Starting phenix.real_space_refine on Tue Mar 3 18:26:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukc_26576/03_2026/7ukc_26576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukc_26576/03_2026/7ukc_26576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ukc_26576/03_2026/7ukc_26576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukc_26576/03_2026/7ukc_26576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukc_26576/03_2026/7ukc_26576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukc_26576/03_2026/7ukc_26576.map" } resolution = 3.0 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= 0.005 sd= 0.060 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 K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.05, per 1000 atoms: 0.26 Number of scatterers: 8000 At special positions: 0 Unit cell: (108.206, 106.554, 83.426, 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) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 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: 0.76 Conformation dependent library (CDL) restraints added in 298.7 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 280 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.507A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 321 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.640A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.538A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 278 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.802A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 347 removed outlier: 5.359A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.844A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.419A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 280 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.507A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 321 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.640A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 424 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.538A pdb=" N TYR A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 278 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.803A pdb=" N LYS A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 347 removed outlier: 5.359A pdb=" N SER A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.844A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.420A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1815 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: 1.25 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2436 1.34 - 1.46: 1525 1.46 - 1.57: 4139 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" CB GLU C 346 " pdb=" CG GLU C 346 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CG GLU A 346 " pdb=" CD GLU A 346 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CG GLU C 346 " pdb=" CD GLU C 346 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CB LEU D 371 " pdb=" CG LEU D 371 " ideal model delta sigma weight residual 1.530 1.504 0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10814 1.68 - 3.37: 244 3.37 - 5.05: 52 5.05 - 6.74: 8 6.74 - 8.42: 6 Bond angle restraints: 11124 Sorted by residual: angle pdb=" C PHE A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 122.38 114.93 7.45 1.81e+00 3.05e-01 1.70e+01 angle pdb=" C PHE C 175 " pdb=" N GLU C 176 " pdb=" CA GLU C 176 " ideal model delta sigma weight residual 122.38 114.93 7.45 1.81e+00 3.05e-01 1.69e+01 angle pdb=" C ILE B 270 " pdb=" CA ILE B 270 " pdb=" CB ILE B 270 " ideal model delta sigma weight residual 111.65 107.18 4.47 1.41e+00 5.03e-01 1.00e+01 angle pdb=" C ILE D 270 " pdb=" CA ILE D 270 " pdb=" CB ILE D 270 " ideal model delta sigma weight residual 111.65 107.20 4.45 1.41e+00 5.03e-01 9.98e+00 angle pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" CB GLU A 176 " ideal model delta sigma weight residual 110.44 114.14 -3.70 1.53e+00 4.27e-01 5.84e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 4334 16.23 - 32.46: 376 32.46 - 48.69: 72 48.69 - 64.93: 6 64.93 - 81.16: 4 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CA ARG C 293 " pdb=" C ARG C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG A 293 " pdb=" C ARG A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR A 370 " pdb=" C THR A 370 " pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 793 0.035 - 0.070: 388 0.070 - 0.106: 92 0.106 - 0.141: 43 0.141 - 0.176: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA GLU B 176 " pdb=" N GLU B 176 " pdb=" C GLU B 176 " pdb=" CB GLU B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA GLU D 176 " pdb=" N GLU D 176 " pdb=" C GLU D 176 " pdb=" CB GLU D 176 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA PHE C 194 " pdb=" N PHE C 194 " pdb=" C PHE C 194 " pdb=" CB PHE C 194 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 172 " 0.020 2.00e-02 2.50e+03 1.61e-02 6.51e+00 pdb=" CG TRP B 172 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 172 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 172 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 172 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 172 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 172 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 172 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 172 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 172 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 172 " -0.020 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP D 172 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 172 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 172 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 172 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 172 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 172 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 172 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 172 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 172 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 346 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" CD GLU D 346 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU D 346 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU D 346 " -0.010 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.73: 661 2.73 - 3.33: 10452 3.33 - 3.93: 15425 3.93 - 4.54: 21774 4.54 - 5.14: 32004 Nonbonded interactions: 80316 Sorted by model distance: nonbonded pdb=" OH TYR C 188 " pdb=" O HIS C 306 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" O HIS A 306 " model vdw 2.128 3.040 nonbonded pdb=" OE2 GLU D 205 " pdb=" NH2 ARG D 293 " model vdw 2.282 3.120 nonbonded pdb=" OE2 GLU B 205 " pdb=" NH2 ARG B 293 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR D 367 " pdb=" OH TYR A 373 " model vdw 2.307 3.040 ... (remaining 80311 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 166 through 424) selection = (chain 'B' and resid 166 through 424) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.200 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.006 0.047 8188 Z= 0.234 Angle : 0.670 8.420 11124 Z= 0.385 Chirality : 0.045 0.176 1320 Planarity : 0.004 0.037 1360 Dihedral : 12.536 81.157 2840 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % 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: 0.47 (0.26), residues: 1028 helix: 0.61 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -0.42 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 296 TYR 0.015 0.002 TYR B 188 PHE 0.017 0.002 PHE C 175 TRP 0.042 0.004 TRP B 172 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 8188) covalent geometry : angle 0.67040 (11124) hydrogen bonds : bond 0.11899 ( 617) hydrogen bonds : angle 5.28877 ( 1815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.310 Fit side-chains REVERT: D 187 PHE cc_start: 0.7783 (t80) cc_final: 0.7431 (t80) REVERT: D 418 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7585 (ptm160) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.5814 time to fit residues: 88.1817 Evaluate side-chains 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.178864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110168 restraints weight = 9428.084| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.23 r_work: 0.3151 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8188 Z= 0.154 Angle : 0.560 7.394 11124 Z= 0.300 Chirality : 0.042 0.142 1320 Planarity : 0.005 0.042 1360 Dihedral : 4.203 23.826 1150 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.90 % Allowed : 11.49 % Favored : 86.61 % 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: 1.21 (0.27), residues: 1028 helix: 1.12 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -0.13 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 247 TYR 0.015 0.001 TYR D 188 PHE 0.015 0.001 PHE A 257 TRP 0.016 0.002 TRP D 172 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8188) covalent geometry : angle 0.56010 (11124) hydrogen bonds : bond 0.04287 ( 617) hydrogen bonds : angle 4.22552 ( 1815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.321 Fit side-chains REVERT: B 207 VAL cc_start: 0.8423 (t) cc_final: 0.8046 (m) REVERT: B 241 THR cc_start: 0.7640 (m) cc_final: 0.7360 (p) REVERT: D 241 THR cc_start: 0.7625 (m) cc_final: 0.7364 (p) REVERT: D 308 GLN cc_start: 0.7287 (tm-30) cc_final: 0.7087 (tm-30) REVERT: D 418 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7547 (ptm160) outliers start: 16 outliers final: 5 residues processed: 133 average time/residue: 0.5733 time to fit residues: 80.9405 Evaluate side-chains 128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 156)---------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121290 restraints weight = 9431.677| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.88 r_work: 0.3195 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8188 Z= 0.136 Angle : 0.516 6.941 11124 Z= 0.275 Chirality : 0.040 0.175 1320 Planarity : 0.005 0.046 1360 Dihedral : 3.955 24.228 1150 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.25 % Allowed : 13.03 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.26), residues: 1028 helix: 1.35 (0.18), residues: 816 sheet: None (None), residues: 0 loop : 0.09 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.015 0.001 TYR D 188 PHE 0.017 0.001 PHE C 257 TRP 0.008 0.002 TRP B 172 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8188) covalent geometry : angle 0.51649 (11124) hydrogen bonds : bond 0.03975 ( 617) hydrogen bonds : angle 4.01587 ( 1815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.230 Fit side-chains REVERT: B 241 THR cc_start: 0.8396 (m) cc_final: 0.8179 (p) outliers start: 19 outliers final: 7 residues processed: 148 average time/residue: 0.5621 time to fit residues: 88.1520 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.175978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130737 restraints weight = 9574.777| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.66 r_work: 0.3182 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8188 Z= 0.194 Angle : 0.570 6.714 11124 Z= 0.305 Chirality : 0.043 0.152 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.971 24.894 1150 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.01 % Allowed : 15.52 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.26), residues: 1028 helix: 1.30 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.09 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.015 0.001 TYR D 188 PHE 0.020 0.001 PHE A 257 TRP 0.010 0.002 TRP A 172 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8188) covalent geometry : angle 0.56992 (11124) hydrogen bonds : bond 0.04302 ( 617) hydrogen bonds : angle 4.02166 ( 1815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.368 Fit side-chains REVERT: B 308 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7393 (tm-30) REVERT: C 275 ILE cc_start: 0.8692 (mp) cc_final: 0.8472 (mt) outliers start: 17 outliers final: 7 residues processed: 130 average time/residue: 0.6235 time to fit residues: 85.6470 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 93 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.176392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130380 restraints weight = 9520.685| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.63 r_work: 0.3164 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8188 Z= 0.188 Angle : 0.556 6.466 11124 Z= 0.296 Chirality : 0.042 0.129 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.877 17.672 1148 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.84 % Allowed : 16.82 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1028 helix: 1.31 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.05 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 293 TYR 0.014 0.001 TYR D 188 PHE 0.025 0.001 PHE A 257 TRP 0.011 0.002 TRP A 172 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8188) covalent geometry : angle 0.55603 (11124) hydrogen bonds : bond 0.04234 ( 617) hydrogen bonds : angle 3.97810 ( 1815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 308 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7377 (tm-30) REVERT: D 279 MET cc_start: 0.5987 (tmm) cc_final: 0.5785 (tmm) REVERT: D 308 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 24 outliers final: 13 residues processed: 132 average time/residue: 0.6086 time to fit residues: 84.9108 Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.0030 chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.0030 chunk 28 optimal weight: 0.8980 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129580 restraints weight = 9461.221| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.62 r_work: 0.3245 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8188 Z= 0.126 Angle : 0.519 6.620 11124 Z= 0.274 Chirality : 0.039 0.181 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.745 17.764 1148 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.25 % Allowed : 18.13 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.26), residues: 1028 helix: 1.54 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.22 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.013 0.001 TYR D 188 PHE 0.026 0.001 PHE A 257 TRP 0.010 0.002 TRP C 172 HIS 0.001 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8188) covalent geometry : angle 0.51890 (11124) hydrogen bonds : bond 0.03772 ( 617) hydrogen bonds : angle 3.85478 ( 1815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 308 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7316 (tm-30) REVERT: D 308 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 275 ILE cc_start: 0.8658 (mp) cc_final: 0.8439 (mt) outliers start: 19 outliers final: 10 residues processed: 133 average time/residue: 0.5890 time to fit residues: 82.8692 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.0030 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.179685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136083 restraints weight = 9554.518| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.64 r_work: 0.3244 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8188 Z= 0.132 Angle : 0.528 7.813 11124 Z= 0.278 Chirality : 0.040 0.159 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.691 17.387 1148 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.25 % Allowed : 19.43 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1028 helix: 1.56 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.05 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 247 TYR 0.013 0.001 TYR B 188 PHE 0.030 0.001 PHE A 257 TRP 0.012 0.002 TRP A 172 HIS 0.001 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8188) covalent geometry : angle 0.52819 (11124) hydrogen bonds : bond 0.03756 ( 617) hydrogen bonds : angle 3.84385 ( 1815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: B 308 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7300 (tm-30) REVERT: D 308 GLN cc_start: 0.7656 (tm-30) cc_final: 0.7393 (tm-30) outliers start: 19 outliers final: 9 residues processed: 137 average time/residue: 0.5701 time to fit residues: 82.4514 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138098 restraints weight = 9554.981| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.58 r_work: 0.3241 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8188 Z= 0.148 Angle : 0.552 9.509 11124 Z= 0.290 Chirality : 0.040 0.149 1320 Planarity : 0.005 0.042 1360 Dihedral : 3.715 18.025 1148 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.90 % Allowed : 20.38 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.26), residues: 1028 helix: 1.56 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -0.09 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.012 0.001 TYR D 188 PHE 0.031 0.001 PHE C 257 TRP 0.013 0.002 TRP A 172 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8188) covalent geometry : angle 0.55151 (11124) hydrogen bonds : bond 0.03873 ( 617) hydrogen bonds : angle 3.85804 ( 1815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.317 Fit side-chains REVERT: B 308 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7299 (tm-30) REVERT: D 308 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7405 (tm-30) outliers start: 16 outliers final: 7 residues processed: 130 average time/residue: 0.6023 time to fit residues: 82.6480 Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127821 restraints weight = 9452.594| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.64 r_work: 0.3218 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8188 Z= 0.162 Angle : 0.581 10.184 11124 Z= 0.301 Chirality : 0.041 0.146 1320 Planarity : 0.005 0.040 1360 Dihedral : 3.754 17.405 1148 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.66 % Allowed : 20.85 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.26), residues: 1028 helix: 1.49 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.06 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 247 TYR 0.012 0.001 TYR D 188 PHE 0.037 0.001 PHE C 257 TRP 0.013 0.002 TRP A 172 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8188) covalent geometry : angle 0.58104 (11124) hydrogen bonds : bond 0.03959 ( 617) hydrogen bonds : angle 3.87342 ( 1815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.244 Fit side-chains REVERT: B 308 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7310 (tm-30) REVERT: D 308 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7417 (tm-30) outliers start: 14 outliers final: 10 residues processed: 130 average time/residue: 0.6123 time to fit residues: 83.9059 Evaluate side-chains 129 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 29 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.178868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138153 restraints weight = 9461.467| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.53 r_work: 0.3253 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8188 Z= 0.143 Angle : 0.572 10.465 11124 Z= 0.297 Chirality : 0.040 0.134 1320 Planarity : 0.005 0.040 1360 Dihedral : 3.721 17.231 1148 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.42 % Allowed : 21.21 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.26), residues: 1028 helix: 1.58 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 0.08 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 170 TYR 0.012 0.001 TYR D 188 PHE 0.043 0.001 PHE C 257 TRP 0.013 0.002 TRP B 172 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8188) covalent geometry : angle 0.57250 (11124) hydrogen bonds : bond 0.03800 ( 617) hydrogen bonds : angle 3.84296 ( 1815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.294 Fit side-chains REVERT: B 308 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7290 (tm-30) REVERT: D 308 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7412 (tm-30) outliers start: 12 outliers final: 10 residues processed: 126 average time/residue: 0.6151 time to fit residues: 81.7092 Evaluate side-chains 127 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.178667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134074 restraints weight = 9407.734| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.66 r_work: 0.3235 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8188 Z= 0.150 Angle : 0.580 10.361 11124 Z= 0.301 Chirality : 0.041 0.143 1320 Planarity : 0.004 0.038 1360 Dihedral : 3.733 17.501 1148 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.30 % Allowed : 21.21 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1028 helix: 1.56 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 0.05 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 247 TYR 0.012 0.001 TYR D 188 PHE 0.046 0.001 PHE C 257 TRP 0.015 0.002 TRP B 172 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8188) covalent geometry : angle 0.58010 (11124) hydrogen bonds : bond 0.03848 ( 617) hydrogen bonds : angle 3.84469 ( 1815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3308.98 seconds wall clock time: 56 minutes 59.57 seconds (3419.57 seconds total)