78 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1326 helix: 0.83 (0.19), residues: 674 sheet: -1.41 (0.54), residues: 110 loop : -2.46 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 12 TYR 0.025 0.001 TYR D 395 PHE 0.021 0.002 PHE C 344 TRP 0.011 0.002 TRP A 81 HIS 0.008 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00598 (10524) covalent geometry : angle 0.65741 (14184) hydrogen bonds : bond 0.04605 ( 528) hydrogen bonds : angle 4.94367 ( 1527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8128 (ptm-80) cc_final: 0.7792 (ptm-80) REVERT: A 110 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8226 (tpp) REVERT: A 171 GLU cc_start: 0.8274 (mp0) cc_final: 0.7244 (pm20) REVERT: A 177 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.6987 (p0) REVERT: C 89 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: D 135 GLU cc_start: 0.5653 (tp30) cc_final: 0.5329 (tp30) REVERT: D 233 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7960 (t80) REVERT: D 251 ASN cc_start: 0.8960 (m-40) cc_final: 0.8294 (p0) REVERT: D 376 MET cc_start: 0.7467 (ttm) cc_final: 0.6538 (mmm) REVERT: D 396 ILE cc_start: 0.4702 (OUTLIER) cc_final: 0.4011 (mp) REVERT: B 31 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8491 (t) REVERT: B 43 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7687 (mtm110) REVERT: B 48 LYS cc_start: 0.8774 (ptmm) cc_final: 0.8462 (ptmt) REVERT: B 95 SER cc_start: 0.8809 (m) cc_final: 0.8131 (t) REVERT: B 106 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7149 (tp30) REVERT: B 132 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8510 (tpt90) REVERT: B 181 GLU cc_start: 0.9079 (tt0) cc_final: 0.8778 (tt0) REVERT: B 219 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7886 (t-90) outliers start: 60 outliers final: 32 residues processed: 218 average time/residue: 0.0952 time to fit residues: 29.6759 Evaluate side-chains 207 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 219 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 76 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.232787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141195 restraints weight = 12897.064| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.41 r_work: 0.3412 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10524 Z= 0.160 Angle : 0.608 9.539 14184 Z= 0.321 Chirality : 0.043 0.138 1660 Planarity : 0.004 0.052 1806 Dihedral : 5.259 57.381 1422 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.65 % Favored : 89.89 % Rotamer: Outliers : 3.99 % Allowed : 28.16 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1326 helix: 1.01 (0.19), residues: 676 sheet: -1.44 (0.53), residues: 110 loop : -2.46 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 323 TYR 0.022 0.001 TYR D 395 PHE 0.017 0.001 PHE C 344 TRP 0.006 0.001 TRP A 81 HIS 0.008 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00361 (10524) covalent geometry : angle 0.60756 (14184) hydrogen bonds : bond 0.04346 ( 528) hydrogen bonds : angle 4.78173 ( 1527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8328 (m-30) cc_final: 0.7817 (t0) REVERT: A 65 ARG cc_start: 0.8102 (ptm-80) cc_final: 0.7804 (ptm-80) REVERT: A 110 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8116 (tpp) REVERT: A 177 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.6983 (p0) REVERT: C 87 VAL cc_start: 0.5529 (OUTLIER) cc_final: 0.4855 (t) REVERT: C 89 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: C 124 MET cc_start: 0.5502 (tmm) cc_final: 0.4895 (tpp) REVERT: C 315 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.8995 (m) REVERT: D 23 MET cc_start: 0.9208 (tpp) cc_final: 0.8958 (mmt) REVERT: D 135 GLU cc_start: 0.5552 (tp30) cc_final: 0.5268 (tp30) REVERT: D 251 ASN cc_start: 0.8934 (m-40) cc_final: 0.8266 (p0) REVERT: D 376 MET cc_start: 0.7437 (ttm) cc_final: 0.6550 (mmm) REVERT: D 396 ILE cc_start: 0.4445 (OUTLIER) cc_final: 0.3891 (mm) REVERT: B 31 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8475 (t) REVERT: B 43 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7682 (mtm110) REVERT: B 48 LYS cc_start: 0.8720 (ptmm) cc_final: 0.8437 (ptmt) REVERT: B 95 SER cc_start: 0.8740 (m) cc_final: 0.8047 (t) REVERT: B 106 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7079 (tp30) REVERT: B 181 GLU cc_start: 0.9046 (tt0) cc_final: 0.8739 (tt0) REVERT: B 219 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7877 (t-90) outliers start: 46 outliers final: 26 residues processed: 210 average time/residue: 0.0796 time to fit residues: 24.4600 Evaluate side-chains 199 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 224 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.235371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.182259 restraints weight = 12770.684| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.78 r_work: 0.3457 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10524 Z= 0.245 Angle : 0.660 9.482 14184 Z= 0.350 Chirality : 0.045 0.144 1660 Planarity : 0.004 0.046 1806 Dihedral : 5.013 45.282 1420 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.95 % Favored : 89.59 % Rotamer: Outliers : 5.03 % Allowed : 28.08 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.23), residues: 1326 helix: 0.80 (0.19), residues: 676 sheet: -1.51 (0.53), residues: 110 loop : -2.49 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.024 0.001 TYR D 395 PHE 0.022 0.002 PHE C 344 TRP 0.009 0.001 TRP A 81 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00574 (10524) covalent geometry : angle 0.65955 (14184) hydrogen bonds : bond 0.04617 ( 528) hydrogen bonds : angle 4.92122 ( 1527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8076 (ptm-80) cc_final: 0.7748 (ptm-80) REVERT: A 110 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8092 (tpp) REVERT: A 177 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.6906 (p0) REVERT: C 89 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: C 124 MET cc_start: 0.5676 (tmm) cc_final: 0.4658 (tpp) REVERT: C 315 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8936 (m) REVERT: D 23 MET cc_start: 0.8788 (tpp) cc_final: 0.8550 (mmt) REVERT: D 251 ASN cc_start: 0.8781 (m-40) cc_final: 0.8155 (p0) REVERT: D 376 MET cc_start: 0.7323 (ttm) cc_final: 0.6800 (mmm) REVERT: D 396 ILE cc_start: 0.4587 (OUTLIER) cc_final: 0.4063 (mm) REVERT: B 25 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8033 (tp) REVERT: B 31 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8420 (t) REVERT: B 43 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7975 (mtm110) REVERT: B 95 SER cc_start: 0.8733 (m) cc_final: 0.8182 (t) REVERT: B 132 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8325 (tpt90) REVERT: B 152 GLN cc_start: 0.8749 (tp40) cc_final: 0.8391 (tp40) REVERT: B 181 GLU cc_start: 0.9001 (tt0) cc_final: 0.8783 (tt0) REVERT: B 219 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7654 (t-90) outliers start: 58 outliers final: 37 residues processed: 225 average time/residue: 0.0915 time to fit residues: 29.3750 Evaluate side-chains 217 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 224 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.228426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.166791 restraints weight = 12590.592| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.87 r_work: 0.3333 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 10524 Z= 0.403 Angle : 0.795 9.212 14184 Z= 0.423 Chirality : 0.050 0.198 1660 Planarity : 0.005 0.056 1806 Dihedral : 5.287 44.379 1420 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.33 % Favored : 89.14 % Rotamer: Outliers : 6.41 % Allowed : 27.38 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.22), residues: 1326 helix: 0.10 (0.18), residues: 675 sheet: -1.62 (0.58), residues: 94 loop : -2.41 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 12 TYR 0.033 0.002 TYR D 395 PHE 0.029 0.002 PHE C 344 TRP 0.014 0.002 TRP A 81 HIS 0.007 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00947 (10524) covalent geometry : angle 0.79487 (14184) hydrogen bonds : bond 0.05156 ( 528) hydrogen bonds : angle 5.32035 ( 1527) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 177 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8270 (m-30) cc_final: 0.7851 (t0) REVERT: A 65 ARG cc_start: 0.8044 (ptm-80) cc_final: 0.7646 (ptm-80) REVERT: A 110 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8065 (tpp) REVERT: C 23 MET cc_start: 0.8848 (tpp) cc_final: 0.8496 (mmp) REVERT: C 89 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: C 124 MET cc_start: 0.5880 (tmm) cc_final: 0.4939 (tpp) REVERT: D 251 ASN cc_start: 0.8865 (m-40) cc_final: 0.8186 (p0) REVERT: D 376 MET cc_start: 0.7622 (ttm) cc_final: 0.6852 (mmm) REVERT: D 396 ILE cc_start: 0.4928 (OUTLIER) cc_final: 0.4376 (mp) REVERT: B 25 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8167 (tp) REVERT: B 43 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7984 (mtm110) REVERT: B 132 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8934 (tpt170) REVERT: B 195 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7388 (ptm160) REVERT: B 219 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7632 (t-90) outliers start: 74 outliers final: 51 residues processed: 238 average time/residue: 0.0941 time to fit residues: 31.6788 Evaluate side-chains 227 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 224 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 88 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 110 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 40.0000 overall best weight: 0.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 57 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.234521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.177338 restraints weight = 12827.122| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.96 r_work: 0.3437 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10524 Z= 0.170 Angle : 0.659 9.088 14184 Z= 0.348 Chirality : 0.044 0.233 1660 Planarity : 0.004 0.049 1806 Dihedral : 5.134 46.942 1420 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.80 % Favored : 89.74 % Rotamer: Outliers : 3.73 % Allowed : 30.24 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.23), residues: 1326 helix: 0.61 (0.19), residues: 673 sheet: -1.68 (0.52), residues: 117 loop : -2.46 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 193 TYR 0.013 0.001 TYR D 395 PHE 0.056 0.002 PHE D 290 TRP 0.005 0.001 TRP A 81 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00391 (10524) covalent geometry : angle 0.65872 (14184) hydrogen bonds : bond 0.04500 ( 528) hydrogen bonds : angle 4.96175 ( 1527) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7720 (ptm-80) REVERT: A 170 ASP cc_start: 0.7967 (t0) cc_final: 0.7690 (t70) REVERT: A 171 GLU cc_start: 0.8229 (mp0) cc_final: 0.7437 (pm20) REVERT: C 23 MET cc_start: 0.8781 (tpp) cc_final: 0.8373 (mmp) REVERT: C 89 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: C 124 MET cc_start: 0.5648 (tmm) cc_final: 0.4859 (tpp) REVERT: C 222 MET cc_start: 0.2624 (OUTLIER) cc_final: 0.0103 (mtm) REVERT: C 315 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8906 (m) REVERT: D 16 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8499 (mmtt) REVERT: D 23 MET cc_start: 0.8785 (tpp) cc_final: 0.8541 (mmt) REVERT: D 137 GLU cc_start: 0.4725 (OUTLIER) cc_final: 0.4192 (tp30) REVERT: D 179 LYS cc_start: 0.8050 (tptt) cc_final: 0.7800 (tmmt) REVERT: D 251 ASN cc_start: 0.8865 (m-40) cc_final: 0.8236 (p0) REVERT: D 376 MET cc_start: 0.7499 (ttm) cc_final: 0.6814 (mmm) REVERT: D 396 ILE cc_start: 0.4642 (OUTLIER) cc_final: 0.3986 (mp) REVERT: B 25 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8129 (tp) REVERT: B 43 ARG cc_start: 0.8225 (mtm110) cc_final: 0.8015 (mtm110) REVERT: B 95 SER cc_start: 0.8678 (m) cc_final: 0.8086 (t) REVERT: B 132 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8318 (tpt90) REVERT: B 195 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7340 (ptm160) REVERT: B 219 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7662 (t-90) REVERT: B 220 ASP cc_start: 0.8294 (m-30) cc_final: 0.7968 (m-30) outliers start: 43 outliers final: 29 residues processed: 211 average time/residue: 0.0961 time to fit residues: 28.6121 Evaluate side-chains 212 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 224 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 chunk 96 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.234082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174487 restraints weight = 12720.714| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.77 r_work: 0.3455 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10524 Z= 0.185 Angle : 0.667 8.811 14184 Z= 0.352 Chirality : 0.045 0.273 1660 Planarity : 0.004 0.045 1806 Dihedral : 5.119 47.532 1420 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.65 % Favored : 89.89 % Rotamer: Outliers : 3.99 % Allowed : 29.81 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1326 helix: 0.67 (0.19), residues: 674 sheet: -1.67 (0.52), residues: 117 loop : -2.46 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 193 TYR 0.014 0.001 TYR D 395 PHE 0.024 0.002 PHE D 3 TRP 0.006 0.001 TRP A 81 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00427 (10524) covalent geometry : angle 0.66692 (14184) hydrogen bonds : bond 0.04528 ( 528) hydrogen bonds : angle 4.93225 ( 1527) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8155 (ptm-80) cc_final: 0.7754 (ptm-80) REVERT: C 23 MET cc_start: 0.9008 (tpp) cc_final: 0.8620 (mmp) REVERT: C 315 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8929 (m) REVERT: D 16 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8495 (mmtt) REVERT: D 23 MET cc_start: 0.8984 (tpp) cc_final: 0.8722 (mmt) REVERT: D 137 GLU cc_start: 0.4759 (OUTLIER) cc_final: 0.4197 (tp30) REVERT: D 251 ASN cc_start: 0.8953 (m-40) cc_final: 0.8277 (p0) REVERT: D 303 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7763 (mm) REVERT: D 376 MET cc_start: 0.7496 (ttm) cc_final: 0.6770 (mmm) REVERT: D 396 ILE cc_start: 0.4975 (OUTLIER) cc_final: 0.4194 (mp) REVERT: B 25 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8134 (tp) REVERT: B 43 ARG cc_start: 0.8234 (mtm110) cc_final: 0.8008 (mtm110) REVERT: B 95 SER cc_start: 0.8715 (m) cc_final: 0.8104 (t) REVERT: B 131 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8443 (tptm) REVERT: B 132 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8403 (tpt90) REVERT: B 195 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7379 (ptm160) REVERT: B 219 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7701 (t-90) outliers start: 46 outliers final: 32 residues processed: 211 average time/residue: 0.1028 time to fit residues: 30.4082 Evaluate side-chains 214 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 224 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 0.3980 chunk 76 optimal weight: 40.0000 chunk 25 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 0.0570 chunk 126 optimal weight: 2.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.235395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179094 restraints weight = 12618.863| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.98 r_work: 0.3470 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10524 Z= 0.165 Angle : 0.672 8.947 14184 Z= 0.354 Chirality : 0.044 0.257 1660 Planarity : 0.004 0.045 1806 Dihedral : 4.807 34.083 1416 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.80 % Favored : 89.74 % Rotamer: Outliers : 3.38 % Allowed : 30.94 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1326 helix: 0.79 (0.19), residues: 675 sheet: -1.38 (0.54), residues: 110 loop : -2.43 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 193 TYR 0.012 0.001 TYR D 395 PHE 0.027 0.002 PHE D 290 TRP 0.005 0.001 TRP A 81 HIS 0.006 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00374 (10524) covalent geometry : angle 0.67192 (14184) hydrogen bonds : bond 0.04467 ( 528) hydrogen bonds : angle 4.89632 ( 1527) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8102 (ptm-80) cc_final: 0.7616 (ptm-80) REVERT: C 23 MET cc_start: 0.8785 (tpp) cc_final: 0.8496 (mmp) REVERT: C 124 MET cc_start: 0.5490 (tmm) cc_final: 0.5214 (ttp) REVERT: C 125 GLU cc_start: 0.2997 (pt0) cc_final: 0.2404 (pm20) REVERT: C 222 MET cc_start: 0.2658 (OUTLIER) cc_final: 0.0095 (mtm) REVERT: C 315 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8887 (m) REVERT: D 23 MET cc_start: 0.8813 (tpp) cc_final: 0.8547 (mmt) REVERT: D 137 GLU cc_start: 0.4714 (OUTLIER) cc_final: 0.4151 (tp30) REVERT: D 251 ASN cc_start: 0.8803 (m-40) cc_final: 0.8186 (p0) REVERT: D 303 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7596 (mm) REVERT: D 376 MET cc_start: 0.7441 (ttm) cc_final: 0.6813 (mmm) REVERT: D 426 THR cc_start: 0.8762 (p) cc_final: 0.7790 (m) REVERT: B 25 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8076 (tp) REVERT: B 43 ARG cc_start: 0.8287 (mtm110) cc_final: 0.8057 (mtm110) REVERT: B 95 SER cc_start: 0.8646 (m) cc_final: 0.8006 (t) REVERT: B 131 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8324 (tptm) REVERT: B 132 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8794 (tpt170) REVERT: B 181 GLU cc_start: 0.9034 (tt0) cc_final: 0.8750 (tt0) REVERT: B 195 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7305 (ptm160) REVERT: B 219 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7655 (t-90) outliers start: 39 outliers final: 28 residues processed: 202 average time/residue: 0.1084 time to fit residues: 30.7896 Evaluate side-chains 211 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 224 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 30.0000 chunk 95 optimal weight: 0.5980 chunk 80 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.235804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178638 restraints weight = 12769.586| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.84 r_work: 0.3503 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10524 Z= 0.157 Angle : 0.667 8.643 14184 Z= 0.350 Chirality : 0.044 0.216 1660 Planarity : 0.004 0.046 1806 Dihedral : 4.757 33.806 1416 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.65 % Favored : 89.89 % Rotamer: Outliers : 3.21 % Allowed : 31.46 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.23), residues: 1326 helix: 0.87 (0.19), residues: 674 sheet: -1.87 (0.50), residues: 123 loop : -2.37 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 193 TYR 0.015 0.001 TYR C 94 PHE 0.021 0.002 PHE A 96 TRP 0.005 0.001 TRP A 81 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00354 (10524) covalent geometry : angle 0.66672 (14184) hydrogen bonds : bond 0.04421 ( 528) hydrogen bonds : angle 4.84204 ( 1527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.74 seconds wall clock time: 52 minutes 57.61 seconds (3177.61 seconds total)