Starting phenix.real_space_refine on Wed Feb 4 16:18:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ln4_63226/02_2026/9ln4_63226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ln4_63226/02_2026/9ln4_63226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ln4_63226/02_2026/9ln4_63226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ln4_63226/02_2026/9ln4_63226.map" model { file = "/net/cci-nas-00/data/ceres_data/9ln4_63226/02_2026/9ln4_63226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ln4_63226/02_2026/9ln4_63226.cif" } resolution = 3.09 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 58 5.16 5 C 7351 2.51 5 N 1960 2.21 5 O 2247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 11636 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2174 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain breaks: 1 Chain: "B" Number of atoms: 2294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2283 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 13, 'TRANS': 275} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 289, 2283 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 13, 'TRANS': 275} Chain breaks: 1 bond proxies already assigned to first conformer: 2308 Chain: "C" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2289 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 74 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG B 74 " occ=0.54 Time building chain proxies: 2.73, per 1000 atoms: 0.23 Number of scatterers: 11636 At special positions: 0 Unit cell: (83.23, 124.64, 134.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 15 15.00 Mg 5 11.99 O 2247 8.00 N 1960 7.00 C 7351 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: 0.81 Conformation dependent library (CDL) restraints added in 637.9 milliseconds 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 5 sheets defined 56.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.722A pdb=" N ALA A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.508A pdb=" N LEU A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.173A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.938A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.919A pdb=" N GLU B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 96 through 106 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.501A pdb=" N LEU B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.173A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.938A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.803A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.174A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.938A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.722A pdb=" N ALA D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.173A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 289 removed outlier: 3.938A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 341 through 348 Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.722A pdb=" N ALA E 65 " --> pdb=" O PRO E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.174A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 289 removed outlier: 3.938A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 319 Processing helix chain 'E' and resid 341 through 348 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 4.191A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 234 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL A 129 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR A 235 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 131 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 4.190A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 234 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL B 129 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR B 235 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU B 131 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 4.190A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL C 129 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR C 235 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 131 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 4.191A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP D 192 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL D 129 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N THR D 235 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU D 131 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 removed outlier: 4.191A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE E 190 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP E 192 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL E 129 " --> pdb=" O GLY E 233 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N THR E 235 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU E 131 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1579 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: 1.75 Time building geometry restraints manager: 1.13 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: 2459 1.33 - 1.45: 2401 1.45 - 1.57: 6835 1.57 - 1.69: 30 1.69 - 1.81: 101 Bond restraints: 11826 Sorted by residual: bond pdb=" CA LEU B 276 " pdb=" C LEU B 276 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.19e-02 7.06e+03 5.96e+00 bond pdb=" C LEU C 103 " pdb=" O LEU C 103 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.19e-02 7.06e+03 5.93e+00 bond pdb=" C LEU D 103 " pdb=" O LEU D 103 " ideal model delta sigma weight residual 1.236 1.209 0.028 1.15e-02 7.56e+03 5.81e+00 bond pdb=" C ARG D 337 " pdb=" N PRO D 338 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.93e+00 bond pdb=" C LEU A 103 " pdb=" O LEU A 103 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.17e-02 7.31e+03 4.76e+00 ... (remaining 11821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 14841 1.58 - 3.16: 849 3.16 - 4.75: 212 4.75 - 6.33: 43 6.33 - 7.91: 40 Bond angle restraints: 15985 Sorted by residual: angle pdb=" CB GLN B 193 " pdb=" CG GLN B 193 " pdb=" CD GLN B 193 " ideal model delta sigma weight residual 112.60 120.51 -7.91 1.70e+00 3.46e-01 2.17e+01 angle pdb=" CB GLN E 193 " pdb=" CG GLN E 193 " pdb=" CD GLN E 193 " ideal model delta sigma weight residual 112.60 120.49 -7.89 1.70e+00 3.46e-01 2.15e+01 angle pdb=" CB GLN A 193 " pdb=" CG GLN A 193 " pdb=" CD GLN A 193 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.70e+00 3.46e-01 2.14e+01 angle pdb=" CB GLN C 193 " pdb=" CG GLN C 193 " pdb=" CD GLN C 193 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.70e+00 3.46e-01 2.14e+01 angle pdb=" CB GLN D 193 " pdb=" CG GLN D 193 " pdb=" CD GLN D 193 " ideal model delta sigma weight residual 112.60 120.45 -7.85 1.70e+00 3.46e-01 2.13e+01 ... (remaining 15980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.53: 6353 18.53 - 37.06: 772 37.06 - 55.59: 215 55.59 - 74.11: 55 74.11 - 92.64: 26 Dihedral angle restraints: 7421 sinusoidal: 3159 harmonic: 4262 Sorted by residual: dihedral pdb=" CA ARG C 349 " pdb=" C ARG C 349 " pdb=" N MET C 350 " pdb=" CA MET C 350 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE B 90 " pdb=" C PHE B 90 " pdb=" N GLN B 91 " pdb=" CA GLN B 91 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE E 90 " pdb=" C PHE E 90 " pdb=" N GLN E 91 " pdb=" CA GLN E 91 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 7418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1460 0.061 - 0.122: 305 0.122 - 0.183: 61 0.183 - 0.244: 6 0.244 - 0.305: 2 Chirality restraints: 1834 Sorted by residual: chirality pdb=" CB VAL C 107 " pdb=" CA VAL C 107 " pdb=" CG1 VAL C 107 " pdb=" CG2 VAL C 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB VAL D 107 " pdb=" CA VAL D 107 " pdb=" CG1 VAL D 107 " pdb=" CG2 VAL D 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB VAL A 107 " pdb=" CA VAL A 107 " pdb=" CG1 VAL A 107 " pdb=" CG2 VAL A 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1831 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 193 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" CD GLN B 193 " -0.056 2.00e-02 2.50e+03 pdb=" OE1 GLN B 193 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN B 193 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 193 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.07e+01 pdb=" CD GLN E 193 " 0.056 2.00e-02 2.50e+03 pdb=" OE1 GLN E 193 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN E 193 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 193 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" CD GLN A 193 " -0.056 2.00e-02 2.50e+03 pdb=" OE1 GLN A 193 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN A 193 " 0.020 2.00e-02 2.50e+03 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 109 2.60 - 3.18: 9803 3.18 - 3.75: 19382 3.75 - 4.33: 26510 4.33 - 4.90: 43082 Nonbonded interactions: 98886 Sorted by model distance: nonbonded pdb=" OG1 THR C 140 " pdb="MG MG C 402 " model vdw 2.026 2.170 nonbonded pdb=" O1G ATP B 401 " pdb="MG MG B 402 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 402 " model vdw 2.039 2.170 nonbonded pdb=" O1G ATP C 401 " pdb="MG MG C 402 " model vdw 2.047 2.170 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG C 403 " model vdw 2.073 2.170 ... (remaining 98881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 48 through 73 or resid 75 through 348)) selection = (chain 'B' and (resid 48 through 73 or resid 75 through 313 or resid 338 through \ 348)) selection = (chain 'C' and (resid 48 through 73 or resid 75 through 313 or resid 338 through \ 348)) selection = (chain 'D' and (resid 48 through 73 or resid 75 through 313 or resid 338 through \ 348)) selection = (chain 'E' and (resid 48 through 73 or resid 75 through 313 or resid 338 through \ 348)) } 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=0.00 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: 11.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.570 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.500 Find NCS groups from input model: 0.180 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.005 0.054 11826 Z= 0.249 Angle : 0.950 7.912 15985 Z= 0.522 Chirality : 0.054 0.305 1834 Planarity : 0.007 0.079 2005 Dihedral : 18.664 92.642 4643 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.90 % Allowed : 8.71 % Favored : 84.39 % 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 (0.21), residues: 1427 helix: -0.27 (0.17), residues: 800 sheet: -0.18 (0.48), residues: 135 loop : -0.59 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 228 TYR 0.022 0.003 TYR A 313 PHE 0.010 0.002 PHE C 190 TRP 0.016 0.003 TRP E 220 HIS 0.008 0.003 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00509 (11826) covalent geometry : angle 0.95017 (15985) hydrogen bonds : bond 0.16161 ( 528) hydrogen bonds : angle 6.49708 ( 1579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 332 time to evaluate : 0.442 Fit side-chains REVERT: A 163 MET cc_start: 0.6174 (mmt) cc_final: 0.4759 (ttm) REVERT: A 215 GLU cc_start: 0.8383 (tp30) cc_final: 0.8010 (tp30) REVERT: B 51 SER cc_start: 0.8536 (m) cc_final: 0.8231 (m) REVERT: B 92 ASP cc_start: 0.6983 (m-30) cc_final: 0.6776 (m-30) REVERT: B 161 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8635 (m) REVERT: C 161 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8309 (m) REVERT: C 200 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7049 (pt0) REVERT: C 264 TYR cc_start: 0.8141 (t80) cc_final: 0.7929 (t80) REVERT: D 163 MET cc_start: 0.4590 (mmt) cc_final: 0.4260 (mmt) REVERT: D 288 ASP cc_start: 0.8053 (m-30) cc_final: 0.7708 (m-30) REVERT: D 335 LYS cc_start: 0.6693 (ptmt) cc_final: 0.6483 (ptmt) REVERT: E 73 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7857 (mt-10) REVERT: E 159 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.6001 (mmt) REVERT: E 163 MET cc_start: 0.4323 (mmt) cc_final: 0.3841 (mmt) REVERT: E 200 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: E 274 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7430 (m) REVERT: E 307 LEU cc_start: 0.8034 (mt) cc_final: 0.7534 (mt) REVERT: E 340 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7405 (mptt) outliers start: 88 outliers final: 9 residues processed: 375 average time/residue: 0.1096 time to fit residues: 56.9036 Evaluate side-chains 229 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120464 restraints weight = 18241.639| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.58 r_work: 0.3216 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11826 Z= 0.164 Angle : 0.638 8.486 15985 Z= 0.317 Chirality : 0.043 0.150 1834 Planarity : 0.004 0.039 2005 Dihedral : 11.818 80.146 1756 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.51 % Allowed : 13.80 % Favored : 83.69 % 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: 0.20 (0.22), residues: 1427 helix: 0.62 (0.18), residues: 778 sheet: -0.21 (0.55), residues: 105 loop : -0.34 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 199 TYR 0.011 0.002 TYR D 109 PHE 0.013 0.002 PHE C 178 TRP 0.014 0.001 TRP B 166 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00388 (11826) covalent geometry : angle 0.63800 (15985) hydrogen bonds : bond 0.03757 ( 528) hydrogen bonds : angle 4.62965 ( 1579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.399 Fit side-chains REVERT: A 88 ILE cc_start: 0.7658 (mm) cc_final: 0.7315 (mm) REVERT: A 115 GLU cc_start: 0.7496 (pm20) cc_final: 0.6233 (mm-30) REVERT: A 219 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (mm) REVERT: B 51 SER cc_start: 0.8675 (m) cc_final: 0.8338 (m) REVERT: B 200 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8261 (tt0) REVERT: C 200 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: C 299 LYS cc_start: 0.8387 (tttt) cc_final: 0.8111 (ttpt) REVERT: E 44 ARG cc_start: 0.6496 (mpt180) cc_final: 0.6128 (mmm-85) REVERT: E 167 TYR cc_start: 0.7040 (t80) cc_final: 0.6826 (t80) REVERT: E 200 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7217 (pt0) REVERT: E 215 GLU cc_start: 0.8151 (tp30) cc_final: 0.7943 (tp30) outliers start: 32 outliers final: 20 residues processed: 264 average time/residue: 0.0971 time to fit residues: 36.4347 Evaluate side-chains 225 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 31 optimal weight: 0.5980 chunk 107 optimal weight: 0.3980 chunk 117 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 236 ASN E 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.170475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125132 restraints weight = 20070.356| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.10 r_work: 0.3192 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11826 Z= 0.157 Angle : 0.580 8.777 15985 Z= 0.285 Chirality : 0.042 0.142 1834 Planarity : 0.004 0.028 2005 Dihedral : 11.402 87.941 1738 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.67 % Allowed : 14.98 % Favored : 82.35 % 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: 0.65 (0.23), residues: 1427 helix: 1.06 (0.19), residues: 783 sheet: -0.62 (0.53), residues: 100 loop : -0.14 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 158 TYR 0.016 0.002 TYR E 264 PHE 0.014 0.002 PHE C 197 TRP 0.011 0.001 TRP A 166 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00375 (11826) covalent geometry : angle 0.57961 (15985) hydrogen bonds : bond 0.03353 ( 528) hydrogen bonds : angle 4.41089 ( 1579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.478 Fit side-chains REVERT: A 88 ILE cc_start: 0.7706 (mm) cc_final: 0.7380 (mm) REVERT: A 115 GLU cc_start: 0.7478 (pm20) cc_final: 0.6660 (mp0) REVERT: A 149 GLU cc_start: 0.7752 (tp30) cc_final: 0.7494 (mm-30) REVERT: A 219 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8225 (mm) REVERT: B 51 SER cc_start: 0.8663 (m) cc_final: 0.8384 (m) REVERT: B 275 LYS cc_start: 0.8378 (tptp) cc_final: 0.8173 (tptp) REVERT: C 207 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8464 (pt0) REVERT: C 299 LYS cc_start: 0.8447 (tttt) cc_final: 0.8091 (ttpt) REVERT: D 113 MET cc_start: 0.8518 (mtt) cc_final: 0.8190 (mtt) REVERT: D 311 LYS cc_start: 0.7521 (mtmt) cc_final: 0.7009 (pttt) REVERT: E 44 ARG cc_start: 0.6542 (mpt180) cc_final: 0.6124 (mmm-85) REVERT: E 76 ILE cc_start: 0.8352 (mm) cc_final: 0.8101 (mm) REVERT: E 252 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7678 (mtm-85) REVERT: E 342 LYS cc_start: 0.8290 (tptt) cc_final: 0.7814 (ttpp) outliers start: 34 outliers final: 17 residues processed: 257 average time/residue: 0.0989 time to fit residues: 36.9628 Evaluate side-chains 233 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 140 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 ASN D 53 GLN E 226 ASN E 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125283 restraints weight = 27528.162| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 4.58 r_work: 0.3089 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11826 Z= 0.145 Angle : 0.550 8.919 15985 Z= 0.267 Chirality : 0.041 0.170 1834 Planarity : 0.003 0.028 2005 Dihedral : 11.143 81.046 1729 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.96 % Allowed : 16.94 % Favored : 81.10 % 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: 0.97 (0.23), residues: 1427 helix: 1.27 (0.19), residues: 789 sheet: -0.56 (0.50), residues: 108 loop : 0.11 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 252 TYR 0.014 0.001 TYR E 264 PHE 0.011 0.001 PHE C 197 TRP 0.017 0.001 TRP A 166 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00355 (11826) covalent geometry : angle 0.55026 (15985) hydrogen bonds : bond 0.02999 ( 528) hydrogen bonds : angle 4.28928 ( 1579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.395 Fit side-chains REVERT: A 88 ILE cc_start: 0.7674 (mm) cc_final: 0.7325 (mm) REVERT: A 115 GLU cc_start: 0.7534 (pm20) cc_final: 0.7247 (pm20) REVERT: A 149 GLU cc_start: 0.7723 (tp30) cc_final: 0.7514 (mm-30) REVERT: A 219 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8318 (mm) REVERT: B 51 SER cc_start: 0.8660 (m) cc_final: 0.8371 (m) REVERT: C 207 GLU cc_start: 0.8810 (pt0) cc_final: 0.8603 (pt0) REVERT: C 299 LYS cc_start: 0.8508 (tttt) cc_final: 0.8184 (ttpt) REVERT: D 84 ASP cc_start: 0.8203 (m-30) cc_final: 0.7982 (m-30) REVERT: D 113 MET cc_start: 0.8577 (mtt) cc_final: 0.8262 (mtt) REVERT: D 207 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7931 (pt0) REVERT: D 311 LYS cc_start: 0.7429 (mtmt) cc_final: 0.6925 (pttt) REVERT: E 44 ARG cc_start: 0.6529 (mpt180) cc_final: 0.6076 (mmm-85) REVERT: E 76 ILE cc_start: 0.8357 (mm) cc_final: 0.8135 (mm) REVERT: E 342 LYS cc_start: 0.8283 (tptt) cc_final: 0.7780 (ttpp) outliers start: 25 outliers final: 17 residues processed: 237 average time/residue: 0.1027 time to fit residues: 34.6336 Evaluate side-chains 224 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 299 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 142 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 ASN E 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.163845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113872 restraints weight = 30700.851| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.62 r_work: 0.3063 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11826 Z= 0.154 Angle : 0.548 8.692 15985 Z= 0.265 Chirality : 0.041 0.139 1834 Planarity : 0.003 0.027 2005 Dihedral : 10.971 78.515 1729 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.35 % Allowed : 17.18 % Favored : 80.47 % 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: 1.14 (0.23), residues: 1427 helix: 1.36 (0.19), residues: 794 sheet: -0.35 (0.47), residues: 121 loop : 0.23 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 237 TYR 0.017 0.001 TYR E 264 PHE 0.011 0.001 PHE B 178 TRP 0.011 0.001 TRP A 166 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00375 (11826) covalent geometry : angle 0.54819 (15985) hydrogen bonds : bond 0.03015 ( 528) hydrogen bonds : angle 4.28666 ( 1579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.466 Fit side-chains REVERT: A 88 ILE cc_start: 0.7662 (mm) cc_final: 0.7314 (mm) REVERT: A 115 GLU cc_start: 0.7538 (pm20) cc_final: 0.7229 (pm20) REVERT: A 149 GLU cc_start: 0.7687 (tp30) cc_final: 0.7410 (mm-30) REVERT: A 219 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8296 (mm) REVERT: B 51 SER cc_start: 0.8606 (m) cc_final: 0.8314 (m) REVERT: B 347 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7606 (mmtt) REVERT: B 350 MET cc_start: 0.6707 (ppp) cc_final: 0.6307 (ptm) REVERT: C 164 ASP cc_start: 0.8580 (t70) cc_final: 0.8321 (t0) REVERT: C 207 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: C 299 LYS cc_start: 0.8505 (tttt) cc_final: 0.8161 (ttpt) REVERT: D 84 ASP cc_start: 0.8222 (m-30) cc_final: 0.8001 (m-30) REVERT: D 113 MET cc_start: 0.8507 (mtt) cc_final: 0.8211 (mtt) REVERT: D 311 LYS cc_start: 0.7399 (mtmt) cc_final: 0.6869 (pttt) REVERT: E 44 ARG cc_start: 0.6515 (mpt180) cc_final: 0.6068 (mmm-85) REVERT: E 76 ILE cc_start: 0.8235 (mm) cc_final: 0.7992 (mm) REVERT: E 172 LYS cc_start: 0.7617 (tppt) cc_final: 0.7032 (ttmt) REVERT: E 273 ASP cc_start: 0.7022 (t0) cc_final: 0.6659 (t0) REVERT: E 342 LYS cc_start: 0.8258 (tptt) cc_final: 0.7753 (ttpp) outliers start: 30 outliers final: 20 residues processed: 232 average time/residue: 0.0973 time to fit residues: 32.1765 Evaluate side-chains 226 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 299 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 126 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS E 236 ASN E 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122227 restraints weight = 24621.245| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.98 r_work: 0.3073 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11826 Z= 0.160 Angle : 0.565 8.716 15985 Z= 0.270 Chirality : 0.041 0.136 1834 Planarity : 0.003 0.028 2005 Dihedral : 10.858 83.878 1729 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.20 % Allowed : 18.59 % Favored : 79.22 % 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: 1.27 (0.23), residues: 1427 helix: 1.53 (0.20), residues: 781 sheet: -0.36 (0.45), residues: 134 loop : 0.28 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 199 TYR 0.018 0.001 TYR E 264 PHE 0.012 0.002 PHE B 178 TRP 0.012 0.001 TRP A 166 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00387 (11826) covalent geometry : angle 0.56520 (15985) hydrogen bonds : bond 0.02974 ( 528) hydrogen bonds : angle 4.25913 ( 1579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7811 (mm) cc_final: 0.7457 (mm) REVERT: A 115 GLU cc_start: 0.7566 (pm20) cc_final: 0.7249 (pm20) REVERT: A 149 GLU cc_start: 0.7645 (tp30) cc_final: 0.7398 (mm-30) REVERT: A 219 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 51 SER cc_start: 0.8687 (m) cc_final: 0.8420 (m) REVERT: B 347 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7686 (mmtt) REVERT: B 350 MET cc_start: 0.6772 (ppp) cc_final: 0.6398 (ptm) REVERT: C 164 ASP cc_start: 0.8658 (t70) cc_final: 0.8366 (t0) REVERT: C 207 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: C 299 LYS cc_start: 0.8536 (tttt) cc_final: 0.8181 (ttpt) REVERT: D 113 MET cc_start: 0.8569 (mtt) cc_final: 0.8309 (mtt) REVERT: D 124 GLN cc_start: 0.8385 (pm20) cc_final: 0.7917 (pm20) REVERT: D 311 LYS cc_start: 0.7448 (mtmt) cc_final: 0.7027 (pttt) REVERT: E 44 ARG cc_start: 0.6542 (mpt180) cc_final: 0.6109 (mmm-85) REVERT: E 248 ARG cc_start: 0.8352 (mtt90) cc_final: 0.8126 (mtt-85) REVERT: E 273 ASP cc_start: 0.7100 (t0) cc_final: 0.6754 (t0) REVERT: E 342 LYS cc_start: 0.8296 (tptt) cc_final: 0.7794 (ttpp) outliers start: 28 outliers final: 20 residues processed: 234 average time/residue: 0.1081 time to fit residues: 35.7336 Evaluate side-chains 223 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 79 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 96 optimal weight: 0.4980 chunk 114 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.171205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127277 restraints weight = 25010.773| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.03 r_work: 0.3090 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11826 Z= 0.118 Angle : 0.549 8.113 15985 Z= 0.260 Chirality : 0.040 0.129 1834 Planarity : 0.003 0.028 2005 Dihedral : 10.696 84.851 1729 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.96 % Allowed : 19.84 % Favored : 78.20 % 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: 1.42 (0.23), residues: 1427 helix: 1.66 (0.20), residues: 776 sheet: -0.30 (0.44), residues: 142 loop : 0.36 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 237 TYR 0.015 0.001 TYR E 264 PHE 0.009 0.001 PHE B 178 TRP 0.009 0.001 TRP A 166 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00287 (11826) covalent geometry : angle 0.54894 (15985) hydrogen bonds : bond 0.02751 ( 528) hydrogen bonds : angle 4.18638 ( 1579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.420 Fit side-chains REVERT: A 88 ILE cc_start: 0.7686 (mm) cc_final: 0.7321 (mm) REVERT: A 115 GLU cc_start: 0.7513 (pm20) cc_final: 0.7198 (pm20) REVERT: A 149 GLU cc_start: 0.7639 (tp30) cc_final: 0.7404 (mm-30) REVERT: A 219 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 272 LYS cc_start: 0.7895 (mmmt) cc_final: 0.6845 (pptt) REVERT: B 51 SER cc_start: 0.8679 (m) cc_final: 0.8410 (m) REVERT: B 207 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: B 347 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7670 (mmtt) REVERT: B 350 MET cc_start: 0.6840 (ppp) cc_final: 0.6524 (ptm) REVERT: C 164 ASP cc_start: 0.8598 (t70) cc_final: 0.8312 (t0) REVERT: C 207 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8393 (pt0) REVERT: C 299 LYS cc_start: 0.8528 (tttt) cc_final: 0.8229 (ttpt) REVERT: D 113 MET cc_start: 0.8548 (mtt) cc_final: 0.8279 (mtt) REVERT: D 124 GLN cc_start: 0.8376 (pm20) cc_final: 0.7959 (pm20) REVERT: D 158 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7194 (ttp80) REVERT: D 311 LYS cc_start: 0.7344 (mtmt) cc_final: 0.6991 (pttt) REVERT: D 346 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7528 (mttm) REVERT: E 44 ARG cc_start: 0.6534 (mpt180) cc_final: 0.6059 (mmm-85) REVERT: E 172 LYS cc_start: 0.7599 (tppt) cc_final: 0.7042 (ttmt) REVERT: E 273 ASP cc_start: 0.7222 (t0) cc_final: 0.6871 (t0) REVERT: E 342 LYS cc_start: 0.8291 (tptt) cc_final: 0.7793 (ttpp) outliers start: 25 outliers final: 16 residues processed: 235 average time/residue: 0.1150 time to fit residues: 37.9589 Evaluate side-chains 226 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 124 optimal weight: 0.0030 chunk 127 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.161963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110520 restraints weight = 21545.632| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.77 r_work: 0.3080 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11826 Z= 0.129 Angle : 0.552 7.853 15985 Z= 0.262 Chirality : 0.041 0.132 1834 Planarity : 0.003 0.029 2005 Dihedral : 10.445 86.124 1729 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.04 % Allowed : 20.00 % Favored : 77.96 % 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: 1.46 (0.23), residues: 1427 helix: 1.63 (0.20), residues: 782 sheet: -0.28 (0.44), residues: 143 loop : 0.45 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 201 TYR 0.016 0.001 TYR E 264 PHE 0.010 0.001 PHE B 178 TRP 0.011 0.001 TRP A 166 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00316 (11826) covalent geometry : angle 0.55225 (15985) hydrogen bonds : bond 0.02760 ( 528) hydrogen bonds : angle 4.16993 ( 1579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.475 Fit side-chains REVERT: A 88 ILE cc_start: 0.7759 (mm) cc_final: 0.7363 (mm) REVERT: A 141 MET cc_start: 0.8388 (mmm) cc_final: 0.8080 (mmt) REVERT: A 159 MET cc_start: 0.7628 (tpp) cc_final: 0.7223 (tpp) REVERT: A 219 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8167 (mm) REVERT: B 51 SER cc_start: 0.8645 (m) cc_final: 0.8348 (m) REVERT: B 207 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8219 (pt0) REVERT: B 350 MET cc_start: 0.6857 (ppp) cc_final: 0.6548 (ptm) REVERT: C 164 ASP cc_start: 0.8570 (t70) cc_final: 0.8263 (t0) REVERT: C 207 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: C 299 LYS cc_start: 0.8522 (tttt) cc_final: 0.8213 (ttpt) REVERT: D 113 MET cc_start: 0.8509 (mtt) cc_final: 0.8225 (mtt) REVERT: D 124 GLN cc_start: 0.8355 (pm20) cc_final: 0.7958 (pm20) REVERT: D 158 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7088 (ttp80) REVERT: D 311 LYS cc_start: 0.7354 (mtmt) cc_final: 0.7010 (pttt) REVERT: D 346 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7546 (mttm) REVERT: E 44 ARG cc_start: 0.6537 (mpt180) cc_final: 0.6069 (mmm-85) REVERT: E 172 LYS cc_start: 0.7616 (tppt) cc_final: 0.7071 (ttmt) REVERT: E 177 MET cc_start: 0.8147 (ttp) cc_final: 0.7912 (mtp) REVERT: E 273 ASP cc_start: 0.7211 (t0) cc_final: 0.6871 (t0) REVERT: E 342 LYS cc_start: 0.8336 (tptt) cc_final: 0.7840 (ttpp) outliers start: 26 outliers final: 19 residues processed: 228 average time/residue: 0.1060 time to fit residues: 33.9575 Evaluate side-chains 226 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 82 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 69 optimal weight: 0.0000 chunk 129 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.161835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119506 restraints weight = 32374.711| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 5.61 r_work: 0.2947 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11826 Z= 0.138 Angle : 0.565 8.165 15985 Z= 0.268 Chirality : 0.041 0.137 1834 Planarity : 0.003 0.030 2005 Dihedral : 10.363 86.937 1729 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.12 % Allowed : 19.92 % Favored : 77.96 % 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: 1.51 (0.24), residues: 1427 helix: 1.65 (0.20), residues: 782 sheet: -0.22 (0.45), residues: 143 loop : 0.50 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 248 TYR 0.015 0.001 TYR E 264 PHE 0.011 0.001 PHE B 178 TRP 0.010 0.001 TRP A 166 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00340 (11826) covalent geometry : angle 0.56485 (15985) hydrogen bonds : bond 0.02756 ( 528) hydrogen bonds : angle 4.15711 ( 1579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7760 (mm) cc_final: 0.7353 (mm) REVERT: A 141 MET cc_start: 0.8408 (mmm) cc_final: 0.8115 (mmt) REVERT: A 159 MET cc_start: 0.7779 (tpp) cc_final: 0.7378 (tpp) REVERT: A 205 ASP cc_start: 0.7932 (m-30) cc_final: 0.7650 (m-30) REVERT: A 219 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 272 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7290 (mtmt) REVERT: B 51 SER cc_start: 0.8689 (m) cc_final: 0.8411 (m) REVERT: B 207 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: B 350 MET cc_start: 0.6918 (ppp) cc_final: 0.6656 (ptm) REVERT: C 164 ASP cc_start: 0.8760 (t70) cc_final: 0.8478 (t0) REVERT: C 207 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8505 (pt0) REVERT: C 299 LYS cc_start: 0.8626 (tttt) cc_final: 0.8323 (ttpt) REVERT: D 113 MET cc_start: 0.8596 (mtt) cc_final: 0.8324 (mtt) REVERT: D 124 GLN cc_start: 0.8468 (pm20) cc_final: 0.8071 (pm20) REVERT: D 158 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7136 (ttp80) REVERT: D 311 LYS cc_start: 0.7367 (mtmt) cc_final: 0.7010 (pttt) REVERT: D 346 LYS cc_start: 0.8350 (ttmt) cc_final: 0.7556 (mttm) REVERT: E 44 ARG cc_start: 0.6493 (mpt180) cc_final: 0.6011 (mmm-85) REVERT: E 273 ASP cc_start: 0.7333 (t0) cc_final: 0.6975 (t0) REVERT: E 342 LYS cc_start: 0.8300 (tptt) cc_final: 0.7799 (ttpp) outliers start: 27 outliers final: 21 residues processed: 221 average time/residue: 0.1133 time to fit residues: 35.1426 Evaluate side-chains 227 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117945 restraints weight = 26891.711| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.29 r_work: 0.2961 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11826 Z= 0.137 Angle : 0.567 8.392 15985 Z= 0.269 Chirality : 0.041 0.131 1834 Planarity : 0.003 0.031 2005 Dihedral : 10.293 87.593 1729 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.96 % Allowed : 20.47 % Favored : 77.57 % 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: 1.52 (0.24), residues: 1427 helix: 1.64 (0.20), residues: 788 sheet: -0.24 (0.45), residues: 144 loop : 0.56 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 248 TYR 0.014 0.001 TYR E 264 PHE 0.011 0.001 PHE B 178 TRP 0.011 0.001 TRP A 166 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00339 (11826) covalent geometry : angle 0.56696 (15985) hydrogen bonds : bond 0.02758 ( 528) hydrogen bonds : angle 4.16061 ( 1579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7761 (mm) cc_final: 0.7429 (mm) REVERT: A 141 MET cc_start: 0.8398 (mmm) cc_final: 0.7936 (mtp) REVERT: A 159 MET cc_start: 0.7729 (tpp) cc_final: 0.7341 (tpp) REVERT: A 205 ASP cc_start: 0.7911 (m-30) cc_final: 0.7625 (m-30) REVERT: A 219 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 272 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7324 (mtmt) REVERT: B 51 SER cc_start: 0.8677 (m) cc_final: 0.8390 (m) REVERT: B 207 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: B 346 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7953 (mtmt) REVERT: B 347 LYS cc_start: 0.8347 (tppt) cc_final: 0.7964 (mptt) REVERT: B 350 MET cc_start: 0.6978 (ppp) cc_final: 0.6723 (ptm) REVERT: C 164 ASP cc_start: 0.8687 (t70) cc_final: 0.8381 (t0) REVERT: C 207 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: C 299 LYS cc_start: 0.8598 (tttt) cc_final: 0.8294 (ttpt) REVERT: D 113 MET cc_start: 0.8565 (mtt) cc_final: 0.8291 (mtt) REVERT: D 124 GLN cc_start: 0.8417 (pm20) cc_final: 0.8036 (pm20) REVERT: D 158 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7138 (ttp80) REVERT: D 311 LYS cc_start: 0.7362 (mtmt) cc_final: 0.6953 (pttt) REVERT: D 346 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7568 (mttm) REVERT: E 44 ARG cc_start: 0.6495 (mpt180) cc_final: 0.6032 (mmm-85) REVERT: E 273 ASP cc_start: 0.7351 (t0) cc_final: 0.7015 (t0) outliers start: 25 outliers final: 21 residues processed: 223 average time/residue: 0.1117 time to fit residues: 35.1790 Evaluate side-chains 228 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.162588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120243 restraints weight = 25650.734| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.11 r_work: 0.3022 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11826 Z= 0.122 Angle : 0.563 8.357 15985 Z= 0.268 Chirality : 0.040 0.131 1834 Planarity : 0.003 0.030 2005 Dihedral : 10.173 87.615 1729 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.73 % Allowed : 20.78 % Favored : 77.49 % 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 (0.24), residues: 1427 helix: 1.66 (0.20), residues: 788 sheet: -0.13 (0.45), residues: 143 loop : 0.60 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 248 TYR 0.014 0.001 TYR E 264 PHE 0.009 0.001 PHE B 178 TRP 0.010 0.001 TRP A 166 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00299 (11826) covalent geometry : angle 0.56269 (15985) hydrogen bonds : bond 0.02677 ( 528) hydrogen bonds : angle 4.12859 ( 1579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.02 seconds wall clock time: 60 minutes 24.91 seconds (3624.91 seconds total)