Starting phenix.real_space_refine on Fri Aug 22 16:21:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fk5_50519/08_2025/9fk5_50519.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fk5_50519/08_2025/9fk5_50519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fk5_50519/08_2025/9fk5_50519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fk5_50519/08_2025/9fk5_50519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fk5_50519/08_2025/9fk5_50519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fk5_50519/08_2025/9fk5_50519.map" } resolution = 4.1 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= 0.016 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 55 5.16 5 C 3636 2.51 5 N 981 2.21 5 O 1093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5765 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 890 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "B" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "C" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 586 Classifications: {'peptide': 77} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 73} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 831 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "E" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2579 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 309} Time building chain proxies: 1.42, per 1000 atoms: 0.25 Number of scatterers: 5765 At special positions: 0 Unit cell: (81.34, 74.7, 138.61, 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 55 16.00 O 1093 8.00 N 981 7.00 C 3636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 409 " distance=2.02 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 411 " distance=2.02 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 104 " distance=2.04 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 71 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 67 " distance=2.03 Simple disulfide: pdb=" SG CYS D 77 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 143 " distance=2.02 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 162.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 18 sheets defined 13.7% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 373 removed outlier: 3.655A pdb=" N SER A 373 " --> pdb=" O PRO A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 373' Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.732A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'E' and resid 58 through 62 removed outlier: 3.793A pdb=" N SER E 62 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 149 removed outlier: 3.797A pdb=" N PHE E 146 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 148 " --> pdb=" O ASN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.519A pdb=" N LEU E 311 " --> pdb=" O ASP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 316 through 318 removed outlier: 3.811A pdb=" N PHE A 343 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 392 removed outlier: 5.717A pdb=" N GLU A 384 " --> pdb=" O ASN A 403 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 403 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 316 through 318 removed outlier: 3.530A pdb=" N SER B 345 " --> pdb=" O CYS B 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 323 Processing sheet with id=AA7, first strand: chain 'B' and resid 333 through 335 removed outlier: 6.570A pdb=" N VAL B 333 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR B 391 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 335 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER B 408 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 383 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 406 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N MET B 404 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR B 387 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N SER B 402 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N LEU B 389 " --> pdb=" O GLN B 400 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N GLN B 400 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N TYR B 391 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL B 398 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 63 through 70 removed outlier: 4.148A pdb=" N VAL C 93 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AB2, first strand: chain 'D' and resid 57 through 58 removed outlier: 4.138A pdb=" N THR D 132 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET D 135 " --> pdb=" O LYS D 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 66 through 68 removed outlier: 6.728A pdb=" N CYS D 121 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 34 through 35 removed outlier: 3.653A pdb=" N LEU E 34 " --> pdb=" O GLY E 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 215 through 220 removed outlier: 4.427A pdb=" N ALA E 44 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE E 353 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE E 255 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU E 355 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP E 257 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU E 357 " --> pdb=" O ASP E 257 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG E 259 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER E 303 " --> pdb=" O VAL E 281 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TRP E 283 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 56 removed outlier: 5.673A pdb=" N VAL E 67 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N SER E 179 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE E 69 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE E 130 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AB8, first strand: chain 'E' and resid 90 through 91 removed outlier: 5.962A pdb=" N HIS E 90 " --> pdb=" O ILE E 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 312 through 314 removed outlier: 7.268A pdb=" N GLY E 292 " --> pdb=" O GLN E 313 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG E 269 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU E 295 " --> pdb=" O ARG E 269 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E 271 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N MET E 297 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU E 273 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR E 344 " --> pdb=" O HIS E 237 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE E 239 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN E 346 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU E 241 " --> pdb=" O ASN E 346 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 429 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: 0.68 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1117 1.33 - 1.45: 1398 1.45 - 1.57: 3320 1.57 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 5901 Sorted by residual: bond pdb=" C SER D 118 " pdb=" O SER D 118 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.28e-02 6.10e+03 6.26e+00 bond pdb=" N SER D 118 " pdb=" CA SER D 118 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.37e-02 5.33e+03 6.12e+00 bond pdb=" N THR E 317 " pdb=" CA THR E 317 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" C PRO D 119 " pdb=" O PRO D 119 " ideal model delta sigma weight residual 1.235 1.205 0.030 1.30e-02 5.92e+03 5.25e+00 bond pdb=" N ASN E 71 " pdb=" CA ASN E 71 " ideal model delta sigma weight residual 1.463 1.487 -0.025 1.28e-02 6.10e+03 3.70e+00 ... (remaining 5896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 7418 0.84 - 1.69: 464 1.69 - 2.53: 83 2.53 - 3.37: 41 3.37 - 4.22: 16 Bond angle restraints: 8022 Sorted by residual: angle pdb=" CA SER D 118 " pdb=" C SER D 118 " pdb=" O SER D 118 " ideal model delta sigma weight residual 120.69 117.06 3.63 1.13e+00 7.83e-01 1.03e+01 angle pdb=" N GLY E 292 " pdb=" CA GLY E 292 " pdb=" C GLY E 292 " ideal model delta sigma weight residual 111.21 114.49 -3.28 1.04e+00 9.25e-01 9.92e+00 angle pdb=" CA ASN E 71 " pdb=" C ASN E 71 " pdb=" O ASN E 71 " ideal model delta sigma weight residual 121.58 118.19 3.39 1.12e+00 7.97e-01 9.17e+00 angle pdb=" CA SER D 118 " pdb=" C SER D 118 " pdb=" N PRO D 119 " ideal model delta sigma weight residual 117.79 121.00 -3.21 1.08e+00 8.57e-01 8.83e+00 angle pdb=" CA SER D 139 " pdb=" C SER D 139 " pdb=" O SER D 139 " ideal model delta sigma weight residual 121.78 118.58 3.20 1.12e+00 7.97e-01 8.17e+00 ... (remaining 8017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.50: 3326 11.50 - 23.00: 236 23.00 - 34.50: 59 34.50 - 45.99: 19 45.99 - 57.49: 8 Dihedral angle restraints: 3648 sinusoidal: 1490 harmonic: 2158 Sorted by residual: dihedral pdb=" CA PHE E 141 " pdb=" C PHE E 141 " pdb=" N GLU E 142 " pdb=" CA GLU E 142 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" N CYS B 316 " pdb=" CA CYS B 316 " pdb=" CB CYS B 316 " pdb=" SG CYS B 316 " ideal model delta sinusoidal sigma weight residual -60.00 -117.49 57.49 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N CYS A 316 " pdb=" CA CYS A 316 " pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " ideal model delta sinusoidal sigma weight residual -180.00 -123.14 -56.86 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 3645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 548 0.030 - 0.061: 243 0.061 - 0.091: 38 0.091 - 0.121: 68 0.121 - 0.151: 12 Chirality restraints: 909 Sorted by residual: chirality pdb=" CA ILE D 76 " pdb=" N ILE D 76 " pdb=" C ILE D 76 " pdb=" CB ILE D 76 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA VAL B 379 " pdb=" N VAL B 379 " pdb=" C VAL B 379 " pdb=" CB VAL B 379 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE E 187 " pdb=" N ILE E 187 " pdb=" C ILE E 187 " pdb=" CB ILE E 187 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 906 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 379 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO B 380 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 92 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO E 93 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 93 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 93 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 47 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO D 48 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 48 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 48 " 0.015 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 85 2.60 - 3.18: 4998 3.18 - 3.75: 8358 3.75 - 4.33: 12057 4.33 - 4.90: 19917 Nonbonded interactions: 45415 Sorted by model distance: nonbonded pdb=" OE2 GLU B 399 " pdb=" OG SER E 246 " model vdw 2.030 3.040 nonbonded pdb=" O GLY E 144 " pdb=" OG SER E 147 " model vdw 2.114 3.040 nonbonded pdb=" O ALA A 372 " pdb=" OG SER A 373 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR C 59 " pdb=" O LYS C 62 " model vdw 2.122 3.040 nonbonded pdb=" OG SER E 222 " pdb=" OG1 THR E 347 " model vdw 2.134 3.040 ... (remaining 45410 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 301 through 324 or resid 326 through 389 or resid 391 thro \ ugh 393 or resid 395 through 412)) selection = (chain 'B' and (resid 301 through 324 or resid 326 through 389 or resid 391 thro \ ugh 393 or resid 395 through 412)) } 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 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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 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 0.034 5923 Z= 0.159 Angle : 0.523 4.218 8066 Z= 0.297 Chirality : 0.044 0.151 909 Planarity : 0.004 0.042 1036 Dihedral : 9.259 57.492 2176 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.25 % Allowed : 4.20 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.88 (0.32), residues: 725 helix: 0.47 (0.59), residues: 86 sheet: -0.46 (0.32), residues: 268 loop : -0.85 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.012 0.001 TYR A 365 PHE 0.012 0.001 PHE E 49 TRP 0.007 0.001 TRP D 88 HIS 0.003 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5901) covalent geometry : angle 0.51791 ( 8022) SS BOND : bond 0.00467 ( 22) SS BOND : angle 1.15289 ( 44) hydrogen bonds : bond 0.26920 ( 162) hydrogen bonds : angle 11.49290 ( 429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8349 (mt) cc_final: 0.7619 (tp) REVERT: B 404 MET cc_start: 0.8193 (mmm) cc_final: 0.7369 (mmm) outliers start: 15 outliers final: 8 residues processed: 169 average time/residue: 0.0715 time to fit residues: 15.4209 Evaluate side-chains 91 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.094190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.080590 restraints weight = 20045.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.082206 restraints weight = 16134.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.084502 restraints weight = 12008.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.084907 restraints weight = 8155.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.085598 restraints weight = 7725.646| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5923 Z= 0.157 Angle : 0.607 6.097 8066 Z= 0.320 Chirality : 0.047 0.198 909 Planarity : 0.005 0.039 1036 Dihedral : 4.440 18.156 779 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.88 (0.31), residues: 725 helix: 0.78 (0.59), residues: 83 sheet: -0.63 (0.32), residues: 262 loop : -0.78 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 80 TYR 0.012 0.002 TYR E 216 PHE 0.012 0.001 PHE B 308 TRP 0.013 0.002 TRP D 88 HIS 0.004 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5901) covalent geometry : angle 0.59254 ( 8022) SS BOND : bond 0.00536 ( 22) SS BOND : angle 1.86113 ( 44) hydrogen bonds : bond 0.04697 ( 162) hydrogen bonds : angle 8.09799 ( 429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8268 (mt) cc_final: 0.7581 (mt) REVERT: B 399 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6966 (mt-10) REVERT: E 257 ASP cc_start: 0.8637 (m-30) cc_final: 0.8327 (m-30) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0791 time to fit residues: 10.7517 Evaluate side-chains 70 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.092866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.079220 restraints weight = 19513.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.081017 restraints weight = 13925.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.082282 restraints weight = 10731.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.083028 restraints weight = 8049.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.084011 restraints weight = 7407.928| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5923 Z= 0.116 Angle : 0.542 6.083 8066 Z= 0.285 Chirality : 0.046 0.172 909 Planarity : 0.004 0.038 1036 Dihedral : 4.267 17.124 779 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.86 (0.31), residues: 725 helix: 0.86 (0.59), residues: 82 sheet: -0.50 (0.33), residues: 249 loop : -0.87 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 80 TYR 0.011 0.001 TYR E 216 PHE 0.010 0.001 PHE D 133 TRP 0.011 0.001 TRP D 88 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 5901) covalent geometry : angle 0.53617 ( 8022) SS BOND : bond 0.00328 ( 22) SS BOND : angle 1.20894 ( 44) hydrogen bonds : bond 0.03720 ( 162) hydrogen bonds : angle 7.27711 ( 429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8189 (mt) cc_final: 0.7529 (mt) REVERT: B 399 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6878 (mt-10) REVERT: D 123 MET cc_start: 0.7447 (mmm) cc_final: 0.6978 (mmm) REVERT: D 124 LYS cc_start: 0.8330 (mmpt) cc_final: 0.8099 (mmmt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0663 time to fit residues: 8.0022 Evaluate side-chains 64 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 GLN D 49 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.091353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.077981 restraints weight = 19912.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.080689 restraints weight = 15952.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.081648 restraints weight = 10900.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.082171 restraints weight = 8415.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.082666 restraints weight = 7526.392| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5923 Z= 0.134 Angle : 0.554 6.241 8066 Z= 0.287 Chirality : 0.046 0.171 909 Planarity : 0.004 0.038 1036 Dihedral : 4.394 16.728 779 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.31 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.94 (0.31), residues: 725 helix: 0.16 (0.55), residues: 94 sheet: -0.41 (0.34), residues: 248 loop : -0.91 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 318 TYR 0.027 0.002 TYR A 306 PHE 0.009 0.001 PHE D 133 TRP 0.011 0.001 TRP D 88 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5901) covalent geometry : angle 0.54405 ( 8022) SS BOND : bond 0.00376 ( 22) SS BOND : angle 1.54531 ( 44) hydrogen bonds : bond 0.03534 ( 162) hydrogen bonds : angle 6.91455 ( 429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8288 (mt) cc_final: 0.7619 (mt) REVERT: D 123 MET cc_start: 0.7426 (mmm) cc_final: 0.6928 (mmm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0775 time to fit residues: 8.9920 Evaluate side-chains 60 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.090913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.077798 restraints weight = 20487.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.079137 restraints weight = 14490.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.080218 restraints weight = 12268.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.080704 restraints weight = 9100.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.082204 restraints weight = 8555.178| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5923 Z= 0.133 Angle : 0.537 4.647 8066 Z= 0.281 Chirality : 0.046 0.168 909 Planarity : 0.004 0.042 1036 Dihedral : 4.417 17.761 779 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.83 (0.31), residues: 725 helix: 0.55 (0.60), residues: 82 sheet: -0.50 (0.33), residues: 247 loop : -0.74 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 259 TYR 0.015 0.002 TYR A 306 PHE 0.008 0.001 PHE D 133 TRP 0.011 0.001 TRP D 88 HIS 0.009 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5901) covalent geometry : angle 0.52815 ( 8022) SS BOND : bond 0.00392 ( 22) SS BOND : angle 1.39985 ( 44) hydrogen bonds : bond 0.03391 ( 162) hydrogen bonds : angle 6.68569 ( 429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8313 (mt) cc_final: 0.7646 (mt) REVERT: D 123 MET cc_start: 0.7370 (mmm) cc_final: 0.7029 (mmm) REVERT: E 90 HIS cc_start: 0.7397 (m90) cc_final: 0.7003 (t-170) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0693 time to fit residues: 8.1992 Evaluate side-chains 62 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 HIS E 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.090278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.077524 restraints weight = 20137.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.079036 restraints weight = 13720.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.080012 restraints weight = 11118.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.080792 restraints weight = 8557.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.080928 restraints weight = 7596.957| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5923 Z= 0.145 Angle : 0.561 6.424 8066 Z= 0.292 Chirality : 0.046 0.166 909 Planarity : 0.004 0.037 1036 Dihedral : 4.608 16.903 779 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.93 (0.31), residues: 725 helix: 0.32 (0.58), residues: 88 sheet: -0.54 (0.33), residues: 247 loop : -0.82 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 259 TYR 0.018 0.002 TYR A 306 PHE 0.008 0.001 PHE D 133 TRP 0.010 0.001 TRP D 88 HIS 0.011 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5901) covalent geometry : angle 0.54955 ( 8022) SS BOND : bond 0.00352 ( 22) SS BOND : angle 1.63900 ( 44) hydrogen bonds : bond 0.03366 ( 162) hydrogen bonds : angle 6.63859 ( 429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8385 (mt) cc_final: 0.7682 (mt) REVERT: D 105 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7281 (pptt) REVERT: D 123 MET cc_start: 0.7244 (mmm) cc_final: 0.6934 (mmm) REVERT: E 90 HIS cc_start: 0.7427 (m90) cc_final: 0.7029 (t-170) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0657 time to fit residues: 7.0613 Evaluate side-chains 65 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.090894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.078545 restraints weight = 20423.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.079758 restraints weight = 13668.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.081116 restraints weight = 11035.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.081710 restraints weight = 8376.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.082632 restraints weight = 7616.058| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5923 Z= 0.111 Angle : 0.534 7.467 8066 Z= 0.276 Chirality : 0.045 0.165 909 Planarity : 0.004 0.039 1036 Dihedral : 4.349 15.670 779 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.31 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.90 (0.31), residues: 725 helix: 0.35 (0.60), residues: 87 sheet: -0.46 (0.33), residues: 256 loop : -0.86 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 259 TYR 0.016 0.001 TYR A 306 PHE 0.009 0.001 PHE D 133 TRP 0.011 0.001 TRP D 88 HIS 0.008 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 5901) covalent geometry : angle 0.52353 ( 8022) SS BOND : bond 0.00285 ( 22) SS BOND : angle 1.51597 ( 44) hydrogen bonds : bond 0.03113 ( 162) hydrogen bonds : angle 6.41866 ( 429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8385 (mt) cc_final: 0.7670 (mt) REVERT: D 105 LYS cc_start: 0.7668 (mmtp) cc_final: 0.7303 (pptt) REVERT: D 123 MET cc_start: 0.7216 (mmm) cc_final: 0.6843 (mmm) REVERT: E 90 HIS cc_start: 0.7320 (m90) cc_final: 0.7079 (t-170) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0602 time to fit residues: 6.8267 Evaluate side-chains 66 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 0.0030 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 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 = 0.4059 r_free = 0.4059 target = 0.090864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.078091 restraints weight = 20105.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.079244 restraints weight = 14991.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.080210 restraints weight = 12777.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.081357 restraints weight = 9800.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.082323 restraints weight = 7985.981| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5923 Z= 0.113 Angle : 0.529 7.771 8066 Z= 0.275 Chirality : 0.045 0.161 909 Planarity : 0.004 0.040 1036 Dihedral : 4.372 15.773 779 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.89 (0.31), residues: 725 helix: 0.35 (0.60), residues: 86 sheet: -0.40 (0.33), residues: 253 loop : -0.88 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 259 TYR 0.023 0.002 TYR B 339 PHE 0.008 0.001 PHE D 133 TRP 0.011 0.001 TRP D 88 HIS 0.007 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5901) covalent geometry : angle 0.51900 ( 8022) SS BOND : bond 0.00274 ( 22) SS BOND : angle 1.50175 ( 44) hydrogen bonds : bond 0.03129 ( 162) hydrogen bonds : angle 6.44825 ( 429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8395 (mt) cc_final: 0.7805 (mt) REVERT: D 105 LYS cc_start: 0.7664 (mmtp) cc_final: 0.7297 (pptt) REVERT: D 123 MET cc_start: 0.7242 (mmm) cc_final: 0.6878 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0591 time to fit residues: 6.7566 Evaluate side-chains 64 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 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 = 0.4052 r_free = 0.4052 target = 0.091318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.077854 restraints weight = 20214.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.079158 restraints weight = 14414.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.080722 restraints weight = 12165.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.081309 restraints weight = 9400.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.081802 restraints weight = 7782.483| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5923 Z= 0.123 Angle : 0.533 7.906 8066 Z= 0.276 Chirality : 0.045 0.157 909 Planarity : 0.004 0.043 1036 Dihedral : 4.480 17.966 779 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.86 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 aren not related in a simple way. whole: -0.98 (0.31), residues: 725 helix: -0.00 (0.57), residues: 92 sheet: -0.43 (0.33), residues: 253 loop : -0.90 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 259 TYR 0.015 0.002 TYR B 339 PHE 0.008 0.001 PHE D 53 TRP 0.010 0.001 TRP D 88 HIS 0.008 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5901) covalent geometry : angle 0.52324 ( 8022) SS BOND : bond 0.00320 ( 22) SS BOND : angle 1.45100 ( 44) hydrogen bonds : bond 0.03108 ( 162) hydrogen bonds : angle 6.36711 ( 429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8390 (mt) cc_final: 0.7789 (mt) REVERT: D 105 LYS cc_start: 0.7731 (mmtp) cc_final: 0.7333 (pptt) REVERT: D 123 MET cc_start: 0.7258 (mmm) cc_final: 0.6899 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0631 time to fit residues: 6.4854 Evaluate side-chains 62 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2317 > 50: distance: 15 - 45: 12.151 distance: 29 - 98: 16.812 distance: 41 - 45: 12.892 distance: 45 - 46: 13.022 distance: 46 - 47: 8.374 distance: 46 - 49: 7.757 distance: 47 - 48: 5.074 distance: 47 - 53: 3.013 distance: 49 - 50: 21.962 distance: 50 - 51: 6.685 distance: 50 - 52: 7.187 distance: 53 - 54: 5.800 distance: 54 - 55: 15.856 distance: 54 - 57: 10.144 distance: 55 - 56: 36.761 distance: 55 - 61: 6.145 distance: 57 - 58: 13.456 distance: 58 - 59: 17.199 distance: 58 - 60: 40.685 distance: 61 - 62: 23.860 distance: 62 - 63: 7.539 distance: 62 - 65: 11.145 distance: 63 - 64: 12.781 distance: 63 - 70: 52.246 distance: 65 - 66: 25.118 distance: 66 - 67: 12.406 distance: 67 - 68: 8.107 distance: 67 - 69: 40.173 distance: 70 - 71: 3.802 distance: 71 - 72: 20.227 distance: 71 - 74: 8.499 distance: 72 - 73: 7.689 distance: 72 - 79: 27.222 distance: 74 - 75: 24.613 distance: 75 - 76: 40.168 distance: 76 - 77: 20.495 distance: 76 - 78: 28.666 distance: 79 - 80: 17.665 distance: 80 - 81: 23.981 distance: 80 - 83: 16.159 distance: 81 - 82: 23.524 distance: 81 - 87: 16.786 distance: 83 - 84: 4.026 distance: 84 - 85: 14.581 distance: 84 - 86: 19.805 distance: 87 - 88: 28.744 distance: 88 - 89: 13.678 distance: 88 - 91: 19.231 distance: 89 - 90: 17.069 distance: 89 - 93: 24.953 distance: 91 - 92: 38.301 distance: 92 - 190: 26.834 distance: 93 - 94: 4.261 distance: 93 - 158: 26.947 distance: 94 - 95: 5.802 distance: 94 - 97: 3.504 distance: 95 - 96: 21.933 distance: 95 - 99: 13.978 distance: 96 - 155: 19.516 distance: 97 - 98: 26.113 distance: 99 - 100: 21.153 distance: 100 - 101: 22.793 distance: 100 - 103: 20.817 distance: 101 - 102: 13.070 distance: 101 - 106: 33.613 distance: 103 - 104: 16.474 distance: 103 - 105: 20.715 distance: 106 - 107: 36.570 distance: 106 - 142: 31.756 distance: 107 - 108: 35.995 distance: 107 - 110: 9.910 distance: 108 - 109: 27.980 distance: 108 - 117: 9.475 distance: 110 - 111: 13.905 distance: 113 - 114: 27.031 distance: 114 - 115: 29.391 distance: 114 - 116: 37.089 distance: 117 - 118: 16.490 distance: 117 - 123: 9.853 distance: 118 - 119: 27.539 distance: 118 - 121: 17.394 distance: 119 - 120: 23.065 distance: 119 - 124: 9.018 distance: 121 - 122: 14.282 distance: 122 - 123: 40.181 distance: 191 - 209: 3.086 distance: 192 - 206: 3.269