Starting phenix.real_space_refine on Tue Feb 3 21:37:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gr0_51516/02_2026/9gr0_51516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gr0_51516/02_2026/9gr0_51516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gr0_51516/02_2026/9gr0_51516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gr0_51516/02_2026/9gr0_51516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gr0_51516/02_2026/9gr0_51516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gr0_51516/02_2026/9gr0_51516.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 8 5.49 5 S 26 5.16 5 C 4556 2.51 5 N 1269 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 7213 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 65 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 65 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "B" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3427 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 1 Chain: "C" Number of atoms: 3439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3439 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 21, 'TRANS': 422} Chain breaks: 1 Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 1.73, per 1000 atoms: 0.24 Number of scatterers: 7213 At special positions: 0 Unit cell: (81.2, 83.52, 114.84, 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 26 16.00 P 8 15.00 O 1354 8.00 N 1269 7.00 C 4556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 223.3 milliseconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1630 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 30.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 140 through 154 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.526A pdb=" N SER B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 309 through 326 Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.683A pdb=" N GLY B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.423A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 471 Processing helix chain 'B' and resid 584 through 594 removed outlier: 3.589A pdb=" N ALA B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 607 removed outlier: 3.642A pdb=" N LEU B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.654A pdb=" N ILE C 220 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 309 through 326 Processing helix chain 'C' and resid 345 through 359 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.742A pdb=" N LYS C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 470 Processing helix chain 'C' and resid 584 through 594 removed outlier: 3.637A pdb=" N ALA C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 606 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 239 Processing sheet with id=AA2, first strand: chain 'F' and resid 234 through 239 removed outlier: 6.254A pdb=" N LEU F 235 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE B 508 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET F 237 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.859A pdb=" N VAL B 132 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 160 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE B 134 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 162 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 136 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS B 131 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B 253 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.859A pdb=" N VAL B 132 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 160 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE B 134 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 162 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 136 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS B 131 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B 253 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 192 through 193 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AA7, first strand: chain 'B' and resid 362 through 364 removed outlier: 6.721A pdb=" N VAL B 330 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N MET B 364 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN B 332 " --> pdb=" O MET B 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 375 Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 422 removed outlier: 5.921A pdb=" N PHE B 421 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N TYR B 443 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 229 removed outlier: 8.217A pdb=" N ARG C 158 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS C 131 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR C 253 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N MET C 242 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU C 236 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS C 244 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 229 removed outlier: 8.217A pdb=" N ARG C 158 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS C 131 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR C 253 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 192 through 194 Processing sheet with id=AB4, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=AB5, first strand: chain 'C' and resid 281 through 282 removed outlier: 6.292A pdb=" N THR C 282 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER C 302 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL C 395 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 304 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 330 " --> pdb=" O LYS C 362 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N MET C 364 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN C 332 " --> pdb=" O MET C 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 375 Processing sheet with id=AB7, first strand: chain 'C' and resid 421 through 422 removed outlier: 5.932A pdb=" N PHE C 421 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TYR C 443 " --> pdb=" O PHE C 421 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 873 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: 1.02 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1437 1.33 - 1.45: 1696 1.45 - 1.57: 4156 1.57 - 1.69: 16 1.69 - 1.81: 44 Bond restraints: 7349 Sorted by residual: bond pdb=" CB VAL C 423 " pdb=" CG1 VAL C 423 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.90e+00 bond pdb=" CA ASP C 237 " pdb=" CB ASP C 237 " ideal model delta sigma weight residual 1.533 1.558 -0.025 2.29e-02 1.91e+03 1.20e+00 bond pdb=" N PRO C 173 " pdb=" CA PRO C 173 " ideal model delta sigma weight residual 1.465 1.484 -0.019 2.03e-02 2.43e+03 8.67e-01 bond pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 7.74e-01 bond pdb=" CA VAL C 550 " pdb=" C VAL C 550 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.82e-01 ... (remaining 7344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 9613 1.21 - 2.42: 285 2.42 - 3.64: 47 3.64 - 4.85: 9 4.85 - 6.06: 8 Bond angle restraints: 9962 Sorted by residual: angle pdb=" N VAL C 238 " pdb=" CA VAL C 238 " pdb=" C VAL C 238 " ideal model delta sigma weight residual 111.81 109.32 2.49 8.60e-01 1.35e+00 8.38e+00 angle pdb=" N PRO C 173 " pdb=" CA PRO C 173 " pdb=" C PRO C 173 " ideal model delta sigma weight residual 110.70 113.91 -3.21 1.22e+00 6.72e-01 6.91e+00 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 109.81 115.35 -5.54 2.21e+00 2.05e-01 6.29e+00 angle pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 109.81 115.31 -5.50 2.21e+00 2.05e-01 6.19e+00 angle pdb=" N PRO B 173 " pdb=" CA PRO B 173 " pdb=" C PRO B 173 " ideal model delta sigma weight residual 110.70 113.52 -2.82 1.22e+00 6.72e-01 5.34e+00 ... (remaining 9957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 3964 16.67 - 33.34: 374 33.34 - 50.02: 111 50.02 - 66.69: 33 66.69 - 83.36: 12 Dihedral angle restraints: 4494 sinusoidal: 1947 harmonic: 2547 Sorted by residual: dihedral pdb=" CA LYS C 177 " pdb=" C LYS C 177 " pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ARG C 450 " pdb=" C ARG C 450 " pdb=" N ARG C 451 " pdb=" CA ARG C 451 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP B 237 " pdb=" CB ASP B 237 " pdb=" CG ASP B 237 " pdb=" OD1 ASP B 237 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 4491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 580 0.026 - 0.052: 290 0.052 - 0.078: 96 0.078 - 0.104: 83 0.104 - 0.130: 49 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA VAL C 423 " pdb=" N VAL C 423 " pdb=" C VAL C 423 " pdb=" CB VAL C 423 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL B 564 " pdb=" N VAL B 564 " pdb=" C VAL B 564 " pdb=" CB VAL B 564 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA VAL C 564 " pdb=" N VAL C 564 " pdb=" C VAL C 564 " pdb=" CB VAL C 564 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1095 not shown) Planarity restraints: 1254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 132 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO C 133 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 174 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C PRO C 174 " -0.029 2.00e-02 2.50e+03 pdb=" O PRO C 174 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 175 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 172 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO C 173 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 173 " 0.023 5.00e-02 4.00e+02 ... (remaining 1251 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 386 2.73 - 3.27: 6671 3.27 - 3.82: 11653 3.82 - 4.36: 14940 4.36 - 4.90: 25567 Nonbonded interactions: 59217 Sorted by model distance: nonbonded pdb=" OE2 GLU B 453 " pdb=" O HOH B 801 " model vdw 2.191 3.040 nonbonded pdb=" OE1 GLU B 336 " pdb=" O2B NAD B 702 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP B 499 " pdb=" OG SER B 501 " model vdw 2.266 3.040 nonbonded pdb=" O2A FAD B 701 " pdb=" O HOH B 802 " model vdw 2.284 3.040 nonbonded pdb=" NH1 ARG C 172 " pdb=" O ARG C 285 " model vdw 2.286 3.120 ... (remaining 59212 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' selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 129 through 702) selection = (chain 'C' and (resid 129 through 510 or resid 551 through 610 or resid 701 thro \ ugh 702)) } 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: 5.120 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: 0.020 Set scattering table: 0.010 Process input model: 6.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 0.045 7349 Z= 0.127 Angle : 0.526 6.062 9962 Z= 0.279 Chirality : 0.045 0.130 1098 Planarity : 0.005 0.049 1254 Dihedral : 15.364 83.359 2864 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 18.01 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.28), residues: 891 helix: 1.15 (0.35), residues: 247 sheet: 0.64 (0.35), residues: 214 loop : -1.30 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 589 TYR 0.009 0.001 TYR B 567 PHE 0.015 0.002 PHE B 482 TRP 0.007 0.001 TRP B 351 HIS 0.004 0.001 HIS C 455 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7349) covalent geometry : angle 0.52581 ( 9962) hydrogen bonds : bond 0.15769 ( 288) hydrogen bonds : angle 6.55552 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.291 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.5888 time to fit residues: 69.6318 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN C 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075541 restraints weight = 13108.869| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.00 r_work: 0.2982 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7349 Z= 0.202 Angle : 0.594 5.998 9962 Z= 0.314 Chirality : 0.047 0.181 1098 Planarity : 0.005 0.060 1254 Dihedral : 6.984 55.701 1177 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.36 % Allowed : 20.03 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.28), residues: 891 helix: 1.26 (0.35), residues: 249 sheet: 0.50 (0.35), residues: 212 loop : -1.30 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 272 TYR 0.010 0.001 TYR C 492 PHE 0.021 0.002 PHE B 482 TRP 0.012 0.001 TRP B 579 HIS 0.003 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 7349) covalent geometry : angle 0.59389 ( 9962) hydrogen bonds : bond 0.04675 ( 288) hydrogen bonds : angle 5.09789 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.227 Fit side-chains REVERT: B 321 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7749 (ttp80) REVERT: B 390 GLU cc_start: 0.8374 (mp0) cc_final: 0.8171 (mp0) REVERT: B 570 ASP cc_start: 0.7918 (p0) cc_final: 0.7587 (p0) REVERT: B 571 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8163 (mtpp) REVERT: B 584 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8490 (mtt-85) REVERT: C 196 TRP cc_start: 0.8328 (p-90) cc_final: 0.8107 (p90) REVERT: C 358 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7922 (mtm110) REVERT: C 362 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7661 (tttm) outliers start: 25 outliers final: 10 residues processed: 99 average time/residue: 0.5687 time to fit residues: 58.9827 Evaluate side-chains 89 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 504 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.093770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072293 restraints weight = 12361.496| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.09 r_work: 0.2894 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7349 Z= 0.134 Angle : 0.537 6.103 9962 Z= 0.283 Chirality : 0.045 0.142 1098 Planarity : 0.005 0.058 1254 Dihedral : 6.633 54.896 1177 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.23 % Allowed : 20.16 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.28), residues: 891 helix: 1.50 (0.35), residues: 249 sheet: 0.45 (0.35), residues: 212 loop : -1.26 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 358 TYR 0.006 0.001 TYR C 492 PHE 0.015 0.001 PHE B 482 TRP 0.012 0.001 TRP B 579 HIS 0.002 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7349) covalent geometry : angle 0.53711 ( 9962) hydrogen bonds : bond 0.03837 ( 288) hydrogen bonds : angle 4.80762 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.212 Fit side-chains REVERT: B 301 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7694 (tptp) outliers start: 24 outliers final: 8 residues processed: 96 average time/residue: 0.5341 time to fit residues: 54.1308 Evaluate side-chains 79 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 504 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.091931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.070369 restraints weight = 12586.705| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.10 r_work: 0.2854 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7349 Z= 0.205 Angle : 0.580 6.414 9962 Z= 0.304 Chirality : 0.047 0.142 1098 Planarity : 0.005 0.060 1254 Dihedral : 7.031 55.306 1177 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 3.63 % Allowed : 19.76 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.28), residues: 891 helix: 1.55 (0.36), residues: 243 sheet: 0.39 (0.34), residues: 223 loop : -1.30 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 358 TYR 0.008 0.001 TYR C 492 PHE 0.019 0.002 PHE C 482 TRP 0.010 0.001 TRP C 579 HIS 0.003 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 7349) covalent geometry : angle 0.57973 ( 9962) hydrogen bonds : bond 0.04512 ( 288) hydrogen bonds : angle 4.88498 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.315 Fit side-chains REVERT: B 242 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7689 (mmm) REVERT: B 301 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7705 (tptp) REVERT: B 321 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7679 (ttp80) REVERT: C 240 ASP cc_start: 0.8712 (m-30) cc_final: 0.8472 (t70) outliers start: 27 outliers final: 12 residues processed: 93 average time/residue: 0.5154 time to fit residues: 50.7060 Evaluate side-chains 87 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 504 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.093271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.071888 restraints weight = 12419.576| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.09 r_work: 0.2887 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7349 Z= 0.131 Angle : 0.525 6.151 9962 Z= 0.276 Chirality : 0.045 0.139 1098 Planarity : 0.005 0.057 1254 Dihedral : 6.623 56.573 1177 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 3.49 % Allowed : 20.30 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.28), residues: 891 helix: 1.59 (0.35), residues: 249 sheet: 0.46 (0.35), residues: 217 loop : -1.27 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 358 TYR 0.014 0.001 TYR B 492 PHE 0.015 0.001 PHE B 482 TRP 0.012 0.001 TRP B 579 HIS 0.002 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7349) covalent geometry : angle 0.52499 ( 9962) hydrogen bonds : bond 0.03650 ( 288) hydrogen bonds : angle 4.65171 ( 873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.233 Fit side-chains REVERT: B 242 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7744 (mmm) REVERT: B 301 LYS cc_start: 0.8071 (tmtt) cc_final: 0.7660 (tptp) REVERT: B 336 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: B 358 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7547 (mpp-170) REVERT: B 390 GLU cc_start: 0.8305 (mp0) cc_final: 0.8028 (mp0) REVERT: B 570 ASP cc_start: 0.7861 (p0) cc_final: 0.7659 (p0) REVERT: B 571 LYS cc_start: 0.8403 (mmpt) cc_final: 0.8187 (mtpp) REVERT: C 240 ASP cc_start: 0.8671 (m-30) cc_final: 0.8408 (t70) REVERT: C 499 ASP cc_start: 0.8794 (t0) cc_final: 0.8438 (t0) outliers start: 26 outliers final: 11 residues processed: 94 average time/residue: 0.4477 time to fit residues: 44.6002 Evaluate side-chains 85 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 568 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 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 = 0.3427 r_free = 0.3427 target = 0.094016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072627 restraints weight = 12487.642| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.10 r_work: 0.2902 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7349 Z= 0.117 Angle : 0.517 6.488 9962 Z= 0.270 Chirality : 0.045 0.252 1098 Planarity : 0.004 0.056 1254 Dihedral : 6.506 58.077 1177 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.85 % Rotamer: Outliers : 2.96 % Allowed : 20.70 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.28), residues: 891 helix: 1.72 (0.35), residues: 249 sheet: 0.46 (0.34), residues: 217 loop : -1.24 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 358 TYR 0.015 0.001 TYR B 492 PHE 0.014 0.001 PHE B 482 TRP 0.012 0.001 TRP B 579 HIS 0.002 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7349) covalent geometry : angle 0.51704 ( 9962) hydrogen bonds : bond 0.03432 ( 288) hydrogen bonds : angle 4.52272 ( 873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.196 Fit side-chains REVERT: B 242 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7753 (mmm) REVERT: B 301 LYS cc_start: 0.8150 (tmtt) cc_final: 0.7685 (tptp) REVERT: B 336 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: B 358 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7531 (mpp-170) REVERT: B 390 GLU cc_start: 0.8307 (mp0) cc_final: 0.8044 (mp0) REVERT: C 240 ASP cc_start: 0.8651 (m-30) cc_final: 0.8370 (t70) REVERT: C 499 ASP cc_start: 0.8788 (t0) cc_final: 0.8409 (t0) outliers start: 22 outliers final: 14 residues processed: 89 average time/residue: 0.4553 time to fit residues: 42.8802 Evaluate side-chains 85 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 504 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.092228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.070950 restraints weight = 12428.936| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.08 r_work: 0.2872 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7349 Z= 0.165 Angle : 0.555 6.220 9962 Z= 0.288 Chirality : 0.046 0.189 1098 Planarity : 0.005 0.058 1254 Dihedral : 6.759 58.052 1177 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.74 % Rotamer: Outliers : 3.23 % Allowed : 20.43 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.28), residues: 891 helix: 1.74 (0.35), residues: 243 sheet: 0.45 (0.34), residues: 223 loop : -1.23 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 358 TYR 0.017 0.001 TYR B 492 PHE 0.017 0.001 PHE B 482 TRP 0.009 0.001 TRP B 579 HIS 0.003 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 7349) covalent geometry : angle 0.55452 ( 9962) hydrogen bonds : bond 0.04014 ( 288) hydrogen bonds : angle 4.65421 ( 873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.216 Fit side-chains REVERT: B 242 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7698 (mmm) REVERT: B 301 LYS cc_start: 0.8124 (tmtt) cc_final: 0.7635 (tptp) REVERT: B 336 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: B 358 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7594 (mpp-170) REVERT: B 390 GLU cc_start: 0.8360 (mp0) cc_final: 0.8076 (mp0) REVERT: C 240 ASP cc_start: 0.8656 (m-30) cc_final: 0.8360 (t70) REVERT: C 499 ASP cc_start: 0.8811 (t0) cc_final: 0.8450 (t0) outliers start: 24 outliers final: 15 residues processed: 89 average time/residue: 0.4434 time to fit residues: 41.7714 Evaluate side-chains 85 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 504 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 0.0010 chunk 88 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.094019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072701 restraints weight = 12507.566| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.11 r_work: 0.2909 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7349 Z= 0.113 Angle : 0.526 6.655 9962 Z= 0.273 Chirality : 0.045 0.170 1098 Planarity : 0.004 0.055 1254 Dihedral : 6.327 59.375 1177 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 2.55 % Allowed : 21.64 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 891 helix: 1.92 (0.35), residues: 243 sheet: 0.50 (0.34), residues: 223 loop : -1.18 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 358 TYR 0.016 0.001 TYR B 492 PHE 0.014 0.001 PHE B 482 TRP 0.013 0.001 TRP B 579 HIS 0.002 0.000 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7349) covalent geometry : angle 0.52575 ( 9962) hydrogen bonds : bond 0.03233 ( 288) hydrogen bonds : angle 4.43153 ( 873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.376 Fit side-chains REVERT: B 242 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7751 (mmm) REVERT: B 301 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7606 (tptp) REVERT: B 336 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: B 358 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7547 (mpp-170) REVERT: B 390 GLU cc_start: 0.8319 (mp0) cc_final: 0.8031 (mp0) REVERT: C 222 ASN cc_start: 0.7877 (p0) cc_final: 0.7441 (t0) REVERT: C 240 ASP cc_start: 0.8637 (m-30) cc_final: 0.8338 (t70) REVERT: C 499 ASP cc_start: 0.8767 (t0) cc_final: 0.8380 (t0) outliers start: 19 outliers final: 10 residues processed: 83 average time/residue: 0.5051 time to fit residues: 44.5052 Evaluate side-chains 79 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.090371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069168 restraints weight = 12493.911| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.07 r_work: 0.2840 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7349 Z= 0.243 Angle : 0.619 6.829 9962 Z= 0.320 Chirality : 0.048 0.151 1098 Planarity : 0.005 0.059 1254 Dihedral : 7.184 57.484 1177 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 2.42 % Allowed : 21.37 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.28), residues: 891 helix: 1.60 (0.35), residues: 243 sheet: 0.44 (0.34), residues: 233 loop : -1.27 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 358 TYR 0.018 0.002 TYR B 492 PHE 0.020 0.002 PHE B 482 TRP 0.007 0.001 TRP C 477 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 7349) covalent geometry : angle 0.61877 ( 9962) hydrogen bonds : bond 0.04718 ( 288) hydrogen bonds : angle 4.83080 ( 873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.195 Fit side-chains REVERT: B 242 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7647 (mmm) REVERT: B 301 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7582 (tptp) REVERT: B 336 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 240 ASP cc_start: 0.8635 (m-30) cc_final: 0.8320 (t70) REVERT: C 499 ASP cc_start: 0.8807 (t0) cc_final: 0.8476 (t0) outliers start: 18 outliers final: 12 residues processed: 82 average time/residue: 0.4580 time to fit residues: 40.0311 Evaluate side-chains 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.092855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.071686 restraints weight = 12435.868| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.09 r_work: 0.2890 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7349 Z= 0.126 Angle : 0.551 6.588 9962 Z= 0.286 Chirality : 0.045 0.142 1098 Planarity : 0.004 0.055 1254 Dihedral : 6.514 58.485 1177 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 2.02 % Allowed : 22.45 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.28), residues: 891 helix: 1.82 (0.35), residues: 243 sheet: 0.49 (0.34), residues: 228 loop : -1.23 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 358 TYR 0.016 0.001 TYR B 492 PHE 0.015 0.001 PHE B 482 TRP 0.013 0.001 TRP B 579 HIS 0.002 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7349) covalent geometry : angle 0.55105 ( 9962) hydrogen bonds : bond 0.03494 ( 288) hydrogen bonds : angle 4.54005 ( 873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.283 Fit side-chains REVERT: B 239 ARG cc_start: 0.7927 (mpp-170) cc_final: 0.7700 (mpp-170) REVERT: B 242 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7761 (mmm) REVERT: B 301 LYS cc_start: 0.8082 (tmtt) cc_final: 0.7593 (tptp) REVERT: B 336 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: B 358 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7588 (mpp-170) REVERT: C 222 ASN cc_start: 0.7867 (p0) cc_final: 0.7458 (t0) REVERT: C 240 ASP cc_start: 0.8619 (m-30) cc_final: 0.8327 (t70) REVERT: C 499 ASP cc_start: 0.8791 (t0) cc_final: 0.8436 (t0) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.4564 time to fit residues: 39.4247 Evaluate side-chains 80 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.093089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.071849 restraints weight = 12519.098| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.11 r_work: 0.2890 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7349 Z= 0.127 Angle : 0.547 6.596 9962 Z= 0.283 Chirality : 0.045 0.137 1098 Planarity : 0.004 0.057 1254 Dihedral : 6.506 59.568 1177 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.85 % Rotamer: Outliers : 1.75 % Allowed : 23.12 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 891 helix: 1.92 (0.35), residues: 243 sheet: 0.52 (0.34), residues: 228 loop : -1.22 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 358 TYR 0.017 0.001 TYR B 492 PHE 0.015 0.001 PHE B 482 TRP 0.013 0.001 TRP B 579 HIS 0.002 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7349) covalent geometry : angle 0.54717 ( 9962) hydrogen bonds : bond 0.03494 ( 288) hydrogen bonds : angle 4.47572 ( 873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.66 seconds wall clock time: 33 minutes 46.29 seconds (2026.29 seconds total)