Starting phenix.real_space_refine on Sun Apr 5 05:34:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ogh_70468/04_2026/9ogh_70468.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ogh_70468/04_2026/9ogh_70468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ogh_70468/04_2026/9ogh_70468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ogh_70468/04_2026/9ogh_70468.map" model { file = "/net/cci-nas-00/data/ceres_data/9ogh_70468/04_2026/9ogh_70468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ogh_70468/04_2026/9ogh_70468.cif" } resolution = 2.7 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= 0.007 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 9 5.49 5 S 42 5.16 5 Na 1 4.78 5 C 5385 2.51 5 N 1299 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8254 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2582 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2582 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2582 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 170 Unusual residues: {' NA': 1, 'NAG': 3, 'POV': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'POV:plan-3': 7, 'POV:plan-1': 4, 'POV:plan-2': 4} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 169 Unusual residues: {'NAG': 3, 'POV': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'POV:plan-3': 7, 'POV:plan-1': 4, 'POV:plan-2': 4} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 169 Unusual residues: {'NAG': 3, 'POV': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'POV:plan-3': 7, 'POV:plan-1': 4, 'POV:plan-2': 4} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 2.21, per 1000 atoms: 0.27 Number of scatterers: 8254 At special positions: 0 Unit cell: (87.98, 86.32, 126.99, 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 42 16.00 P 9 15.00 Na 1 11.00 O 1518 8.00 N 1299 7.00 C 5385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.00 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.00 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.00 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 194 " " NAG A 503 " - " ASN A 310 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG B 503 " - " ASN B 310 " " NAG C 501 " - " ASN C 133 " " NAG C 502 " - " ASN C 194 " " NAG C 503 " - " ASN C 310 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 310.7 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 21.0% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 38 through 60 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 337 through 363 removed outlier: 3.768A pdb=" N THR A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 60 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 337 through 363 removed outlier: 3.768A pdb=" N THR C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 60 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 337 through 363 removed outlier: 3.769A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 72 current: chain 'A' and resid 154 through 161 removed outlier: 4.729A pdb=" N GLU A 171 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ARG A 158 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR A 169 " --> pdb=" O ARG A 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 281 through 287 current: chain 'A' and resid 312 through 336 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 removed outlier: 3.501A pdb=" N LYS A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 72 current: chain 'C' and resid 154 through 161 removed outlier: 4.729A pdb=" N GLU C 171 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ARG C 158 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR C 169 " --> pdb=" O ARG C 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 281 through 287 current: chain 'C' and resid 312 through 336 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 88 removed outlier: 3.502A pdb=" N LYS C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 72 current: chain 'B' and resid 154 through 161 removed outlier: 4.729A pdb=" N GLU B 171 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ARG B 158 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR B 169 " --> pdb=" O ARG B 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 281 through 287 current: chain 'B' and resid 312 through 336 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 83 Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.501A pdb=" N LYS B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 543 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: 1.18 Time building geometry restraints manager: 0.89 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: 1389 1.32 - 1.45: 2239 1.45 - 1.57: 4736 1.57 - 1.69: 12 1.69 - 1.81: 51 Bond restraints: 8427 Sorted by residual: bond pdb=" CA SER B 232 " pdb=" CB SER B 232 " ideal model delta sigma weight residual 1.529 1.486 0.043 1.55e-02 4.16e+03 7.64e+00 bond pdb=" CA SER A 232 " pdb=" CB SER A 232 " ideal model delta sigma weight residual 1.529 1.487 0.042 1.55e-02 4.16e+03 7.42e+00 bond pdb=" CA SER C 232 " pdb=" CB SER C 232 " ideal model delta sigma weight residual 1.529 1.488 0.041 1.55e-02 4.16e+03 7.14e+00 bond pdb=" CA ALA B 231 " pdb=" CB ALA B 231 " ideal model delta sigma weight residual 1.534 1.496 0.039 1.55e-02 4.16e+03 6.19e+00 bond pdb=" N TYR B 235 " pdb=" CA TYR B 235 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.10e-02 8.26e+03 6.19e+00 ... (remaining 8422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 10898 1.77 - 3.54: 341 3.54 - 5.30: 65 5.30 - 7.07: 15 7.07 - 8.84: 3 Bond angle restraints: 11322 Sorted by residual: angle pdb=" C CYS C 236 " pdb=" CA CYS C 236 " pdb=" CB CYS C 236 " ideal model delta sigma weight residual 111.29 102.45 8.84 1.92e+00 2.71e-01 2.12e+01 angle pdb=" C CYS B 236 " pdb=" CA CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sigma weight residual 111.29 102.49 8.80 1.92e+00 2.71e-01 2.10e+01 angle pdb=" C CYS A 236 " pdb=" CA CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sigma weight residual 111.29 102.51 8.78 1.92e+00 2.71e-01 2.09e+01 angle pdb=" N LEU B 234 " pdb=" CA LEU B 234 " pdb=" C LEU B 234 " ideal model delta sigma weight residual 113.23 107.97 5.26 1.24e+00 6.50e-01 1.80e+01 angle pdb=" N LEU A 234 " pdb=" CA LEU A 234 " pdb=" C LEU A 234 " ideal model delta sigma weight residual 113.23 107.97 5.26 1.24e+00 6.50e-01 1.80e+01 ... (remaining 11317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.77: 4584 20.77 - 41.53: 423 41.53 - 62.30: 111 62.30 - 83.07: 21 83.07 - 103.84: 27 Dihedral angle restraints: 5166 sinusoidal: 2322 harmonic: 2844 Sorted by residual: dihedral pdb=" CA PHE C 366 " pdb=" C PHE C 366 " pdb=" N MET C 367 " pdb=" CA MET C 367 " ideal model delta harmonic sigma weight residual 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 366 " pdb=" C PHE A 366 " pdb=" N MET A 367 " pdb=" CA MET A 367 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE B 366 " pdb=" C PHE B 366 " pdb=" N MET B 367 " pdb=" CA MET B 367 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 5163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 949 0.052 - 0.104: 213 0.104 - 0.156: 92 0.156 - 0.209: 3 0.209 - 0.261: 3 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA CYS C 236 " pdb=" N CYS C 236 " pdb=" C CYS C 236 " pdb=" CB CYS C 236 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA CYS B 236 " pdb=" N CYS B 236 " pdb=" C CYS B 236 " pdb=" CB CYS B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA CYS A 236 " pdb=" N CYS A 236 " pdb=" C CYS A 236 " pdb=" CB CYS A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1257 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 225 " -0.207 9.50e-02 1.11e+02 9.26e-02 5.27e+00 pdb=" NE ARG C 225 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 225 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 225 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 225 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 225 " -0.207 9.50e-02 1.11e+02 9.26e-02 5.26e+00 pdb=" NE ARG B 225 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 225 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 225 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 225 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 225 " 0.206 9.50e-02 1.11e+02 9.24e-02 5.24e+00 pdb=" NE ARG A 225 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 225 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 225 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 225 " 0.007 2.00e-02 2.50e+03 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 765 2.75 - 3.29: 7496 3.29 - 3.82: 13123 3.82 - 4.36: 16074 4.36 - 4.90: 28427 Nonbonded interactions: 65885 Sorted by model distance: nonbonded pdb=" O GLY C 84 " pdb=" OH TYR C 98 " model vdw 2.209 3.040 nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.210 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.210 3.040 nonbonded pdb=" OE1 GLN A 49 " pdb=" OG SER A 356 " model vdw 2.273 3.040 nonbonded pdb=" OE1 GLN C 49 " pdb=" OG SER C 356 " model vdw 2.273 3.040 ... (remaining 65880 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 38 through 511) selection = chain 'B' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.930 Find NCS groups from input model: 0.150 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.004 0.043 8451 Z= 0.237 Angle : 0.730 8.838 11379 Z= 0.430 Chirality : 0.051 0.261 1260 Planarity : 0.006 0.093 1398 Dihedral : 18.664 103.837 3309 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.12 % Allowed : 15.19 % Favored : 82.69 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 6.67 % 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: -0.38 (0.27), residues: 984 helix: 0.98 (0.38), residues: 231 sheet: 0.66 (0.29), residues: 339 loop : -1.80 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.008 0.001 TYR B 235 PHE 0.008 0.001 PHE B 228 TRP 0.007 0.001 TRP C 361 HIS 0.005 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8427) covalent geometry : angle 0.72662 (11322) SS BOND : bond 0.01355 ( 15) SS BOND : angle 1.30196 ( 30) hydrogen bonds : bond 0.18396 ( 199) hydrogen bonds : angle 5.50138 ( 543) link_NAG-ASN : bond 0.00232 ( 9) link_NAG-ASN : angle 1.01056 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.307 Fit side-chains outliers start: 18 outliers final: 5 residues processed: 74 average time/residue: 0.5594 time to fit residues: 44.4137 Evaluate side-chains 60 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain B residue 190 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN C 49 GLN B 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.074179 restraints weight = 11733.530| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.70 r_work: 0.2844 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8451 Z= 0.249 Angle : 0.665 7.296 11379 Z= 0.340 Chirality : 0.052 0.189 1260 Planarity : 0.004 0.033 1398 Dihedral : 13.319 105.307 1549 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.42 % Allowed : 12.84 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.42 (0.27), residues: 984 helix: 0.89 (0.37), residues: 231 sheet: 0.64 (0.28), residues: 342 loop : -1.81 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 287 TYR 0.011 0.002 TYR C 235 PHE 0.019 0.002 PHE C 357 TRP 0.011 0.001 TRP B 268 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 8427) covalent geometry : angle 0.65951 (11322) SS BOND : bond 0.00494 ( 15) SS BOND : angle 1.41563 ( 30) hydrogen bonds : bond 0.05395 ( 199) hydrogen bonds : angle 4.54010 ( 543) link_NAG-ASN : bond 0.00316 ( 9) link_NAG-ASN : angle 1.21557 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.329 Fit side-chains REVERT: C 89 GLU cc_start: 0.8487 (tp30) cc_final: 0.8115 (tm-30) REVERT: C 265 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8433 (mm) outliers start: 29 outliers final: 7 residues processed: 70 average time/residue: 0.4622 time to fit residues: 35.1339 Evaluate side-chains 61 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 246 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.109282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.075601 restraints weight = 11534.440| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.83 r_work: 0.2822 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8451 Z= 0.122 Angle : 0.559 6.342 11379 Z= 0.285 Chirality : 0.048 0.207 1260 Planarity : 0.004 0.035 1398 Dihedral : 11.239 105.488 1544 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.36 % Allowed : 14.72 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.15 (0.27), residues: 984 helix: 1.06 (0.37), residues: 231 sheet: 0.78 (0.29), residues: 336 loop : -1.55 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.009 0.001 TYR B 45 PHE 0.008 0.001 PHE A 252 TRP 0.006 0.001 TRP A 93 HIS 0.004 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8427) covalent geometry : angle 0.55417 (11322) SS BOND : bond 0.00352 ( 15) SS BOND : angle 0.98806 ( 30) hydrogen bonds : bond 0.04233 ( 199) hydrogen bonds : angle 4.31320 ( 543) link_NAG-ASN : bond 0.00352 ( 9) link_NAG-ASN : angle 1.38165 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.259 Fit side-chains REVERT: A 265 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8873 (mm) REVERT: C 89 GLU cc_start: 0.8388 (tp30) cc_final: 0.8045 (tm-30) REVERT: C 191 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7839 (mtt) outliers start: 20 outliers final: 3 residues processed: 71 average time/residue: 0.3848 time to fit residues: 29.9193 Evaluate side-chains 64 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.108711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.074994 restraints weight = 11648.115| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.84 r_work: 0.2823 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8451 Z= 0.133 Angle : 0.547 5.986 11379 Z= 0.281 Chirality : 0.047 0.153 1260 Planarity : 0.004 0.035 1398 Dihedral : 10.926 106.576 1544 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.18 % Allowed : 14.96 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.15 (0.27), residues: 984 helix: 1.02 (0.37), residues: 231 sheet: 0.71 (0.29), residues: 339 loop : -1.48 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.012 0.001 TYR B 45 PHE 0.021 0.001 PHE A 357 TRP 0.006 0.001 TRP B 268 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8427) covalent geometry : angle 0.54267 (11322) SS BOND : bond 0.00348 ( 15) SS BOND : angle 1.02752 ( 30) hydrogen bonds : bond 0.04168 ( 199) hydrogen bonds : angle 4.27106 ( 543) link_NAG-ASN : bond 0.00291 ( 9) link_NAG-ASN : angle 1.25847 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.297 Fit side-chains REVERT: A 265 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8867 (mm) REVERT: C 89 GLU cc_start: 0.8435 (tp30) cc_final: 0.8097 (tm-30) REVERT: C 191 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: C 265 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8748 (mm) REVERT: B 191 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7935 (mtt) outliers start: 27 outliers final: 11 residues processed: 72 average time/residue: 0.4040 time to fit residues: 31.8508 Evaluate side-chains 70 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 191 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.108439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.074803 restraints weight = 11645.276| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.83 r_work: 0.2832 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8451 Z= 0.134 Angle : 0.543 6.063 11379 Z= 0.281 Chirality : 0.047 0.148 1260 Planarity : 0.004 0.036 1398 Dihedral : 10.737 106.462 1544 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.06 % Allowed : 15.78 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.14 (0.27), residues: 984 helix: 1.03 (0.37), residues: 231 sheet: 0.75 (0.29), residues: 339 loop : -1.49 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.012 0.001 TYR B 45 PHE 0.009 0.001 PHE B 252 TRP 0.006 0.001 TRP C 93 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8427) covalent geometry : angle 0.53909 (11322) SS BOND : bond 0.00352 ( 15) SS BOND : angle 0.99659 ( 30) hydrogen bonds : bond 0.04085 ( 199) hydrogen bonds : angle 4.25595 ( 543) link_NAG-ASN : bond 0.00271 ( 9) link_NAG-ASN : angle 1.14650 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.302 Fit side-chains REVERT: A 265 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8877 (mm) REVERT: C 89 GLU cc_start: 0.8447 (tp30) cc_final: 0.8116 (tm-30) REVERT: C 191 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7808 (mtt) REVERT: C 265 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8739 (mm) outliers start: 26 outliers final: 12 residues processed: 70 average time/residue: 0.4252 time to fit residues: 32.4541 Evaluate side-chains 71 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.106588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.072822 restraints weight = 11496.659| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.79 r_work: 0.2792 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8451 Z= 0.198 Angle : 0.592 9.098 11379 Z= 0.307 Chirality : 0.049 0.164 1260 Planarity : 0.004 0.039 1398 Dihedral : 10.951 105.940 1544 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.94 % Allowed : 17.20 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.30 (0.27), residues: 984 helix: 0.89 (0.37), residues: 231 sheet: 0.56 (0.28), residues: 342 loop : -1.51 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.012 0.001 TYR B 235 PHE 0.023 0.002 PHE A 357 TRP 0.009 0.001 TRP B 268 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 8427) covalent geometry : angle 0.58721 (11322) SS BOND : bond 0.00438 ( 15) SS BOND : angle 1.19623 ( 30) hydrogen bonds : bond 0.04521 ( 199) hydrogen bonds : angle 4.39395 ( 543) link_NAG-ASN : bond 0.00219 ( 9) link_NAG-ASN : angle 1.17662 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.343 Fit side-chains REVERT: C 89 GLU cc_start: 0.8456 (tp30) cc_final: 0.8145 (tm-30) REVERT: C 191 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7840 (mtm) REVERT: C 265 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8749 (mm) outliers start: 25 outliers final: 13 residues processed: 66 average time/residue: 0.4588 time to fit residues: 32.8730 Evaluate side-chains 66 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.105282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.071193 restraints weight = 11540.732| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.98 r_work: 0.2784 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8451 Z= 0.132 Angle : 0.548 7.813 11379 Z= 0.284 Chirality : 0.047 0.147 1260 Planarity : 0.004 0.039 1398 Dihedral : 10.658 106.054 1544 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.24 % Allowed : 17.90 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.27), residues: 984 helix: 1.01 (0.37), residues: 231 sheet: 0.65 (0.29), residues: 339 loop : -1.49 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.009 0.001 TYR C 235 PHE 0.009 0.001 PHE B 252 TRP 0.006 0.001 TRP C 93 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8427) covalent geometry : angle 0.54481 (11322) SS BOND : bond 0.00374 ( 15) SS BOND : angle 0.98656 ( 30) hydrogen bonds : bond 0.04010 ( 199) hydrogen bonds : angle 4.31495 ( 543) link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 1.00072 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.283 Fit side-chains REVERT: A 44 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7386 (tp) REVERT: A 265 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8809 (mm) REVERT: C 89 GLU cc_start: 0.8461 (tp30) cc_final: 0.8099 (tm-30) REVERT: C 265 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8681 (mm) outliers start: 19 outliers final: 10 residues processed: 65 average time/residue: 0.4420 time to fit residues: 31.3564 Evaluate side-chains 65 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.105688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.072152 restraints weight = 11565.265| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.77 r_work: 0.2801 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8451 Z= 0.137 Angle : 0.552 8.405 11379 Z= 0.285 Chirality : 0.047 0.150 1260 Planarity : 0.004 0.037 1398 Dihedral : 10.565 106.787 1544 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.12 % Allowed : 18.14 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.17 (0.27), residues: 984 helix: 1.03 (0.37), residues: 231 sheet: 0.67 (0.29), residues: 339 loop : -1.47 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.010 0.001 TYR C 235 PHE 0.025 0.001 PHE A 357 TRP 0.006 0.001 TRP B 268 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8427) covalent geometry : angle 0.54851 (11322) SS BOND : bond 0.00359 ( 15) SS BOND : angle 1.00046 ( 30) hydrogen bonds : bond 0.03995 ( 199) hydrogen bonds : angle 4.29836 ( 543) link_NAG-ASN : bond 0.00250 ( 9) link_NAG-ASN : angle 0.95576 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.336 Fit side-chains REVERT: A 44 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7386 (tp) REVERT: A 265 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8912 (mm) REVERT: C 89 GLU cc_start: 0.8615 (tp30) cc_final: 0.8212 (tm-30) REVERT: C 265 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8788 (mm) outliers start: 18 outliers final: 11 residues processed: 64 average time/residue: 0.4440 time to fit residues: 31.0301 Evaluate side-chains 67 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 90 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.105310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.071890 restraints weight = 11520.345| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.75 r_work: 0.2794 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8451 Z= 0.149 Angle : 0.566 8.917 11379 Z= 0.293 Chirality : 0.047 0.151 1260 Planarity : 0.004 0.038 1398 Dihedral : 10.557 106.818 1544 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.71 % Allowed : 17.55 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.18 (0.27), residues: 984 helix: 1.01 (0.37), residues: 231 sheet: 0.73 (0.29), residues: 336 loop : -1.53 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.010 0.001 TYR C 235 PHE 0.010 0.001 PHE B 252 TRP 0.007 0.001 TRP B 268 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8427) covalent geometry : angle 0.56339 (11322) SS BOND : bond 0.00373 ( 15) SS BOND : angle 1.01960 ( 30) hydrogen bonds : bond 0.04070 ( 199) hydrogen bonds : angle 4.32209 ( 543) link_NAG-ASN : bond 0.00240 ( 9) link_NAG-ASN : angle 0.96371 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.308 Fit side-chains REVERT: A 44 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7355 (tp) REVERT: A 265 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8916 (mm) REVERT: C 89 GLU cc_start: 0.8620 (tp30) cc_final: 0.8224 (tm-30) REVERT: C 191 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7755 (mtm) REVERT: C 265 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8793 (mm) REVERT: B 149 MET cc_start: 0.8508 (mmm) cc_final: 0.8141 (mtt) outliers start: 23 outliers final: 13 residues processed: 65 average time/residue: 0.4455 time to fit residues: 31.4756 Evaluate side-chains 70 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.105970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.072647 restraints weight = 11467.069| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.75 r_work: 0.2810 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8451 Z= 0.132 Angle : 0.563 9.432 11379 Z= 0.288 Chirality : 0.047 0.154 1260 Planarity : 0.004 0.039 1398 Dihedral : 10.432 107.158 1544 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.24 % Allowed : 18.02 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.09 (0.27), residues: 984 helix: 1.07 (0.37), residues: 231 sheet: 0.84 (0.29), residues: 333 loop : -1.50 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 315 TYR 0.009 0.001 TYR B 98 PHE 0.026 0.001 PHE A 357 TRP 0.005 0.001 TRP C 93 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8427) covalent geometry : angle 0.55997 (11322) SS BOND : bond 0.00350 ( 15) SS BOND : angle 0.97190 ( 30) hydrogen bonds : bond 0.03896 ( 199) hydrogen bonds : angle 4.28669 ( 543) link_NAG-ASN : bond 0.00251 ( 9) link_NAG-ASN : angle 0.92548 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.308 Fit side-chains REVERT: A 44 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7365 (tp) REVERT: A 265 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8906 (mm) REVERT: C 89 GLU cc_start: 0.8618 (tp30) cc_final: 0.8221 (tm-30) REVERT: C 265 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8784 (mm) REVERT: B 149 MET cc_start: 0.8496 (mmm) cc_final: 0.8105 (mtt) outliers start: 19 outliers final: 12 residues processed: 63 average time/residue: 0.4359 time to fit residues: 29.9574 Evaluate side-chains 69 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 0.0000 chunk 57 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.106917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.073886 restraints weight = 11294.818| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.87 r_work: 0.2817 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8451 Z= 0.117 Angle : 0.555 9.457 11379 Z= 0.284 Chirality : 0.046 0.158 1260 Planarity : 0.004 0.038 1398 Dihedral : 10.236 106.631 1544 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.12 % Allowed : 18.14 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.10 (0.27), residues: 984 helix: 1.13 (0.37), residues: 231 sheet: 0.71 (0.29), residues: 342 loop : -1.46 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.008 0.001 TYR C 235 PHE 0.007 0.001 PHE B 252 TRP 0.005 0.001 TRP A 93 HIS 0.002 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8427) covalent geometry : angle 0.55260 (11322) SS BOND : bond 0.00326 ( 15) SS BOND : angle 0.91835 ( 30) hydrogen bonds : bond 0.03729 ( 199) hydrogen bonds : angle 4.25477 ( 543) link_NAG-ASN : bond 0.00264 ( 9) link_NAG-ASN : angle 0.90169 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.77 seconds wall clock time: 40 minutes 43.53 seconds (2443.53 seconds total)