Starting phenix.real_space_refine on Wed Feb 4 12:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kcu_62261/02_2026/9kcu_62261.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kcu_62261/02_2026/9kcu_62261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kcu_62261/02_2026/9kcu_62261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kcu_62261/02_2026/9kcu_62261.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kcu_62261/02_2026/9kcu_62261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kcu_62261/02_2026/9kcu_62261.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.053 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 56 5.16 5 C 7020 2.51 5 N 1648 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 10512 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2588 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 1 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2588 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 1 Chain: "C" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2588 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 1 Chain: "D" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2588 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 2.30, per 1000 atoms: 0.22 Number of scatterers: 10512 At special positions: 0 Unit cell: (101.92, 101.92, 101.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 4 15.00 O 1784 8.00 N 1648 7.00 C 7020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 281 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 267 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 281 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 267 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 281 " distance=2.03 Simple disulfide: pdb=" SG CYS D 262 " - pdb=" SG CYS D 302 " distance=2.03 Simple disulfide: pdb=" SG CYS D 267 " - pdb=" SG CYS D 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 431.0 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 75.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.693A pdb=" N VAL A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 103 through 129 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.932A pdb=" N ARG A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 171 through 180 removed outlier: 3.723A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.529A pdb=" N GLY A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 222 removed outlier: 3.833A pdb=" N ILE A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.952A pdb=" N ILE A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 232 through 270 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.684A pdb=" N VAL A 284 " --> pdb=" O CYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.683A pdb=" N THR A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.581A pdb=" N VAL A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 Processing helix chain 'A' and resid 354 through 385 Processing helix chain 'B' and resid 65 through 85 removed outlier: 3.561A pdb=" N VAL B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.778A pdb=" N ARG B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 160 Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 171 through 180 removed outlier: 3.838A pdb=" N VAL B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 192 through 197 removed outlier: 4.267A pdb=" N ARG B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 222 removed outlier: 3.518A pdb=" N GLN B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Proline residue: B 206 - end of helix removed outlier: 3.603A pdb=" N ILE B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Proline residue: B 213 - end of helix Processing helix chain 'B' and resid 232 through 270 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.551A pdb=" N VAL B 284 " --> pdb=" O CYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 311 through 314 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 354 through 385 Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.674A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 103 through 129 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.611A pdb=" N ARG C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 160 Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 171 through 180 removed outlier: 3.789A pdb=" N VAL C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 222 removed outlier: 3.927A pdb=" N ILE C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Proline residue: C 206 - end of helix removed outlier: 3.818A pdb=" N ILE C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Proline residue: C 213 - end of helix Processing helix chain 'C' and resid 229 through 270 removed outlier: 4.588A pdb=" N ALA C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 234 " --> pdb=" O TRP C 230 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 311 through 314 Processing helix chain 'C' and resid 315 through 320 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 326 through 344 Processing helix chain 'C' and resid 354 through 385 Processing helix chain 'D' and resid 65 through 85 removed outlier: 3.664A pdb=" N VAL D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 103 through 130 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.804A pdb=" N ARG D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 160 Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.692A pdb=" N GLY D 186 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 4.232A pdb=" N ARG D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 222 removed outlier: 3.953A pdb=" N ILE D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Proline residue: D 206 - end of helix removed outlier: 3.935A pdb=" N PHE D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Proline residue: D 213 - end of helix Processing helix chain 'D' and resid 233 through 270 Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.656A pdb=" N THR D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 311 through 314 Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 326 through 344 Processing helix chain 'D' and resid 354 through 385 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 95 removed outlier: 3.941A pdb=" N CYS A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.946A pdb=" N CYS B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 92 through 95 removed outlier: 3.905A pdb=" N CYS C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 94 664 hydrogen bonds defined for protein. 1911 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: 1.32 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1638 1.32 - 1.45: 3073 1.45 - 1.57: 5993 1.57 - 1.69: 8 1.69 - 1.81: 76 Bond restraints: 10788 Sorted by residual: bond pdb=" C5 PTY C 701 " pdb=" O14 PTY C 701 " ideal model delta sigma weight residual 1.409 1.460 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" C5 PTY B 701 " pdb=" O14 PTY B 701 " ideal model delta sigma weight residual 1.409 1.458 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C5 PTY A 701 " pdb=" O14 PTY A 701 " ideal model delta sigma weight residual 1.409 1.457 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C5 PTY D 701 " pdb=" O14 PTY D 701 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" O14 PTY B 701 " pdb=" P1 PTY B 701 " ideal model delta sigma weight residual 1.646 1.606 0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 10783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 14506 2.44 - 4.88: 117 4.88 - 7.32: 15 7.32 - 9.76: 3 9.76 - 12.21: 3 Bond angle restraints: 14644 Sorted by residual: angle pdb=" C ASN B 183 " pdb=" CA ASN B 183 " pdb=" CB ASN B 183 " ideal model delta sigma weight residual 116.63 110.51 6.12 1.16e+00 7.43e-01 2.78e+01 angle pdb=" C ASN A 183 " pdb=" CA ASN A 183 " pdb=" CB ASN A 183 " ideal model delta sigma weight residual 116.63 110.64 5.99 1.16e+00 7.43e-01 2.67e+01 angle pdb=" O11 PTY D 701 " pdb=" P1 PTY D 701 " pdb=" O14 PTY D 701 " ideal model delta sigma weight residual 92.90 105.11 -12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" N ASP B 277 " pdb=" CA ASP B 277 " pdb=" C ASP B 277 " ideal model delta sigma weight residual 114.56 109.59 4.97 1.27e+00 6.20e-01 1.53e+01 angle pdb=" CA ASN A 183 " pdb=" C ASN A 183 " pdb=" N LEU A 184 " ideal model delta sigma weight residual 119.63 116.81 2.82 8.10e-01 1.52e+00 1.21e+01 ... (remaining 14639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.48: 5719 18.48 - 36.96: 449 36.96 - 55.44: 74 55.44 - 73.92: 30 73.92 - 92.40: 4 Dihedral angle restraints: 6276 sinusoidal: 2496 harmonic: 3780 Sorted by residual: dihedral pdb=" CA ASP C 277 " pdb=" C ASP C 277 " pdb=" N PHE C 278 " pdb=" CA PHE C 278 " ideal model delta harmonic sigma weight residual 180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ARG A 128 " pdb=" C ARG A 128 " pdb=" N PHE A 129 " pdb=" CA PHE A 129 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CB CYS D 267 " pdb=" SG CYS D 267 " pdb=" SG CYS D 274 " pdb=" CB CYS D 274 " ideal model delta sinusoidal sigma weight residual -86.00 -116.11 30.11 1 1.00e+01 1.00e-02 1.30e+01 ... (remaining 6273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1258 0.041 - 0.082: 351 0.082 - 0.123: 74 0.123 - 0.164: 4 0.164 - 0.205: 1 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CB ILE D 179 " pdb=" CA ILE D 179 " pdb=" CG1 ILE D 179 " pdb=" CG2 ILE D 179 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1685 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 277 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C ASP B 277 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP B 277 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE B 278 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 63 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ARG B 63 " -0.028 2.00e-02 2.50e+03 pdb=" O ARG B 63 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY B 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 63 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ARG C 63 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG C 63 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 64 " 0.008 2.00e-02 2.50e+03 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1859 2.76 - 3.30: 10748 3.30 - 3.83: 18202 3.83 - 4.37: 20696 4.37 - 4.90: 35150 Nonbonded interactions: 86655 Sorted by model distance: nonbonded pdb=" O GLU A 97 " pdb=" NH2 ARG A 289 " model vdw 2.228 3.120 nonbonded pdb=" O GLU B 97 " pdb=" NH2 ARG B 289 " model vdw 2.238 3.120 nonbonded pdb=" OG SER A 115 " pdb=" OE1 GLN A 174 " model vdw 2.242 3.040 nonbonded pdb=" OG SER A 81 " pdb=" NH1 ARG A 207 " model vdw 2.252 3.120 nonbonded pdb=" OG SER C 115 " pdb=" OE1 GLN C 174 " model vdw 2.258 3.040 ... (remaining 86650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.180 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10800 Z= 0.156 Angle : 0.569 12.205 14668 Z= 0.292 Chirality : 0.038 0.205 1688 Planarity : 0.003 0.030 1768 Dihedral : 14.177 92.401 3792 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 1.61 (0.25), residues: 1276 helix: 1.76 (0.18), residues: 860 sheet: -1.58 (0.90), residues: 40 loop : -0.16 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.011 0.001 TYR C 121 PHE 0.014 0.001 PHE A 129 TRP 0.008 0.001 TRP B 70 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00322 (10788) covalent geometry : angle 0.56948 (14644) SS BOND : bond 0.00094 ( 12) SS BOND : angle 0.58000 ( 24) hydrogen bonds : bond 0.13992 ( 664) hydrogen bonds : angle 4.93037 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.235 Fit side-chains REVERT: A 127 MET cc_start: 0.6248 (mtp) cc_final: 0.5994 (ttm) REVERT: A 170 LEU cc_start: 0.8554 (mt) cc_final: 0.8296 (mt) REVERT: D 130 HIS cc_start: 0.6264 (m170) cc_final: 0.5897 (m170) REVERT: D 199 ILE cc_start: 0.7484 (pt) cc_final: 0.7246 (pt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0645 time to fit residues: 11.3968 Evaluate side-chains 99 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN C 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.202071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140644 restraints weight = 10909.055| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.03 r_work: 0.3174 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10800 Z= 0.122 Angle : 0.476 5.624 14668 Z= 0.247 Chirality : 0.038 0.138 1688 Planarity : 0.003 0.030 1768 Dihedral : 9.576 87.385 1508 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 0.70 % Allowed : 5.28 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.25), residues: 1276 helix: 2.16 (0.18), residues: 856 sheet: -1.44 (0.94), residues: 40 loop : 0.02 (0.38), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.012 0.001 TYR C 121 PHE 0.011 0.001 PHE D 109 TRP 0.010 0.001 TRP C 70 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00273 (10788) covalent geometry : angle 0.47642 (14644) SS BOND : bond 0.00159 ( 12) SS BOND : angle 0.49289 ( 24) hydrogen bonds : bond 0.03607 ( 664) hydrogen bonds : angle 3.65254 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.327 Fit side-chains REVERT: A 127 MET cc_start: 0.6612 (mtp) cc_final: 0.6286 (ttm) REVERT: A 170 LEU cc_start: 0.8373 (mt) cc_final: 0.8155 (mt) REVERT: A 203 GLN cc_start: 0.7435 (tt0) cc_final: 0.7227 (tt0) REVERT: D 130 HIS cc_start: 0.5988 (m170) cc_final: 0.5451 (m170) outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.0695 time to fit residues: 11.8960 Evaluate side-chains 102 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain D residue 125 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.195521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.151040 restraints weight = 10919.584| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.23 r_work: 0.3266 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10800 Z= 0.192 Angle : 0.536 6.397 14668 Z= 0.276 Chirality : 0.041 0.176 1688 Planarity : 0.004 0.032 1768 Dihedral : 10.530 89.455 1508 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 1.14 % Allowed : 7.83 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1276 helix: 1.83 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -0.31 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.023 0.002 TYR D 240 PHE 0.016 0.001 PHE B 332 TRP 0.010 0.001 TRP A 70 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00469 (10788) covalent geometry : angle 0.53637 (14644) SS BOND : bond 0.00258 ( 12) SS BOND : angle 0.46875 ( 24) hydrogen bonds : bond 0.03954 ( 664) hydrogen bonds : angle 3.70048 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.383 Fit side-chains REVERT: A 170 LEU cc_start: 0.8649 (mt) cc_final: 0.8438 (mt) REVERT: A 286 ASP cc_start: 0.7089 (t0) cc_final: 0.6679 (t0) REVERT: B 278 PHE cc_start: 0.7874 (m-80) cc_final: 0.7549 (m-80) REVERT: C 283 MET cc_start: 0.7479 (ttm) cc_final: 0.7267 (mtp) REVERT: D 199 ILE cc_start: 0.7656 (pt) cc_final: 0.7453 (pt) REVERT: D 241 MET cc_start: 0.8048 (mmt) cc_final: 0.7718 (mmm) outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.0654 time to fit residues: 11.9131 Evaluate side-chains 112 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain D residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.0060 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.198680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.150042 restraints weight = 11091.201| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.36 r_work: 0.3272 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10800 Z= 0.113 Angle : 0.451 5.641 14668 Z= 0.234 Chirality : 0.038 0.135 1688 Planarity : 0.003 0.031 1768 Dihedral : 9.962 89.410 1508 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.14 % Allowed : 9.33 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1276 helix: 1.97 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -0.13 (0.38), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.010 0.001 TYR D 204 PHE 0.009 0.001 PHE B 332 TRP 0.013 0.001 TRP C 70 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00255 (10788) covalent geometry : angle 0.45073 (14644) SS BOND : bond 0.00095 ( 12) SS BOND : angle 0.44684 ( 24) hydrogen bonds : bond 0.03386 ( 664) hydrogen bonds : angle 3.43399 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.277 Fit side-chains REVERT: A 286 ASP cc_start: 0.6939 (t0) cc_final: 0.6651 (t0) REVERT: B 278 PHE cc_start: 0.7919 (m-80) cc_final: 0.7552 (m-80) REVERT: C 241 MET cc_start: 0.8014 (mmt) cc_final: 0.7800 (mmm) REVERT: D 241 MET cc_start: 0.8030 (mmt) cc_final: 0.7659 (mmm) REVERT: D 379 MET cc_start: 0.7268 (mmt) cc_final: 0.6976 (mmt) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.0674 time to fit residues: 13.1575 Evaluate side-chains 115 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain D residue 125 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 61 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 124 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 overall best weight: 0.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.199353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155495 restraints weight = 10824.930| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.22 r_work: 0.3256 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10800 Z= 0.112 Angle : 0.455 7.250 14668 Z= 0.234 Chirality : 0.038 0.191 1688 Planarity : 0.003 0.030 1768 Dihedral : 9.761 88.893 1508 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 1.50 % Allowed : 9.51 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.25), residues: 1276 helix: 2.24 (0.17), residues: 880 sheet: -1.42 (0.94), residues: 40 loop : 0.08 (0.39), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.011 0.001 TYR D 204 PHE 0.009 0.001 PHE B 332 TRP 0.010 0.001 TRP C 70 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00255 (10788) covalent geometry : angle 0.45490 (14644) SS BOND : bond 0.00092 ( 12) SS BOND : angle 0.41423 ( 24) hydrogen bonds : bond 0.03302 ( 664) hydrogen bonds : angle 3.37284 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.282 Fit side-chains REVERT: A 240 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8420 (t80) REVERT: B 278 PHE cc_start: 0.7993 (m-80) cc_final: 0.7672 (m-80) outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 0.0683 time to fit residues: 13.0294 Evaluate side-chains 113 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain D residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.197632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146492 restraints weight = 11049.843| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.40 r_work: 0.3230 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10800 Z= 0.117 Angle : 0.463 7.777 14668 Z= 0.238 Chirality : 0.038 0.199 1688 Planarity : 0.003 0.037 1768 Dihedral : 9.668 88.885 1508 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 1.85 % Allowed : 9.77 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.25), residues: 1276 helix: 2.25 (0.17), residues: 880 sheet: -1.38 (0.95), residues: 40 loop : 0.07 (0.38), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 128 TYR 0.012 0.001 TYR A 204 PHE 0.010 0.001 PHE B 332 TRP 0.009 0.001 TRP C 70 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00271 (10788) covalent geometry : angle 0.46345 (14644) SS BOND : bond 0.00087 ( 12) SS BOND : angle 0.37556 ( 24) hydrogen bonds : bond 0.03290 ( 664) hydrogen bonds : angle 3.35756 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.267 Fit side-chains REVERT: B 97 GLU cc_start: 0.8210 (mp0) cc_final: 0.7887 (mp0) REVERT: D 379 MET cc_start: 0.7230 (mmt) cc_final: 0.6807 (mmt) outliers start: 21 outliers final: 14 residues processed: 124 average time/residue: 0.0688 time to fit residues: 13.2177 Evaluate side-chains 115 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain D residue 125 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.198384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.154914 restraints weight = 10935.711| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.24 r_work: 0.3304 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10800 Z= 0.123 Angle : 0.480 9.686 14668 Z= 0.244 Chirality : 0.039 0.203 1688 Planarity : 0.003 0.028 1768 Dihedral : 9.619 89.116 1508 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 1.67 % Allowed : 10.65 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.25), residues: 1276 helix: 2.22 (0.17), residues: 884 sheet: -1.38 (0.95), residues: 40 loop : 0.08 (0.39), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 289 TYR 0.012 0.001 TYR A 204 PHE 0.010 0.001 PHE B 332 TRP 0.009 0.001 TRP C 70 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00287 (10788) covalent geometry : angle 0.48058 (14644) SS BOND : bond 0.00080 ( 12) SS BOND : angle 0.38234 ( 24) hydrogen bonds : bond 0.03306 ( 664) hydrogen bonds : angle 3.37757 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.308 Fit side-chains REVERT: B 210 LEU cc_start: 0.7608 (mt) cc_final: 0.7228 (mt) REVERT: B 241 MET cc_start: 0.8488 (mmt) cc_final: 0.7949 (mmt) REVERT: B 278 PHE cc_start: 0.7458 (m-80) cc_final: 0.7205 (m-80) REVERT: C 241 MET cc_start: 0.8073 (mmt) cc_final: 0.7675 (mmm) REVERT: D 99 CYS cc_start: 0.7546 (p) cc_final: 0.7346 (p) REVERT: D 241 MET cc_start: 0.8137 (mmt) cc_final: 0.7754 (mmm) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.0636 time to fit residues: 12.5131 Evaluate side-chains 120 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 240 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 109 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.198613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.149665 restraints weight = 10871.514| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.31 r_work: 0.3257 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10800 Z= 0.123 Angle : 0.483 9.474 14668 Z= 0.245 Chirality : 0.038 0.196 1688 Planarity : 0.003 0.028 1768 Dihedral : 9.539 89.267 1508 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.76 % Allowed : 10.83 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.25), residues: 1276 helix: 2.05 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 289 TYR 0.013 0.001 TYR A 204 PHE 0.010 0.001 PHE B 332 TRP 0.009 0.001 TRP C 70 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00287 (10788) covalent geometry : angle 0.48347 (14644) SS BOND : bond 0.00081 ( 12) SS BOND : angle 0.36626 ( 24) hydrogen bonds : bond 0.03297 ( 664) hydrogen bonds : angle 3.36655 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.290 Fit side-chains REVERT: A 240 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8370 (t80) REVERT: B 97 GLU cc_start: 0.8161 (mp0) cc_final: 0.7865 (mm-30) REVERT: B 214 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6970 (tt) REVERT: B 241 MET cc_start: 0.8446 (mmt) cc_final: 0.7891 (mmt) REVERT: B 278 PHE cc_start: 0.7501 (m-80) cc_final: 0.7237 (m-80) REVERT: C 241 MET cc_start: 0.8115 (mmt) cc_final: 0.7723 (mmm) REVERT: D 99 CYS cc_start: 0.7445 (p) cc_final: 0.7233 (p) REVERT: D 241 MET cc_start: 0.8082 (mmt) cc_final: 0.7694 (mmm) REVERT: D 379 MET cc_start: 0.7206 (mmt) cc_final: 0.6744 (mmt) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.0680 time to fit residues: 13.2614 Evaluate side-chains 119 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 240 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 40 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.198213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154580 restraints weight = 11008.878| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.24 r_work: 0.3299 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10800 Z= 0.126 Angle : 0.490 9.438 14668 Z= 0.249 Chirality : 0.038 0.137 1688 Planarity : 0.003 0.028 1768 Dihedral : 9.507 89.342 1508 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 1.85 % Allowed : 11.36 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.25), residues: 1276 helix: 2.04 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -0.20 (0.37), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.013 0.001 TYR A 204 PHE 0.011 0.001 PHE B 332 TRP 0.009 0.001 TRP C 70 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00295 (10788) covalent geometry : angle 0.49046 (14644) SS BOND : bond 0.00077 ( 12) SS BOND : angle 0.36531 ( 24) hydrogen bonds : bond 0.03314 ( 664) hydrogen bonds : angle 3.39755 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.373 Fit side-chains REVERT: A 240 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8386 (t80) REVERT: B 97 GLU cc_start: 0.8248 (mp0) cc_final: 0.7953 (mm-30) REVERT: B 214 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7079 (tt) REVERT: B 241 MET cc_start: 0.8471 (mmt) cc_final: 0.7933 (mmt) REVERT: B 278 PHE cc_start: 0.7407 (m-80) cc_final: 0.7201 (m-80) REVERT: C 241 MET cc_start: 0.8128 (mmt) cc_final: 0.7767 (mmm) REVERT: D 99 CYS cc_start: 0.7546 (p) cc_final: 0.7338 (p) REVERT: D 241 MET cc_start: 0.8200 (mmt) cc_final: 0.7842 (mmm) REVERT: D 379 MET cc_start: 0.7217 (mmt) cc_final: 0.6771 (mmt) outliers start: 21 outliers final: 16 residues processed: 122 average time/residue: 0.0660 time to fit residues: 12.8966 Evaluate side-chains 123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 275 GLN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 240 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 0.0030 chunk 26 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.199843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156347 restraints weight = 10936.169| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.23 r_work: 0.3273 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10800 Z= 0.119 Angle : 0.485 9.458 14668 Z= 0.246 Chirality : 0.038 0.137 1688 Planarity : 0.003 0.028 1768 Dihedral : 9.399 89.287 1508 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 1.85 % Allowed : 11.44 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.25), residues: 1276 helix: 2.08 (0.18), residues: 912 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.013 0.001 TYR A 204 PHE 0.010 0.001 PHE B 332 TRP 0.014 0.001 TRP D 70 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00275 (10788) covalent geometry : angle 0.48477 (14644) SS BOND : bond 0.00075 ( 12) SS BOND : angle 0.38214 ( 24) hydrogen bonds : bond 0.03259 ( 664) hydrogen bonds : angle 3.36399 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.361 Fit side-chains REVERT: A 240 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8327 (t80) REVERT: B 97 GLU cc_start: 0.8228 (mp0) cc_final: 0.7937 (mm-30) REVERT: B 214 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6911 (tt) REVERT: B 241 MET cc_start: 0.8403 (mmt) cc_final: 0.7842 (mmt) REVERT: B 278 PHE cc_start: 0.7406 (m-80) cc_final: 0.7112 (m-80) REVERT: C 241 MET cc_start: 0.8078 (mmt) cc_final: 0.7705 (mmm) REVERT: D 99 CYS cc_start: 0.7385 (p) cc_final: 0.7169 (p) REVERT: D 241 MET cc_start: 0.8096 (mmt) cc_final: 0.7722 (mmm) REVERT: D 379 MET cc_start: 0.7164 (mmt) cc_final: 0.6709 (mmt) outliers start: 21 outliers final: 15 residues processed: 119 average time/residue: 0.0710 time to fit residues: 13.3267 Evaluate side-chains 118 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 275 GLN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain D residue 240 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.198546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150314 restraints weight = 10991.997| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.30 r_work: 0.3262 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10800 Z= 0.121 Angle : 0.489 9.346 14668 Z= 0.248 Chirality : 0.038 0.138 1688 Planarity : 0.003 0.028 1768 Dihedral : 9.329 89.121 1508 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 1.76 % Allowed : 11.53 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.25), residues: 1276 helix: 2.10 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -0.24 (0.37), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 289 TYR 0.013 0.001 TYR A 204 PHE 0.010 0.001 PHE B 332 TRP 0.009 0.001 TRP A 70 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00281 (10788) covalent geometry : angle 0.48922 (14644) SS BOND : bond 0.00074 ( 12) SS BOND : angle 0.34779 ( 24) hydrogen bonds : bond 0.03274 ( 664) hydrogen bonds : angle 3.36981 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.93 seconds wall clock time: 44 minutes 11.07 seconds (2651.07 seconds total)