Starting phenix.real_space_refine on Fri Sep 11 11:19:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zpa_14852/09_2026/7zpa_14852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpa_14852/09_2026/7zpa_14852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zpa_14852/09_2026/7zpa_14852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpa_14852/09_2026/7zpa_14852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zpa_14852/09_2026/7zpa_14852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpa_14852/09_2026/7zpa_14852.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zpa_14852/09_2026/7zpa_14852.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zpa_14852/09_2026/7zpa_14852.cif" } resolution = 3.9 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= 0.008 sd= 0.925 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 18 5.16 5 C 5544 2.51 5 N 1574 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9121 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3605 Chain: "B" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3636 Classifications: {'peptide': 443} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 972 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Time building chain proxies: 2.62, per 1000 atoms: 0.29 Number of scatterers: 9121 At special positions: 0 Unit cell: (83.566, 101.346, 136.906, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 97 15.00 O 1888 8.00 N 1574 7.00 C 5544 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: 0.70 Conformation dependent library (CDL) restraints added in 279.2 milliseconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 46.5% alpha, 9.0% beta 12 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 15 through 31 removed outlier: 4.480A pdb=" N TYR A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 52 through 66 removed outlier: 3.592A pdb=" N VAL A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.779A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.545A pdb=" N GLY A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 4.366A pdb=" N THR A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.344A pdb=" N HIS A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.727A pdb=" N ARG A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.936A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 381 removed outlier: 4.065A pdb=" N LYS A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'B' and resid 15 through 31 removed outlier: 4.711A pdb=" N TYR B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 52 through 67 removed outlier: 3.601A pdb=" N VAL B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.876A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 190 removed outlier: 4.357A pdb=" N THR B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.872A pdb=" N HIS B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.709A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 381 removed outlier: 3.804A pdb=" N LYS B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 450 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.991A pdb=" N GLY A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.618A pdb=" N TYR A 107 " --> pdb=" O LYS A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.609A pdb=" N GLY A 175 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 273 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 304 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLU A 275 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 239 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP A 276 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR A 241 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 194 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR A 240 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 196 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 195 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE A 219 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 197 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.815A pdb=" N LEU A 388 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 401 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 440 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR A 423 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.592A pdb=" N GLY B 175 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.285A pdb=" N VAL B 194 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TYR B 240 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 196 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 239 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP B 276 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR B 241 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 387 through 389 removed outlier: 3.643A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 401 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 440 " --> pdb=" O TYR B 423 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR B 423 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2305 1.33 - 1.45: 2293 1.45 - 1.57: 4711 1.57 - 1.69: 190 1.69 - 1.81: 32 Bond restraints: 9531 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.542 0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.546 0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C4 LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.464 1.614 -0.150 2.00e-02 2.50e+03 5.61e+01 ... (remaining 9526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 13093 2.47 - 4.94: 200 4.94 - 7.40: 17 7.40 - 9.87: 3 9.87 - 12.34: 3 Bond angle restraints: 13316 Sorted by residual: angle pdb=" N VAL B 297 " pdb=" CA VAL B 297 " pdb=" C VAL B 297 " ideal model delta sigma weight residual 113.53 107.41 6.12 9.80e-01 1.04e+00 3.89e+01 angle pdb=" N3 DT D 27 " pdb=" C4 DT D 27 " pdb=" O4 DT D 27 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT C 33 " pdb=" C4 DT C 33 " pdb=" O4 DT C 33 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT D 45 " pdb=" C4 DT D 45 " pdb=" O4 DT D 45 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 16 " pdb=" C4 DT C 16 " pdb=" O4 DT C 16 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 13311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.53: 4922 27.53 - 55.07: 486 55.07 - 82.60: 55 82.60 - 110.14: 5 110.14 - 137.67: 1 Dihedral angle restraints: 5469 sinusoidal: 2885 harmonic: 2584 Sorted by residual: dihedral pdb=" CA ARG A 74 " pdb=" C ARG A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA GLU B 83 " pdb=" C GLU B 83 " pdb=" N ASP B 84 " pdb=" CA ASP B 84 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DA D 33 " pdb=" C3' DA D 33 " pdb=" O3' DA D 33 " pdb=" P DA D 34 " ideal model delta sinusoidal sigma weight residual 220.00 82.33 137.67 1 3.50e+01 8.16e-04 1.36e+01 ... (remaining 5466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 845 0.032 - 0.064: 381 0.064 - 0.097: 170 0.097 - 0.129: 57 0.129 - 0.161: 8 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CB ILE B 273 " pdb=" CA ILE B 273 " pdb=" CG1 ILE B 273 " pdb=" CG2 ILE B 273 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA GLU B 154 " pdb=" N GLU B 154 " pdb=" C GLU B 154 " pdb=" CB GLU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CB VAL A 315 " pdb=" CA VAL A 315 " pdb=" CG1 VAL A 315 " pdb=" CG2 VAL A 315 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1458 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.159 2.00e-02 2.50e+03 2.67e-01 7.10e+02 pdb=" NZ LLP A 309 " -0.359 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.335 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " 0.078 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" NZ LLP B 309 " -0.082 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " 0.070 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 247 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 248 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.024 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1177 2.75 - 3.29: 8854 3.29 - 3.83: 15249 3.83 - 4.36: 16908 4.36 - 4.90: 27536 Nonbonded interactions: 69724 Sorted by model distance: nonbonded pdb=" OG1 THR B 168 " pdb=" OE1 GLN B 171 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 308 " pdb=" O ILE A 312 " model vdw 2.221 3.040 nonbonded pdb=" OE1 GLN B 184 " pdb=" OH TYR B 330 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 240 " pdb=" OD2 ASP B 276 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 162 " pdb=" OE2 GLU B 281 " model vdw 2.284 3.040 ... (remaining 69719 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 15 through 81 or resid 103 through 442 or resid 444 throug \ h 464)) selection = (chain 'B' and (resid 15 through 81 or resid 84 or resid 104 through 442 or resi \ d 444 through 464)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.070 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.007 0.184 9531 Z= 0.433 Angle : 0.773 12.341 13316 Z= 0.556 Chirality : 0.045 0.161 1461 Planarity : 0.009 0.267 1363 Dihedral : 19.492 137.671 3815 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.40 (0.29), residues: 861 helix: 0.90 (0.28), residues: 370 sheet: -0.29 (0.50), residues: 107 loop : -1.43 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 316 TYR 0.018 0.002 TYR A 337 PHE 0.020 0.002 PHE A 128 TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.43 ( 9531) covalent geometry : angle 0.77253 / 0.56 (13316) hydrogen bonds : bond 0.16407 / 10.57 ( 309) hydrogen bonds : angle 7.02334 / 4.92 ( 866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7443 (ttm-80) REVERT: A 291 SER cc_start: 0.7372 (m) cc_final: 0.7086 (m) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0821 time to fit residues: 10.5525 Evaluate side-chains 66 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN B 142 ASN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.118859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093669 restraints weight = 21277.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095742 restraints weight = 12491.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097163 restraints weight = 8491.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098116 restraints weight = 6450.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098519 restraints weight = 5326.642| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9531 Z= 0.166 Angle : 0.674 7.251 13316 Z= 0.384 Chirality : 0.046 0.214 1461 Planarity : 0.005 0.050 1363 Dihedral : 21.650 138.974 2059 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.42 % Allowed : 7.61 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.54 (0.28), residues: 861 helix: 0.82 (0.27), residues: 375 sheet: -0.67 (0.47), residues: 114 loop : -1.48 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 343 TYR 0.021 0.002 TYR B 21 PHE 0.014 0.002 PHE A 128 TRP 0.008 0.001 TRP A 264 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 ( 9531) covalent geometry : angle 0.67393 / 0.38 (13316) hydrogen bonds : bond 0.06387 / 3.86 ( 309) hydrogen bonds : angle 4.74761 / 3.27 ( 866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7449 (ttm-80) REVERT: A 291 SER cc_start: 0.7376 (m) cc_final: 0.7076 (m) REVERT: B 413 GLU cc_start: 0.7069 (pp20) cc_final: 0.6779 (pp20) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.0790 time to fit residues: 9.0648 Evaluate side-chains 71 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN B 142 ASN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.092832 restraints weight = 21479.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094847 restraints weight = 12712.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.096230 restraints weight = 8711.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097176 restraints weight = 6637.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097769 restraints weight = 5495.886| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9531 Z= 0.181 Angle : 0.646 7.340 13316 Z= 0.373 Chirality : 0.045 0.165 1461 Planarity : 0.005 0.049 1363 Dihedral : 21.627 139.792 2059 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.42 % Allowed : 11.48 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.62 (0.28), residues: 861 helix: 0.78 (0.27), residues: 376 sheet: -0.76 (0.47), residues: 112 loop : -1.54 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.019 0.002 TYR B 21 PHE 0.014 0.002 PHE B 352 TRP 0.010 0.001 TRP A 124 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 ( 9531) covalent geometry : angle 0.64615 / 0.37 (13316) hydrogen bonds : bond 0.06255 / 3.76 ( 309) hydrogen bonds : angle 4.57437 / 3.15 ( 866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7467 (ttm-80) REVERT: A 291 SER cc_start: 0.7409 (m) cc_final: 0.7127 (m) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.0691 time to fit residues: 7.7995 Evaluate side-chains 74 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 8.9990 chunk 60 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.119167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.093753 restraints weight = 21442.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095818 restraints weight = 12570.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097262 restraints weight = 8544.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098252 restraints weight = 6456.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098612 restraints weight = 5297.084| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9531 Z= 0.146 Angle : 0.605 7.823 13316 Z= 0.352 Chirality : 0.043 0.160 1461 Planarity : 0.005 0.049 1363 Dihedral : 21.622 140.570 2059 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.55 % Allowed : 13.16 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.44 (0.28), residues: 861 helix: 0.94 (0.27), residues: 376 sheet: -0.57 (0.48), residues: 106 loop : -1.47 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 138 TYR 0.017 0.001 TYR B 21 PHE 0.012 0.002 PHE A 128 TRP 0.011 0.001 TRP A 124 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 9531) covalent geometry : angle 0.60464 / 0.35 (13316) hydrogen bonds : bond 0.05665 / 3.46 ( 309) hydrogen bonds : angle 4.28661 / 2.95 ( 866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.213 Fit side-chains REVERT: A 291 SER cc_start: 0.7162 (m) cc_final: 0.6880 (m) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.0729 time to fit residues: 8.3689 Evaluate side-chains 74 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.118582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093117 restraints weight = 21509.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095190 restraints weight = 12630.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096617 restraints weight = 8579.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097546 restraints weight = 6487.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098189 restraints weight = 5378.484| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9531 Z= 0.167 Angle : 0.620 6.325 13316 Z= 0.360 Chirality : 0.044 0.161 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.699 140.773 2059 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.81 % Allowed : 14.19 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.53 (0.28), residues: 861 helix: 0.89 (0.27), residues: 376 sheet: -0.71 (0.48), residues: 106 loop : -1.52 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.018 0.002 TYR B 21 PHE 0.014 0.002 PHE B 352 TRP 0.010 0.001 TRP A 264 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 ( 9531) covalent geometry : angle 0.62008 / 0.36 (13316) hydrogen bonds : bond 0.05645 / 3.46 ( 309) hydrogen bonds : angle 4.31903 / 2.98 ( 866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.293 Fit side-chains REVERT: A 291 SER cc_start: 0.7283 (m) cc_final: 0.7008 (m) REVERT: B 115 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.6048 (m-30) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.0727 time to fit residues: 8.2969 Evaluate side-chains 72 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 350 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 142 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093507 restraints weight = 21348.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095564 restraints weight = 12475.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096995 restraints weight = 8475.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097953 restraints weight = 6417.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098358 restraints weight = 5296.022| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9531 Z= 0.144 Angle : 0.597 8.163 13316 Z= 0.347 Chirality : 0.043 0.168 1461 Planarity : 0.005 0.050 1363 Dihedral : 21.779 141.193 2059 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.81 % Allowed : 15.35 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.44 (0.29), residues: 861 helix: 0.97 (0.27), residues: 376 sheet: -0.64 (0.47), residues: 107 loop : -1.49 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.019 0.001 TYR B 21 PHE 0.011 0.002 PHE A 77 TRP 0.011 0.001 TRP A 264 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 9531) covalent geometry : angle 0.59720 / 0.35 (13316) hydrogen bonds : bond 0.05393 / 3.34 ( 309) hydrogen bonds : angle 4.16524 / 2.87 ( 866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.235 Fit side-chains REVERT: A 144 ASP cc_start: 0.6513 (m-30) cc_final: 0.6270 (m-30) REVERT: A 291 SER cc_start: 0.7190 (m) cc_final: 0.6904 (m) REVERT: B 115 ASP cc_start: 0.6304 (m-30) cc_final: 0.5993 (m-30) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.0696 time to fit residues: 8.4045 Evaluate side-chains 76 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.120855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094886 restraints weight = 21266.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097125 restraints weight = 12066.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098649 restraints weight = 8035.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.099698 restraints weight = 5997.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100242 restraints weight = 4907.103| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9531 Z= 0.127 Angle : 0.574 8.374 13316 Z= 0.335 Chirality : 0.042 0.156 1461 Planarity : 0.005 0.050 1363 Dihedral : 21.816 141.596 2059 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.29 % Allowed : 16.77 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.29 (0.29), residues: 861 helix: 1.11 (0.27), residues: 376 sheet: -0.59 (0.48), residues: 108 loop : -1.42 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 432 TYR 0.020 0.001 TYR A 336 PHE 0.012 0.001 PHE A 77 TRP 0.012 0.001 TRP A 264 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 ( 9531) covalent geometry : angle 0.57408 / 0.34 (13316) hydrogen bonds : bond 0.05099 / 3.17 ( 309) hydrogen bonds : angle 4.00052 / 2.75 ( 866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.317 Fit side-chains REVERT: A 144 ASP cc_start: 0.6563 (m-30) cc_final: 0.6339 (m-30) REVERT: A 291 SER cc_start: 0.7186 (m) cc_final: 0.6921 (m) REVERT: B 115 ASP cc_start: 0.6256 (m-30) cc_final: 0.5953 (m-30) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.0804 time to fit residues: 8.9864 Evaluate side-chains 73 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 GLN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.118482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093273 restraints weight = 21186.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095368 restraints weight = 12210.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096785 restraints weight = 8179.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097752 restraints weight = 6137.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098322 restraints weight = 5049.563| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 0.046 9531 Z= 0.162 Angle : 0.616 7.989 13316 Z= 0.352 Chirality : 0.043 0.161 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.883 141.905 2059 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.55 % Allowed : 17.42 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.29), residues: 861 helix: 1.00 (0.27), residues: 377 sheet: -0.70 (0.48), residues: 109 loop : -1.47 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.020 0.002 TYR A 336 PHE 0.014 0.002 PHE B 352 TRP 0.012 0.001 TRP A 124 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 9531) covalent geometry : angle 0.61572 / 0.35 (13316) hydrogen bonds : bond 0.05333 / 3.32 ( 309) hydrogen bonds : angle 4.17417 / 2.88 ( 866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.269 Fit side-chains REVERT: A 291 SER cc_start: 0.7268 (m) cc_final: 0.6996 (m) REVERT: A 413 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7699 (tp30) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.0701 time to fit residues: 7.9756 Evaluate side-chains 75 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.117368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092177 restraints weight = 21339.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094201 restraints weight = 12288.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095632 restraints weight = 8273.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096601 restraints weight = 6217.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097167 restraints weight = 5095.074| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9531 Z= 0.186 Angle : 0.639 7.860 13316 Z= 0.363 Chirality : 0.045 0.303 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.942 141.948 2059 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.68 % Allowed : 18.06 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.51 (0.29), residues: 861 helix: 0.93 (0.27), residues: 377 sheet: -0.82 (0.48), residues: 109 loop : -1.51 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 316 TYR 0.022 0.002 TYR B 21 PHE 0.016 0.002 PHE A 352 TRP 0.009 0.001 TRP A 124 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 9531) covalent geometry : angle 0.63907 / 0.36 (13316) hydrogen bonds : bond 0.05450 / 3.41 ( 309) hydrogen bonds : angle 4.25591 / 2.94 ( 866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.220 Fit side-chains REVERT: A 291 SER cc_start: 0.7355 (m) cc_final: 0.7079 (m) REVERT: A 413 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7676 (tp30) outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.0743 time to fit residues: 8.5138 Evaluate side-chains 77 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 350 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 80 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 91 optimal weight: 40.0000 chunk 20 optimal weight: 0.0010 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.120160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094655 restraints weight = 20914.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096835 restraints weight = 11861.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.098332 restraints weight = 7870.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099333 restraints weight = 5874.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099954 restraints weight = 4809.179| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9531 Z= 0.130 Angle : 0.594 8.143 13316 Z= 0.342 Chirality : 0.042 0.240 1461 Planarity : 0.005 0.049 1363 Dihedral : 21.900 142.352 2059 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.77 % Allowed : 19.10 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.29 (0.29), residues: 861 helix: 1.10 (0.27), residues: 377 sheet: -0.60 (0.48), residues: 109 loop : -1.41 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.025 0.001 TYR B 21 PHE 0.013 0.001 PHE A 77 TRP 0.013 0.001 TRP A 124 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 9531) covalent geometry : angle 0.59421 / 0.34 (13316) hydrogen bonds : bond 0.05004 / 3.18 ( 309) hydrogen bonds : angle 4.02417 / 2.77 ( 866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.312 Fit side-chains REVERT: A 291 SER cc_start: 0.7184 (m) cc_final: 0.6917 (m) REVERT: A 413 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7761 (tp30) REVERT: B 61 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7749 (tm-30) outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.0797 time to fit residues: 8.4154 Evaluate side-chains 73 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 145 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 40.0000 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.118303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092847 restraints weight = 20976.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094932 restraints weight = 12081.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096357 restraints weight = 8107.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097337 restraints weight = 6098.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097991 restraints weight = 5018.559| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9531 Z= 0.169 Angle : 0.623 8.461 13316 Z= 0.354 Chirality : 0.044 0.220 1461 Planarity : 0.005 0.051 1363 Dihedral : 21.968 142.282 2059 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.42 % Allowed : 18.45 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.45 (0.29), residues: 861 helix: 0.98 (0.27), residues: 377 sheet: -0.79 (0.48), residues: 109 loop : -1.47 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.023 0.002 TYR B 21 PHE 0.015 0.002 PHE A 352 TRP 0.010 0.001 TRP A 124 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 9531) covalent geometry : angle 0.62309 / 0.35 (13316) hydrogen bonds : bond 0.05235 / 3.30 ( 309) hydrogen bonds : angle 4.19085 / 2.89 ( 866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.06 seconds wall clock time: 29 minutes 30.80 seconds (1770.80 seconds total)