Starting phenix.real_space_refine on Wed Feb 4 06:31:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nk7_49495/02_2026/9nk7_49495.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nk7_49495/02_2026/9nk7_49495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nk7_49495/02_2026/9nk7_49495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nk7_49495/02_2026/9nk7_49495.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nk7_49495/02_2026/9nk7_49495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nk7_49495/02_2026/9nk7_49495.map" } resolution = 2.84 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= 0.013 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 5806 2.51 5 N 1533 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8970 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2430 Classifications: {'peptide': 311} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 285} Chain breaks: 1 Chain: "B" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3529 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 28, 'TRANS': 448} Chain: "C" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2663 Classifications: {'peptide': 354} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 325} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ERG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 203 Unusual residues: {'ERG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ERG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.51, per 1000 atoms: 0.28 Number of scatterers: 8970 At special positions: 0 Unit cell: (78.28, 117.832, 131.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1616 8.00 N 1533 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 358.9 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 45.1% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 4.090A pdb=" N LEU A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU A 23 " --> pdb=" O PRO A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 57 through 64 removed outlier: 3.749A pdb=" N LEU A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.731A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 119 through 130 removed outlier: 4.617A pdb=" N LEU A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.781A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 193 through 214 removed outlier: 3.507A pdb=" N THR A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.686A pdb=" N ILE A 234 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.611A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.564A pdb=" N GLY A 264 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 286 removed outlier: 3.815A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.923A pdb=" N GLU A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.576A pdb=" N LEU B 41 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 42 " --> pdb=" O HIS B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 38 through 42' Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.813A pdb=" N LEU B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 72 through 76 removed outlier: 4.176A pdb=" N ALA B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'B' and resid 446 through 463 removed outlier: 3.638A pdb=" N LEU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 105 through 132 removed outlier: 4.861A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Proline residue: C 125 - end of helix Processing helix chain 'C' and resid 134 through 141 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 157 through 170 removed outlier: 3.553A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 234 through 254 removed outlier: 3.731A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.734A pdb=" N LEU C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 300 through 315 Processing helix chain 'C' and resid 315 through 320 removed outlier: 3.937A pdb=" N LYS C 320 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 327 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.755A pdb=" N ALA C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 357 through 378 Processing helix chain 'C' and resid 385 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 30 through 32 current: chain 'B' and resid 167 through 171 removed outlier: 5.789A pdb=" N LEU B 197 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP B 196 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 263 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 333 " --> pdb=" O VAL B 322 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 395 through 400 current: chain 'B' and resid 416 through 421 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 416 through 421 current: chain 'B' and resid 467 through 476 removed outlier: 6.494A pdb=" N LEU B 468 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 3.537A pdb=" N PHE A 103 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 111 removed outlier: 5.813A pdb=" N GLY B 104 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 127 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 126 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 48 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 128 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 50 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.826A pdb=" N VAL C 3 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C 40 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 5 " --> pdb=" O ILE C 40 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1263 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: 1.45 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2924 1.34 - 1.46: 2018 1.46 - 1.58: 4248 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 9215 Sorted by residual: bond pdb=" N PHE B 105 " pdb=" CA PHE B 105 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.23e-02 6.61e+03 6.44e+00 bond pdb=" N ASP B 72 " pdb=" CA ASP B 72 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.35e-02 5.49e+03 6.28e+00 bond pdb=" N LYS B 101 " pdb=" CA LYS B 101 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.25e-02 6.40e+03 6.00e+00 bond pdb=" N LEU A 84 " pdb=" CA LEU A 84 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.22e-02 6.72e+03 5.88e+00 bond pdb=" N VAL B 107 " pdb=" CA VAL B 107 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.44e-02 4.82e+03 5.81e+00 ... (remaining 9210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 12424 2.02 - 4.04: 167 4.04 - 6.06: 34 6.06 - 8.08: 9 8.08 - 10.10: 3 Bond angle restraints: 12637 Sorted by residual: angle pdb=" CA ASP A 25 " pdb=" CB ASP A 25 " pdb=" CG ASP A 25 " ideal model delta sigma weight residual 112.60 116.50 -3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" CB LYS B 67 " pdb=" CG LYS B 67 " pdb=" CD LYS B 67 " ideal model delta sigma weight residual 111.30 119.92 -8.62 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CB MET B 283 " pdb=" CG MET B 283 " pdb=" SD MET B 283 " ideal model delta sigma weight residual 112.70 122.80 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C20 ERG B 601 " pdb=" C22 ERG B 601 " pdb=" C23 ERG B 601 " ideal model delta sigma weight residual 125.47 135.48 -10.01 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA GLU B 111 " pdb=" CB GLU B 111 " pdb=" CG GLU B 111 " ideal model delta sigma weight residual 114.10 120.69 -6.59 2.00e+00 2.50e-01 1.08e+01 ... (remaining 12632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 5419 16.17 - 32.34: 462 32.34 - 48.51: 146 48.51 - 64.67: 33 64.67 - 80.84: 5 Dihedral angle restraints: 6065 sinusoidal: 2821 harmonic: 3244 Sorted by residual: dihedral pdb=" CA ASN B 423 " pdb=" CB ASN B 423 " pdb=" CG ASN B 423 " pdb=" OD1 ASN B 423 " ideal model delta sinusoidal sigma weight residual 120.00 -171.21 -68.79 2 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CG ARG B 482 " pdb=" CD ARG B 482 " pdb=" NE ARG B 482 " pdb=" CZ ARG B 482 " ideal model delta sinusoidal sigma weight residual -180.00 -136.80 -43.20 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CA PRO C 151 " pdb=" C PRO C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual -180.00 -164.27 -15.73 0 5.00e+00 4.00e-02 9.89e+00 ... (remaining 6062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1150 0.046 - 0.092: 211 0.092 - 0.138: 79 0.138 - 0.184: 8 0.184 - 0.230: 1 Chirality restraints: 1449 Sorted by residual: chirality pdb=" C20 ERG B 601 " pdb=" C17 ERG B 601 " pdb=" C21 ERG B 601 " pdb=" C22 ERG B 601 " both_signs ideal model delta sigma weight residual False 2.58 2.35 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C20 ERG B 603 " pdb=" C17 ERG B 603 " pdb=" C21 ERG B 603 " pdb=" C22 ERG B 603 " both_signs ideal model delta sigma weight residual False 2.58 2.41 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CB VAL B 107 " pdb=" CA VAL B 107 " pdb=" CG1 VAL B 107 " pdb=" CG2 VAL B 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1446 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 98 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C ASP B 98 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP B 98 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE B 99 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 113 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 114 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 158 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO C 159 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " -0.020 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 107 2.66 - 3.22: 8152 3.22 - 3.78: 13842 3.78 - 4.34: 18774 4.34 - 4.90: 31469 Nonbonded interactions: 72344 Sorted by model distance: nonbonded pdb=" O ASP C 36 " pdb=" OD1 ASP C 36 " model vdw 2.102 3.040 nonbonded pdb=" O PHE A 55 " pdb=" OG SER A 67 " model vdw 2.245 3.040 nonbonded pdb=" O ILE B 40 " pdb=" OG1 THR B 78 " model vdw 2.266 3.040 nonbonded pdb=" O ARG B 86 " pdb=" NE ARG B 86 " model vdw 2.282 3.120 nonbonded pdb=" OG SER A 217 " pdb=" OG SER A 242 " model vdw 2.287 3.040 ... (remaining 72339 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.820 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 0.040 9215 Z= 0.161 Angle : 0.610 10.101 12637 Z= 0.304 Chirality : 0.041 0.230 1449 Planarity : 0.004 0.039 1586 Dihedral : 13.319 80.843 3985 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 17.42 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.26), residues: 1130 helix: 2.19 (0.26), residues: 430 sheet: 0.29 (0.38), residues: 215 loop : -0.17 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.010 0.001 TYR A 53 PHE 0.019 0.001 PHE C 405 TRP 0.008 0.001 TRP A 325 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9215) covalent geometry : angle 0.60997 (12637) hydrogen bonds : bond 0.16312 ( 441) hydrogen bonds : angle 6.59686 ( 1263) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 206 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7332 (mtm110) REVERT: C 330 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8694 (mm-40) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.5926 time to fit residues: 55.8630 Evaluate side-chains 63 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077577 restraints weight = 15460.877| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.58 r_work: 0.2838 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9215 Z= 0.145 Angle : 0.575 10.126 12637 Z= 0.278 Chirality : 0.042 0.223 1449 Planarity : 0.005 0.037 1586 Dihedral : 6.958 57.814 2048 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.37 % Allowed : 16.63 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.24 (0.26), residues: 1130 helix: 2.22 (0.26), residues: 435 sheet: 0.36 (0.37), residues: 217 loop : -0.22 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 292 TYR 0.012 0.001 TYR A 53 PHE 0.011 0.001 PHE A 68 TRP 0.007 0.001 TRP C 156 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9215) covalent geometry : angle 0.57539 (12637) hydrogen bonds : bond 0.03586 ( 441) hydrogen bonds : angle 5.02856 ( 1263) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.310 Fit side-chains REVERT: A 210 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: B 482 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7861 (ttm170) outliers start: 30 outliers final: 12 residues processed: 88 average time/residue: 0.5809 time to fit residues: 54.7914 Evaluate side-chains 76 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.077403 restraints weight = 15357.001| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.61 r_work: 0.2832 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9215 Z= 0.141 Angle : 0.563 10.118 12637 Z= 0.269 Chirality : 0.041 0.223 1449 Planarity : 0.005 0.037 1586 Dihedral : 6.963 58.185 2048 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.15 % Allowed : 17.30 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.25 (0.26), residues: 1130 helix: 2.22 (0.26), residues: 435 sheet: 0.45 (0.37), residues: 215 loop : -0.25 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.012 0.001 TYR A 53 PHE 0.011 0.001 PHE A 68 TRP 0.007 0.001 TRP A 325 HIS 0.002 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9215) covalent geometry : angle 0.56278 (12637) hydrogen bonds : bond 0.03157 ( 441) hydrogen bonds : angle 4.77712 ( 1263) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.279 Fit side-chains REVERT: A 210 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8668 (tt0) outliers start: 28 outliers final: 14 residues processed: 89 average time/residue: 0.4893 time to fit residues: 46.9825 Evaluate side-chains 77 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 41 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.078462 restraints weight = 15513.090| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.61 r_work: 0.2848 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9215 Z= 0.110 Angle : 0.556 9.921 12637 Z= 0.262 Chirality : 0.041 0.236 1449 Planarity : 0.004 0.037 1586 Dihedral : 6.880 57.889 2048 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.92 % Allowed : 18.09 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.35 (0.26), residues: 1130 helix: 2.31 (0.26), residues: 435 sheet: 0.52 (0.37), residues: 214 loop : -0.21 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 86 TYR 0.008 0.001 TYR A 53 PHE 0.025 0.001 PHE C 405 TRP 0.008 0.001 TRP A 325 HIS 0.002 0.000 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9215) covalent geometry : angle 0.55610 (12637) hydrogen bonds : bond 0.02762 ( 441) hydrogen bonds : angle 4.59347 ( 1263) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.354 Fit side-chains REVERT: A 210 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: B 482 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.6391 (ttm170) outliers start: 26 outliers final: 11 residues processed: 86 average time/residue: 0.5645 time to fit residues: 52.2792 Evaluate side-chains 75 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077777 restraints weight = 15341.008| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.59 r_work: 0.2838 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9215 Z= 0.127 Angle : 0.557 10.031 12637 Z= 0.262 Chirality : 0.041 0.228 1449 Planarity : 0.004 0.037 1586 Dihedral : 6.903 58.688 2048 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.26 % Allowed : 18.09 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.34 (0.26), residues: 1130 helix: 2.31 (0.26), residues: 434 sheet: 0.55 (0.37), residues: 213 loop : -0.24 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.011 0.001 TYR A 53 PHE 0.020 0.001 PHE C 405 TRP 0.007 0.001 TRP C 156 HIS 0.002 0.000 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9215) covalent geometry : angle 0.55680 (12637) hydrogen bonds : bond 0.02803 ( 441) hydrogen bonds : angle 4.54333 ( 1263) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.356 Fit side-chains REVERT: A 210 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: B 63 ASP cc_start: 0.8387 (t0) cc_final: 0.8067 (t70) REVERT: B 482 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.6415 (ttm170) outliers start: 29 outliers final: 10 residues processed: 90 average time/residue: 0.5372 time to fit residues: 52.1675 Evaluate side-chains 74 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.076341 restraints weight = 15414.594| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.61 r_work: 0.2812 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9215 Z= 0.169 Angle : 0.587 10.294 12637 Z= 0.277 Chirality : 0.042 0.212 1449 Planarity : 0.005 0.038 1586 Dihedral : 7.025 59.452 2048 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.26 % Allowed : 18.20 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.28 (0.26), residues: 1130 helix: 2.26 (0.26), residues: 434 sheet: 0.47 (0.38), residues: 212 loop : -0.25 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.015 0.001 TYR A 53 PHE 0.034 0.001 PHE C 405 TRP 0.009 0.001 TRP C 156 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9215) covalent geometry : angle 0.58673 (12637) hydrogen bonds : bond 0.03078 ( 441) hydrogen bonds : angle 4.60040 ( 1263) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.356 Fit side-chains REVERT: A 210 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8712 (tt0) REVERT: B 63 ASP cc_start: 0.8502 (t0) cc_final: 0.8199 (t70) REVERT: B 482 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.6413 (ttm170) outliers start: 29 outliers final: 12 residues processed: 91 average time/residue: 0.5588 time to fit residues: 54.7191 Evaluate side-chains 76 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 111 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.077780 restraints weight = 15426.845| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.60 r_work: 0.2833 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9215 Z= 0.121 Angle : 0.575 10.020 12637 Z= 0.272 Chirality : 0.041 0.231 1449 Planarity : 0.004 0.037 1586 Dihedral : 6.933 58.285 2048 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.36 % Allowed : 19.21 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.34 (0.26), residues: 1130 helix: 2.29 (0.26), residues: 435 sheet: 0.54 (0.37), residues: 214 loop : -0.22 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.009 0.001 TYR A 53 PHE 0.023 0.001 PHE C 405 TRP 0.008 0.001 TRP A 325 HIS 0.002 0.000 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9215) covalent geometry : angle 0.57503 (12637) hydrogen bonds : bond 0.02733 ( 441) hydrogen bonds : angle 4.49316 ( 1263) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.355 Fit side-chains REVERT: A 210 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: B 63 ASP cc_start: 0.8518 (t0) cc_final: 0.8241 (t70) REVERT: B 482 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.6416 (ttm170) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 0.5393 time to fit residues: 49.4401 Evaluate side-chains 78 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 102 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 27 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.078413 restraints weight = 15309.125| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.60 r_work: 0.2846 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9215 Z= 0.112 Angle : 0.569 9.929 12637 Z= 0.268 Chirality : 0.041 0.234 1449 Planarity : 0.004 0.037 1586 Dihedral : 6.879 58.366 2048 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.25 % Allowed : 19.78 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.36 (0.26), residues: 1130 helix: 2.30 (0.26), residues: 436 sheet: 0.51 (0.37), residues: 217 loop : -0.20 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.009 0.001 TYR A 53 PHE 0.041 0.001 PHE C 405 TRP 0.008 0.001 TRP A 325 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9215) covalent geometry : angle 0.56894 (12637) hydrogen bonds : bond 0.02622 ( 441) hydrogen bonds : angle 4.45554 ( 1263) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.348 Fit side-chains REVERT: A 210 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: B 63 ASP cc_start: 0.8453 (t0) cc_final: 0.8176 (t70) REVERT: B 482 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.6393 (ttm170) outliers start: 20 outliers final: 11 residues processed: 82 average time/residue: 0.5190 time to fit residues: 46.1461 Evaluate side-chains 77 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 93 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078160 restraints weight = 15264.850| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.60 r_work: 0.2842 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9215 Z= 0.121 Angle : 0.574 9.966 12637 Z= 0.270 Chirality : 0.041 0.232 1449 Planarity : 0.004 0.037 1586 Dihedral : 6.879 58.722 2048 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.25 % Allowed : 19.89 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.35 (0.26), residues: 1130 helix: 2.30 (0.26), residues: 436 sheet: 0.53 (0.37), residues: 216 loop : -0.21 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 292 TYR 0.009 0.001 TYR A 53 PHE 0.022 0.001 PHE C 405 TRP 0.007 0.001 TRP A 325 HIS 0.002 0.000 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9215) covalent geometry : angle 0.57395 (12637) hydrogen bonds : bond 0.02650 ( 441) hydrogen bonds : angle 4.44245 ( 1263) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.359 Fit side-chains REVERT: A 210 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: B 63 ASP cc_start: 0.8475 (t0) cc_final: 0.8197 (t70) REVERT: B 482 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.6359 (ttm170) outliers start: 20 outliers final: 11 residues processed: 82 average time/residue: 0.4937 time to fit residues: 43.8105 Evaluate side-chains 77 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 0.0170 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 82 GLN B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.079237 restraints weight = 15274.480| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.57 r_work: 0.2872 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9215 Z= 0.104 Angle : 0.576 10.093 12637 Z= 0.272 Chirality : 0.041 0.242 1449 Planarity : 0.004 0.037 1586 Dihedral : 6.815 58.410 2048 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.80 % Allowed : 20.34 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.40 (0.26), residues: 1130 helix: 2.34 (0.26), residues: 436 sheet: 0.55 (0.37), residues: 217 loop : -0.18 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 421 TYR 0.008 0.001 TYR A 26 PHE 0.042 0.001 PHE C 405 TRP 0.009 0.001 TRP A 325 HIS 0.002 0.000 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9215) covalent geometry : angle 0.57583 (12637) hydrogen bonds : bond 0.02495 ( 441) hydrogen bonds : angle 4.38817 ( 1263) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.357 Fit side-chains REVERT: A 210 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8608 (tt0) REVERT: B 63 ASP cc_start: 0.8409 (t0) cc_final: 0.8143 (t70) REVERT: B 85 ASP cc_start: 0.8161 (m-30) cc_final: 0.7906 (p0) REVERT: B 482 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.6323 (ttm170) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.5380 time to fit residues: 47.6836 Evaluate side-chains 79 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 chunk 27 optimal weight: 0.0370 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS A 203 GLN B 82 GLN B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.078969 restraints weight = 15160.475| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.56 r_work: 0.2866 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9215 Z= 0.114 Angle : 0.579 9.855 12637 Z= 0.275 Chirality : 0.041 0.236 1449 Planarity : 0.004 0.037 1586 Dihedral : 6.815 58.958 2048 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.91 % Allowed : 20.45 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.40 (0.26), residues: 1130 helix: 2.34 (0.26), residues: 436 sheet: 0.55 (0.37), residues: 217 loop : -0.18 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 421 TYR 0.025 0.001 TYR C 138 PHE 0.011 0.001 PHE B 396 TRP 0.008 0.001 TRP A 325 HIS 0.002 0.000 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9215) covalent geometry : angle 0.57853 (12637) hydrogen bonds : bond 0.02568 ( 441) hydrogen bonds : angle 4.38412 ( 1263) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3192.36 seconds wall clock time: 55 minutes 10.57 seconds (3310.57 seconds total)