Starting phenix.real_space_refine on Tue Mar 3 16:20:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ybv_10774/03_2026/6ybv_10774.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ybv_10774/03_2026/6ybv_10774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ybv_10774/03_2026/6ybv_10774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ybv_10774/03_2026/6ybv_10774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ybv_10774/03_2026/6ybv_10774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ybv_10774/03_2026/6ybv_10774.map" } resolution = 3.8 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 21 5.16 5 C 3877 2.51 5 N 1250 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6731 Number of models: 1 Model: "" Number of chains: 5 Chain: "s" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1123 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "r" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2215 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "w" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 29} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {' A%rna3p_pur:plan': 2, ' A%rna3p_pur:plan2': 2, ' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 33 Chain: "t" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 1750 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 298} Link IDs: {'PTRANS': 15, 'TRANS': 340} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1009 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLU:plan': 23, 'ARG:plan': 17, 'GLN:plan1': 13, 'ASN:plan1': 12, 'HIS:plan': 9, 'PHE:plan': 8, 'TYR:plan': 6, 'ASP:plan': 9, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 445 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA t 51 " occ=0.32 ... (3 atoms not shown) pdb=" CB ALA t 51 " occ=0.32 residue: pdb=" N GLN t 206 " occ=0.55 ... (3 atoms not shown) pdb=" CB GLN t 206 " occ=0.55 residue: pdb=" N LEU t 208 " occ=0.35 ... (3 atoms not shown) pdb=" CB LEU t 208 " occ=0.35 residue: pdb=" N ASN t 431 " occ=0.42 ... (3 atoms not shown) pdb=" CB ASN t 431 " occ=0.42 Time building chain proxies: 1.86, per 1000 atoms: 0.28 Number of scatterers: 6731 At special positions: 0 Unit cell: (111.696, 117.066, 106.326, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 77 15.00 O 1506 8.00 N 1250 7.00 C 3877 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: 0.65 Conformation dependent library (CDL) restraints added in 231.9 milliseconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 33.7% alpha, 16.4% beta 14 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 's' and resid 176 through 186 Processing helix chain 's' and resid 221 through 229 Processing helix chain 's' and resid 234 through 243 removed outlier: 4.012A pdb=" N ALA s 238 " --> pdb=" O LYS s 234 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE s 239 " --> pdb=" O HIS s 235 " (cutoff:3.500A) Processing helix chain 's' and resid 244 through 246 No H-bonds generated for 'chain 's' and resid 244 through 246' Processing helix chain 's' and resid 263 through 278 Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.609A pdb=" N LEU r 62 " --> pdb=" O SER r 58 " (cutoff:3.500A) Processing helix chain 'r' and resid 91 through 119 Processing helix chain 'r' and resid 123 through 134 Processing helix chain 'r' and resid 134 through 142 Processing helix chain 'r' and resid 146 through 157 Processing helix chain 'r' and resid 161 through 166 removed outlier: 3.694A pdb=" N LEU r 166 " --> pdb=" O LEU r 163 " (cutoff:3.500A) Processing helix chain 'r' and resid 169 through 181 removed outlier: 3.697A pdb=" N ARG r 173 " --> pdb=" O ASN r 169 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU r 174 " --> pdb=" O GLU r 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 203 through 218 Processing helix chain 'r' and resid 243 through 262 removed outlier: 3.720A pdb=" N GLY r 247 " --> pdb=" O GLU r 243 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER r 249 " --> pdb=" O THR r 245 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 63 Processing helix chain 't' and resid 69 through 76 Processing helix chain 't' and resid 141 through 152 removed outlier: 3.949A pdb=" N MET t 145 " --> pdb=" O LEU t 141 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL t 151 " --> pdb=" O ASN t 147 " (cutoff:3.500A) Processing helix chain 't' and resid 168 through 181 Processing helix chain 't' and resid 196 through 212 Processing helix chain 't' and resid 214 through 219 removed outlier: 4.131A pdb=" N GLY t 218 " --> pdb=" O VAL t 215 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 243 Processing helix chain 't' and resid 344 through 349 Processing sheet with id=AA1, first strand: chain 's' and resid 218 through 219 removed outlier: 4.107A pdb=" N VAL s 257 " --> pdb=" O SER s 249 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER s 249 " --> pdb=" O VAL s 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 's' and resid 291 through 293 removed outlier: 3.693A pdb=" N GLN s 292 " --> pdb=" O PHE s 299 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE s 299 " --> pdb=" O GLN s 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'r' and resid 19 through 24 removed outlier: 8.870A pdb=" N LEU r 85 " --> pdb=" O GLU r 43 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET r 45 " --> pdb=" O LEU r 85 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP r 84 " --> pdb=" O ILE r 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'r' and resid 226 through 229 removed outlier: 3.751A pdb=" N ASN r 228 " --> pdb=" O VAL r 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU r 196 " --> pdb=" O ASN r 270 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN r 270 " --> pdb=" O GLU r 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 't' and resid 84 through 86 removed outlier: 3.615A pdb=" N ALA t 84 " --> pdb=" O PHE t 132 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE t 44 " --> pdb=" O VAL t 133 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLY t 45 " --> pdb=" O LEU t 156 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU t 158 " --> pdb=" O GLY t 45 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE t 47 " --> pdb=" O LEU t 158 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA t 155 " --> pdb=" O LEU t 186 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU t 188 " --> pdb=" O ALA t 155 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU t 157 " --> pdb=" O LEU t 188 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE t 222 " --> pdb=" O ILE t 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 't' and resid 283 through 285 removed outlier: 6.429A pdb=" N ARG t 255 " --> pdb=" O LEU t 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 't' and resid 279 through 281 removed outlier: 3.777A pdb=" N ALA t 279 " --> pdb=" O VAL t 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 't' and resid 367 through 368 removed outlier: 3.908A pdb=" N VAL t 433 " --> pdb=" O PHE t 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 't' and resid 411 through 413 removed outlier: 3.756A pdb=" N ASN t 407 " --> pdb=" O ALA t 442 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA t 442 " --> pdb=" O ASN t 407 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE t 441 " --> pdb=" O TRP t 456 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TRP t 456 " --> pdb=" O ILE t 441 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU t 443 " --> pdb=" O ILE t 454 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP t 456 " --> pdb=" O PHE t 376 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE t 373 " --> pdb=" O GLY t 425 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY t 425 " --> pdb=" O ILE t 373 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU t 424 " --> pdb=" O VAL t 420 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL t 420 " --> pdb=" O LEU t 424 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LYS t 426 " --> pdb=" O SER t 418 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER t 418 " --> pdb=" O LYS t 426 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL t 428 " --> pdb=" O ARG t 416 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1471 1.33 - 1.45: 1866 1.45 - 1.57: 3452 1.57 - 1.70: 150 1.70 - 1.82: 31 Bond restraints: 6970 Sorted by residual: bond pdb=" C VAL r 90 " pdb=" N SER r 91 " ideal model delta sigma weight residual 1.339 1.213 0.126 5.57e-02 3.22e+02 5.13e+00 bond pdb=" C CYS t 311 " pdb=" N LYS t 312 " ideal model delta sigma weight residual 1.335 1.256 0.079 3.59e-02 7.76e+02 4.81e+00 bond pdb=" N GLU t 324 " pdb=" CA GLU t 324 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.64e+00 bond pdb=" C5' G w 10 " pdb=" C4' G w 10 " ideal model delta sigma weight residual 1.508 1.480 0.028 1.50e-02 4.44e+03 3.59e+00 bond pdb=" CB VAL r 71 " pdb=" CG2 VAL r 71 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 ... (remaining 6965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 9310 3.00 - 6.01: 484 6.01 - 9.01: 35 9.01 - 12.01: 6 12.01 - 15.02: 5 Bond angle restraints: 9840 Sorted by residual: angle pdb=" N PRO t 168 " pdb=" CA PRO t 168 " pdb=" C PRO t 168 " ideal model delta sigma weight residual 112.47 124.78 -12.31 2.06e+00 2.36e-01 3.57e+01 angle pdb=" N VAL s 203 " pdb=" CA VAL s 203 " pdb=" C VAL s 203 " ideal model delta sigma weight residual 109.34 97.09 12.25 2.08e+00 2.31e-01 3.47e+01 angle pdb=" N GLY s 252 " pdb=" CA GLY s 252 " pdb=" C GLY s 252 " ideal model delta sigma weight residual 112.18 105.50 6.68 1.34e+00 5.57e-01 2.48e+01 angle pdb=" CA ARG s 272 " pdb=" CB ARG s 272 " pdb=" CG ARG s 272 " ideal model delta sigma weight residual 114.10 124.02 -9.92 2.00e+00 2.50e-01 2.46e+01 angle pdb=" C4' G w 52 " pdb=" C3' G w 52 " pdb=" O3' G w 52 " ideal model delta sigma weight residual 113.00 120.35 -7.35 1.50e+00 4.44e-01 2.40e+01 ... (remaining 9835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 3765 24.56 - 49.11: 386 49.11 - 73.67: 141 73.67 - 98.23: 18 98.23 - 122.78: 2 Dihedral angle restraints: 4312 sinusoidal: 2090 harmonic: 2222 Sorted by residual: dihedral pdb=" O4' C w 73 " pdb=" C1' C w 73 " pdb=" N1 C w 73 " pdb=" C2 C w 73 " ideal model delta sinusoidal sigma weight residual -128.00 -44.83 -83.17 1 1.70e+01 3.46e-03 2.93e+01 dihedral pdb=" O4' A k 17 " pdb=" C2' A k 17 " pdb=" C1' A k 17 " pdb=" C3' A k 17 " ideal model delta sinusoidal sigma weight residual 25.00 -9.51 34.51 1 8.00e+00 1.56e-02 2.64e+01 dihedral pdb=" O4' A k 16 " pdb=" C2' A k 16 " pdb=" C1' A k 16 " pdb=" C3' A k 16 " ideal model delta sinusoidal sigma weight residual 25.00 -9.08 34.08 1 8.00e+00 1.56e-02 2.58e+01 ... (remaining 4309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 883 0.068 - 0.136: 271 0.136 - 0.204: 68 0.204 - 0.272: 9 0.272 - 0.340: 4 Chirality restraints: 1235 Sorted by residual: chirality pdb=" C1' C w 73 " pdb=" O4' C w 73 " pdb=" C2' C w 73 " pdb=" N1 C w 73 " both_signs ideal model delta sigma weight residual False 2.45 2.11 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB VAL r 34 " pdb=" CA VAL r 34 " pdb=" CG1 VAL r 34 " pdb=" CG2 VAL r 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA PRO t 168 " pdb=" N PRO t 168 " pdb=" C PRO t 168 " pdb=" CB PRO t 168 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 1232 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN s 292 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" CD GLN s 292 " 0.063 2.00e-02 2.50e+03 pdb=" OE1 GLN s 292 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN s 292 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G w 12 " -0.008 2.00e-02 2.50e+03 2.03e-02 1.24e+01 pdb=" N9 G w 12 " 0.037 2.00e-02 2.50e+03 pdb=" C8 G w 12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G w 12 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G w 12 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G w 12 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G w 12 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G w 12 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G w 12 " 0.033 2.00e-02 2.50e+03 pdb=" N2 G w 12 " -0.017 2.00e-02 2.50e+03 pdb=" N3 G w 12 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G w 12 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA t 323 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ALA t 323 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA t 323 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU t 324 " 0.019 2.00e-02 2.50e+03 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 888 2.74 - 3.28: 6205 3.28 - 3.82: 11334 3.82 - 4.36: 12440 4.36 - 4.90: 19659 Nonbonded interactions: 50526 Sorted by model distance: nonbonded pdb=" O6 G w 9 " pdb=" O2' A w 19 " model vdw 2.202 3.040 nonbonded pdb=" O ALA s 196 " pdb=" NH2 ARG s 285 " model vdw 2.245 3.120 nonbonded pdb=" OG1 THR s 246 " pdb=" O LYS s 259 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR r 220 " pdb=" O MET r 223 " model vdw 2.259 3.040 nonbonded pdb=" O LYS r 104 " pdb=" OG1 THR r 107 " model vdw 2.277 3.040 ... (remaining 50521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 6970 Z= 0.427 Angle : 1.466 15.017 9840 Z= 0.842 Chirality : 0.071 0.340 1235 Planarity : 0.009 0.069 1011 Dihedral : 21.435 122.782 2868 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.09 % Favored : 93.38 % Rotamer: Outliers : 6.67 % Allowed : 22.67 % Favored : 70.67 % 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: -2.26 (0.26), residues: 755 helix: -0.78 (0.32), residues: 214 sheet: 0.05 (0.50), residues: 109 loop : -2.41 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG s 285 TYR 0.030 0.004 TYR s 176 PHE 0.032 0.005 PHE r 131 TRP 0.009 0.004 TRP r 136 HIS 0.007 0.003 HIS r 155 Details of bonding type rmsd covalent geometry : bond 0.00840 ( 6970) covalent geometry : angle 1.46567 ( 9840) hydrogen bonds : bond 0.24647 ( 253) hydrogen bonds : angle 9.06598 ( 680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 74 ILE cc_start: 0.7523 (mm) cc_final: 0.7291 (mm) REVERT: r 89 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.4586 (mmt180) REVERT: r 121 TYR cc_start: 0.2630 (OUTLIER) cc_final: 0.1330 (m-80) REVERT: r 182 ARG cc_start: 0.7039 (mtm180) cc_final: 0.6591 (ttp-170) REVERT: r 273 MET cc_start: 0.3051 (mtt) cc_final: 0.0830 (ttt) outliers start: 25 outliers final: 6 residues processed: 120 average time/residue: 0.1263 time to fit residues: 18.6076 Evaluate side-chains 62 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 244 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 121 TYR Chi-restraints excluded: chain r residue 271 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 181 ASN ** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 306 HIS ** r 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.113221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.105072 restraints weight = 41508.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.105459 restraints weight = 41216.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.106749 restraints weight = 29186.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.106558 restraints weight = 25179.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.107250 restraints weight = 19307.280| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 6970 Z= 0.391 Angle : 1.033 12.100 9840 Z= 0.546 Chirality : 0.054 0.248 1235 Planarity : 0.008 0.078 1011 Dihedral : 21.585 124.644 2021 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.81 % Favored : 91.92 % Rotamer: Outliers : 6.67 % Allowed : 31.47 % Favored : 61.87 % 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: -2.56 (0.27), residues: 755 helix: -0.90 (0.31), residues: 220 sheet: -0.90 (0.53), residues: 94 loop : -2.41 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG r 234 TYR 0.019 0.004 TYR r 147 PHE 0.023 0.003 PHE s 239 TRP 0.015 0.003 TRP r 136 HIS 0.018 0.004 HIS s 306 Details of bonding type rmsd covalent geometry : bond 0.00784 ( 6970) covalent geometry : angle 1.03269 ( 9840) hydrogen bonds : bond 0.09320 ( 253) hydrogen bonds : angle 7.33577 ( 680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 264 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: r 48 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8576 (tm) REVERT: r 89 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.5839 (mmt180) REVERT: r 182 ARG cc_start: 0.7372 (mtm180) cc_final: 0.6893 (ttp80) outliers start: 25 outliers final: 13 residues processed: 83 average time/residue: 0.0950 time to fit residues: 10.3878 Evaluate side-chains 63 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 221 ASN Chi-restraints excluded: chain s residue 228 LEU Chi-restraints excluded: chain s residue 264 GLN Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 280 THR Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 121 TYR Chi-restraints excluded: chain r residue 230 ILE Chi-restraints excluded: chain r residue 268 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 292 GLN r 40 ASN ** r 179 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 = 0.4259 r_free = 0.4259 target = 0.111712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.105289 restraints weight = 40230.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.105543 restraints weight = 35016.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.105946 restraints weight = 28356.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.105887 restraints weight = 24031.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.105963 restraints weight = 23475.216| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4147 r_free = 0.4147 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4147 r_free = 0.4147 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 6970 Z= 0.344 Angle : 0.976 17.367 9840 Z= 0.504 Chirality : 0.052 0.258 1235 Planarity : 0.007 0.065 1011 Dihedral : 21.579 134.199 2018 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.54 % Favored : 90.20 % Rotamer: Outliers : 6.93 % Allowed : 30.40 % Favored : 62.67 % 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: -3.21 (0.26), residues: 755 helix: -1.25 (0.30), residues: 220 sheet: -2.39 (0.45), residues: 108 loop : -2.62 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG s 296 TYR 0.025 0.003 TYR r 109 PHE 0.015 0.003 PHE s 299 TRP 0.009 0.002 TRP r 136 HIS 0.006 0.002 HIS s 235 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 6970) covalent geometry : angle 0.97579 ( 9840) hydrogen bonds : bond 0.08803 ( 253) hydrogen bonds : angle 7.09753 ( 680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: s 226 CYS cc_start: 0.5660 (t) cc_final: 0.4977 (t) REVERT: s 264 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: r 30 MET cc_start: 0.6005 (ptt) cc_final: 0.5734 (ptm) REVERT: r 89 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.5780 (mmt180) REVERT: r 103 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7309 (t) REVERT: r 182 ARG cc_start: 0.7047 (mtm180) cc_final: 0.6770 (ttp80) outliers start: 26 outliers final: 6 residues processed: 79 average time/residue: 0.1163 time to fit residues: 11.5331 Evaluate side-chains 52 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 264 GLN Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain r residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 221 ASN ** r 179 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.114555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.106832 restraints weight = 41438.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.107163 restraints weight = 39198.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.108508 restraints weight = 28974.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.108402 restraints weight = 21725.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.109024 restraints weight = 17950.310| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4209 r_free = 0.4209 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4209 r_free = 0.4209 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6970 Z= 0.156 Angle : 0.698 9.476 9840 Z= 0.369 Chirality : 0.046 0.212 1235 Planarity : 0.005 0.049 1011 Dihedral : 21.032 125.335 2014 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.75 % Favored : 92.98 % Rotamer: Outliers : 5.60 % Allowed : 30.93 % Favored : 63.47 % 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: -2.51 (0.28), residues: 755 helix: -0.56 (0.31), residues: 229 sheet: -1.69 (0.49), residues: 92 loop : -2.38 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG r 7 TYR 0.016 0.002 TYR r 150 PHE 0.020 0.002 PHE s 239 TRP 0.004 0.001 TRP r 136 HIS 0.003 0.001 HIS s 230 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6970) covalent geometry : angle 0.69844 ( 9840) hydrogen bonds : bond 0.07146 ( 253) hydrogen bonds : angle 6.00887 ( 680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.213 Fit side-chains REVERT: s 204 MET cc_start: 0.3973 (pmm) cc_final: 0.2744 (pmm) REVERT: s 226 CYS cc_start: 0.5185 (t) cc_final: 0.4902 (t) REVERT: r 30 MET cc_start: 0.5588 (ptt) cc_final: 0.5363 (ptm) REVERT: r 89 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.5427 (mmt180) REVERT: r 182 ARG cc_start: 0.7582 (mtm180) cc_final: 0.6795 (ttp80) REVERT: r 220 THR cc_start: 0.3903 (OUTLIER) cc_final: 0.3651 (m) outliers start: 21 outliers final: 9 residues processed: 67 average time/residue: 0.0911 time to fit residues: 8.0758 Evaluate side-chains 57 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 280 THR Chi-restraints excluded: chain s residue 306 HIS Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 220 THR Chi-restraints excluded: chain r residue 229 LEU Chi-restraints excluded: chain r residue 268 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.112174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.105126 restraints weight = 41709.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.105232 restraints weight = 37365.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.105885 restraints weight = 30303.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.105860 restraints weight = 24090.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.105919 restraints weight = 22751.258| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6970 Z= 0.246 Angle : 0.821 16.102 9840 Z= 0.424 Chirality : 0.048 0.204 1235 Planarity : 0.006 0.056 1011 Dihedral : 21.331 110.161 2014 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.46 % Favored : 89.27 % Rotamer: Outliers : 5.33 % Allowed : 32.00 % Favored : 62.67 % 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: -2.79 (0.27), residues: 755 helix: -0.67 (0.31), residues: 222 sheet: -2.81 (0.48), residues: 86 loop : -2.36 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG s 296 TYR 0.018 0.003 TYR r 82 PHE 0.023 0.002 PHE s 239 TRP 0.007 0.002 TRP r 136 HIS 0.006 0.002 HIS s 306 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 6970) covalent geometry : angle 0.82082 ( 9840) hydrogen bonds : bond 0.07580 ( 253) hydrogen bonds : angle 6.46077 ( 680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: s 204 MET cc_start: 0.3922 (pmm) cc_final: 0.3021 (pmm) REVERT: s 208 GLN cc_start: 0.3537 (OUTLIER) cc_final: 0.2471 (tm-30) REVERT: s 231 ARG cc_start: 0.5334 (tpt-90) cc_final: 0.5089 (tpt-90) REVERT: r 89 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.5696 (mmt180) REVERT: r 182 ARG cc_start: 0.7316 (mtm180) cc_final: 0.6797 (ttp80) outliers start: 20 outliers final: 11 residues processed: 65 average time/residue: 0.0809 time to fit residues: 7.1800 Evaluate side-chains 58 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 208 GLN Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain s residue 280 THR Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 0.0570 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.116332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.108413 restraints weight = 42065.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.109336 restraints weight = 29191.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.110010 restraints weight = 21984.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.110473 restraints weight = 17703.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.110782 restraints weight = 15034.020| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6970 Z= 0.124 Angle : 0.627 8.576 9840 Z= 0.324 Chirality : 0.043 0.212 1235 Planarity : 0.004 0.041 1011 Dihedral : 20.729 104.139 2014 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.23 % Favored : 93.51 % Rotamer: Outliers : 4.27 % Allowed : 34.13 % Favored : 61.60 % 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: -1.91 (0.29), residues: 755 helix: 0.27 (0.33), residues: 225 sheet: -1.78 (0.50), residues: 92 loop : -2.07 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG s 182 TYR 0.011 0.001 TYR r 82 PHE 0.010 0.001 PHE s 239 TRP 0.005 0.001 TRP r 136 HIS 0.002 0.001 HIS s 306 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6970) covalent geometry : angle 0.62679 ( 9840) hydrogen bonds : bond 0.06700 ( 253) hydrogen bonds : angle 5.50459 ( 680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.182 Fit side-chains REVERT: s 298 TYR cc_start: 0.5981 (m-80) cc_final: 0.5772 (m-80) REVERT: r 89 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.5421 (mmt180) REVERT: r 272 GLN cc_start: 0.3775 (tp40) cc_final: 0.3407 (mm110) outliers start: 16 outliers final: 8 residues processed: 63 average time/residue: 0.0851 time to fit residues: 6.9743 Evaluate side-chains 52 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 306 HIS Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 80 optimal weight: 30.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.114645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.106691 restraints weight = 41305.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.107595 restraints weight = 28471.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.108248 restraints weight = 21771.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.108680 restraints weight = 17598.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.108857 restraints weight = 15041.080| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6970 Z= 0.164 Angle : 0.666 12.243 9840 Z= 0.346 Chirality : 0.044 0.198 1235 Planarity : 0.005 0.057 1011 Dihedral : 20.824 100.201 2013 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.54 % Favored : 90.20 % Rotamer: Outliers : 4.27 % Allowed : 33.07 % Favored : 62.67 % 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: -2.00 (0.29), residues: 755 helix: 0.11 (0.33), residues: 224 sheet: -1.72 (0.53), residues: 85 loop : -2.10 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG s 211 TYR 0.017 0.002 TYR s 274 PHE 0.010 0.002 PHE s 299 TRP 0.006 0.002 TRP r 136 HIS 0.003 0.001 HIS s 230 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6970) covalent geometry : angle 0.66570 ( 9840) hydrogen bonds : bond 0.06769 ( 253) hydrogen bonds : angle 5.68488 ( 680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: s 226 CYS cc_start: 0.6270 (p) cc_final: 0.5803 (t) REVERT: r 89 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.5645 (mmt180) REVERT: r 182 ARG cc_start: 0.6776 (mtm180) cc_final: 0.6474 (ttp80) REVERT: r 209 LYS cc_start: 0.2961 (OUTLIER) cc_final: 0.2340 (mmtt) outliers start: 16 outliers final: 9 residues processed: 58 average time/residue: 0.0911 time to fit residues: 7.0239 Evaluate side-chains 57 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 279 VAL Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 209 LYS Chi-restraints excluded: chain r residue 242 LEU Chi-restraints excluded: chain r residue 274 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 0.0030 chunk 46 optimal weight: 9.9990 chunk 70 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.116674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.108943 restraints weight = 42025.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.109830 restraints weight = 29482.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.110438 restraints weight = 22586.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.110854 restraints weight = 18369.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.111151 restraints weight = 15808.676| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4233 r_free = 0.4233 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4233 r_free = 0.4233 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6970 Z= 0.123 Angle : 0.599 8.631 9840 Z= 0.311 Chirality : 0.042 0.208 1235 Planarity : 0.004 0.064 1011 Dihedral : 20.564 103.014 2013 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.23 % Favored : 93.51 % Rotamer: Outliers : 3.47 % Allowed : 32.80 % Favored : 63.73 % 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: -1.65 (0.30), residues: 755 helix: 0.71 (0.34), residues: 221 sheet: -1.78 (0.48), residues: 103 loop : -1.98 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG s 296 TYR 0.010 0.001 TYR s 278 PHE 0.007 0.001 PHE r 131 TRP 0.008 0.003 TRP r 136 HIS 0.003 0.001 HIS s 235 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6970) covalent geometry : angle 0.59928 ( 9840) hydrogen bonds : bond 0.06358 ( 253) hydrogen bonds : angle 5.26887 ( 680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.218 Fit side-chains REVERT: s 226 CYS cc_start: 0.6146 (p) cc_final: 0.5691 (t) REVERT: s 288 ASP cc_start: 0.5901 (m-30) cc_final: 0.5188 (p0) REVERT: r 89 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.5491 (mmt180) REVERT: r 179 ASN cc_start: 0.6588 (p0) cc_final: 0.6111 (p0) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.0892 time to fit residues: 7.3034 Evaluate side-chains 55 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 280 THR Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.116157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.108290 restraints weight = 41857.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.109204 restraints weight = 29337.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.109742 restraints weight = 22264.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.110236 restraints weight = 18501.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.110575 restraints weight = 15784.537| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4221 r_free = 0.4221 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4221 r_free = 0.4221 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6970 Z= 0.127 Angle : 0.617 10.136 9840 Z= 0.317 Chirality : 0.042 0.206 1235 Planarity : 0.004 0.061 1011 Dihedral : 20.517 100.957 2012 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.05 % Rotamer: Outliers : 3.20 % Allowed : 32.80 % Favored : 64.00 % 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: -1.68 (0.29), residues: 755 helix: 0.62 (0.34), residues: 224 sheet: -1.82 (0.48), residues: 105 loop : -1.96 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG s 285 TYR 0.018 0.002 TYR r 9 PHE 0.011 0.001 PHE r 8 TRP 0.003 0.001 TRP r 136 HIS 0.002 0.001 HIS s 235 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6970) covalent geometry : angle 0.61650 ( 9840) hydrogen bonds : bond 0.06219 ( 253) hydrogen bonds : angle 5.26454 ( 680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 89 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.5514 (mmt180) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.0898 time to fit residues: 6.9432 Evaluate side-chains 53 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 280 THR Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 229 LEU Chi-restraints excluded: chain r residue 274 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 76 optimal weight: 0.0050 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 0.0070 overall best weight: 1.1216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.116422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.108847 restraints weight = 40778.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.109505 restraints weight = 35133.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.110562 restraints weight = 25022.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.110436 restraints weight = 21313.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.110780 restraints weight = 17003.872| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6970 Z= 0.125 Angle : 0.620 10.242 9840 Z= 0.317 Chirality : 0.042 0.213 1235 Planarity : 0.004 0.066 1011 Dihedral : 20.459 101.268 2012 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.75 % Favored : 93.11 % Rotamer: Outliers : 3.73 % Allowed : 32.00 % Favored : 64.27 % 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: -1.56 (0.30), residues: 755 helix: 0.66 (0.34), residues: 225 sheet: -1.58 (0.49), residues: 96 loop : -1.91 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG r 89 TYR 0.011 0.002 TYR r 9 PHE 0.012 0.001 PHE r 8 TRP 0.002 0.001 TRP r 136 HIS 0.002 0.001 HIS s 230 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6970) covalent geometry : angle 0.61965 ( 9840) hydrogen bonds : bond 0.06048 ( 253) hydrogen bonds : angle 5.16551 ( 680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: r 89 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.5466 (mmt180) outliers start: 14 outliers final: 12 residues processed: 56 average time/residue: 0.0935 time to fit residues: 6.9731 Evaluate side-chains 54 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 217 THR Chi-restraints excluded: chain s residue 224 ASP Chi-restraints excluded: chain s residue 280 THR Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 119 LEU Chi-restraints excluded: chain r residue 229 LEU Chi-restraints excluded: chain r residue 242 LEU Chi-restraints excluded: chain r residue 274 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 71 optimal weight: 50.0000 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.116986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.110112 restraints weight = 40810.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.110208 restraints weight = 42761.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.110568 restraints weight = 35915.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.110407 restraints weight = 35680.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.110579 restraints weight = 30039.769| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6970 Z= 0.117 Angle : 0.609 10.041 9840 Z= 0.310 Chirality : 0.042 0.212 1235 Planarity : 0.004 0.066 1011 Dihedral : 20.380 101.816 2012 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.55 % Favored : 92.32 % Rotamer: Outliers : 3.47 % Allowed : 32.53 % Favored : 64.00 % 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: -1.47 (0.30), residues: 755 helix: 0.73 (0.34), residues: 225 sheet: -1.58 (0.48), residues: 101 loop : -1.84 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG r 67 TYR 0.010 0.001 TYR r 9 PHE 0.009 0.001 PHE r 8 TRP 0.002 0.001 TRP r 136 HIS 0.001 0.000 HIS r 114 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6970) covalent geometry : angle 0.60881 ( 9840) hydrogen bonds : bond 0.05881 ( 253) hydrogen bonds : angle 5.11688 ( 680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1416.75 seconds wall clock time: 25 minutes 11.03 seconds (1511.03 seconds total)