Starting phenix.real_space_refine on Fri Oct 10 14:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q97_18270/10_2025/8q97_18270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q97_18270/10_2025/8q97_18270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q97_18270/10_2025/8q97_18270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q97_18270/10_2025/8q97_18270.map" model { file = "/net/cci-nas-00/data/ceres_data/8q97_18270/10_2025/8q97_18270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q97_18270/10_2025/8q97_18270.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 H 3396 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6642 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "D" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "C" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "B" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "E" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "F" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Time building chain proxies: 2.41, per 1000 atoms: 0.36 Number of scatterers: 6642 At special positions: 0 Unit cell: (99.704, 139.256, 39.552, 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 6 16.00 O 606 8.00 N 588 7.00 C 2046 6.00 H 3396 1.00 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: 0.57 Conformation dependent library (CDL) restraints added in 440.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 46.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 309 through 310 removed outlier: 6.520A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.750A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.621A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER D 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS A 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.629A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.657A pdb=" N GLN A 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILE D 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 357 through 361 removed outlier: 6.162A pdb=" N ASP A 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR D 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.612A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.463A pdb=" N VAL B 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.770A pdb=" N VAL B 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.335A pdb=" N LYS B 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER E 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS E 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS B 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER E 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY B 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342 Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.683A pdb=" N ASP B 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.602A pdb=" N GLN B 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE E 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS B 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 361 removed outlier: 6.192A pdb=" N ASP B 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR E 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.656A pdb=" N LYS B 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLU E 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE B 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS E 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR B 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU E 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS B 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 79 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.33: 4134 1.33 - 1.76: 2546 1.76 - 2.18: 10 2.18 - 2.61: 0 2.61 - 3.04: 6 Bond restraints: 6696 Sorted by residual: bond pdb=" N LYS A 343 " pdb=" H BLYS A 343 " ideal model delta sigma weight residual 0.860 3.040 -2.180 2.00e-02 2.50e+03 1.19e+04 bond pdb=" N LYS B 343 " pdb=" H BLYS B 343 " ideal model delta sigma weight residual 0.860 3.013 -2.153 2.00e-02 2.50e+03 1.16e+04 bond pdb=" N LYS E 343 " pdb=" H BLYS E 343 " ideal model delta sigma weight residual 0.860 2.872 -2.012 2.00e-02 2.50e+03 1.01e+04 bond pdb=" N LYS D 343 " pdb=" H BLYS D 343 " ideal model delta sigma weight residual 0.860 2.852 -1.992 2.00e-02 2.50e+03 9.92e+03 bond pdb=" N LYS F 343 " pdb=" H BLYS F 343 " ideal model delta sigma weight residual 0.860 2.840 -1.980 2.00e-02 2.50e+03 9.80e+03 ... (remaining 6691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 22.33: 12204 22.33 - 44.65: 0 44.65 - 66.98: 6 66.98 - 89.31: 2 89.31 - 111.64: 10 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C LYS E 340 " pdb=" N SER E 341 " pdb=" H BSER E 341 " ideal model delta sigma weight residual 123.78 12.14 111.64 3.00e+00 1.11e-01 1.38e+03 angle pdb=" C LYS B 340 " pdb=" N SER B 341 " pdb=" H BSER B 341 " ideal model delta sigma weight residual 123.78 12.97 110.81 3.00e+00 1.11e-01 1.36e+03 angle pdb=" C LYS D 340 " pdb=" N SER D 341 " pdb=" H BSER D 341 " ideal model delta sigma weight residual 123.78 14.67 109.11 3.00e+00 1.11e-01 1.32e+03 angle pdb=" C LYS F 340 " pdb=" N SER F 341 " pdb=" H BSER F 341 " ideal model delta sigma weight residual 123.78 15.25 108.53 3.00e+00 1.11e-01 1.31e+03 angle pdb=" C LYS A 340 " pdb=" N SER A 341 " pdb=" H BSER A 341 " ideal model delta sigma weight residual 123.65 15.28 108.37 3.00e+00 1.11e-01 1.30e+03 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 2728 14.98 - 29.96: 164 29.96 - 44.93: 92 44.93 - 59.91: 56 59.91 - 74.89: 56 Dihedral angle restraints: 3096 sinusoidal: 1770 harmonic: 1326 Sorted by residual: dihedral pdb=" CA GLY A 355 " pdb=" C GLY A 355 " pdb=" N SER A 356 " pdb=" CA SER A 356 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA VAL A 318 " pdb=" C VAL A 318 " pdb=" N THR A 319 " pdb=" CA THR A 319 " ideal model delta harmonic sigma weight residual -180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N GLN A 351 " pdb=" CA GLN A 351 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 283 0.072 - 0.144: 157 0.144 - 0.216: 37 0.216 - 0.287: 13 0.287 - 0.359: 8 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA HIS C 329 " pdb=" N HIS C 329 " pdb=" C HIS C 329 " pdb=" CB HIS C 329 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA HIS D 329 " pdb=" N HIS D 329 " pdb=" C HIS D 329 " pdb=" CB HIS D 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA HIS F 329 " pdb=" N HIS F 329 " pdb=" C HIS F 329 " pdb=" CB HIS F 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 495 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 338 " 0.198 2.00e-02 2.50e+03 2.62e-01 6.87e+02 pdb=" N VAL A 339 " -0.443 2.00e-02 2.50e+03 pdb=" CA VAL A 339 " 0.189 2.00e-02 2.50e+03 pdb=" H BVAL A 339 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 338 " 0.199 2.00e-02 2.50e+03 2.61e-01 6.83e+02 pdb=" N VAL F 339 " -0.442 2.00e-02 2.50e+03 pdb=" CA VAL F 339 " 0.189 2.00e-02 2.50e+03 pdb=" H BVAL F 339 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 338 " 0.199 2.00e-02 2.50e+03 2.61e-01 6.80e+02 pdb=" N VAL C 339 " -0.441 2.00e-02 2.50e+03 pdb=" CA VAL C 339 " 0.188 2.00e-02 2.50e+03 pdb=" H BVAL C 339 " 0.053 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.34: 8 1.34 - 2.16: 448 2.16 - 2.97: 16746 2.97 - 3.79: 26158 3.79 - 4.60: 42109 Warning: very small nonbonded interaction distances. Nonbonded interactions: 85469 Sorted by model distance: nonbonded pdb=" O LYS C 340 " pdb=" H BSER C 341 " model vdw 0.527 1.960 nonbonded pdb=" O LYS A 340 " pdb=" H BSER A 341 " model vdw 0.551 1.960 nonbonded pdb=" O LYS F 340 " pdb=" H BSER F 341 " model vdw 0.589 1.960 nonbonded pdb=" O LYS B 340 " pdb=" H BSER B 341 " model vdw 0.604 1.960 nonbonded pdb=" O LYS D 340 " pdb=" H BSER D 341 " model vdw 0.748 1.960 ... (remaining 85464 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 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'B' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'C' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'D' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'E' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'F' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 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: 0.080 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.630 Find NCS groups from input model: 0.100 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:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.011 0.033 3300 Z= 0.703 Angle : 2.017 9.222 4416 Z= 1.331 Chirality : 0.099 0.359 498 Planarity : 0.012 0.107 558 Dihedral : 12.244 74.889 1260 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.32), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 349 TYR 0.192 0.059 TYR B 310 PHE 0.044 0.015 PHE B 346 HIS 0.017 0.005 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.01109 ( 3300) covalent geometry : angle 2.01715 ( 4416) hydrogen bonds : bond 0.10581 ( 79) hydrogen bonds : angle 7.56356 ( 237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.215 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: symmetry clash REVERT: A 345 ASP cc_start: 0.8224 (m-30) cc_final: 0.7960 (t0) REVERT: D 345 ASP cc_start: 0.8509 (m-30) cc_final: 0.8221 (t0) REVERT: D 349 ARG cc_start: 0.8006 (mtp180) cc_final: 0.6879 (ppt90) REVERT: C 370 LYS cc_start: 0.6995 (tttt) cc_final: 0.6401 (mttt) REVERT: B 345 ASP cc_start: 0.8449 (m-30) cc_final: 0.8052 (OUTLIER) REVERT: E 349 ARG cc_start: 0.8049 (mtp180) cc_final: 0.6871 (pmt-80) REVERT: F 345 ASP cc_start: 0.8292 (m-30) cc_final: 0.7904 (t0) REVERT: F 370 LYS cc_start: 0.7061 (tttt) cc_final: 0.6629 (mttt) outliers start: 0 outliers final: 1 residues processed: 91 average time/residue: 1.5312 time to fit residues: 142.2800 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN F 368 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.152606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.138691 restraints weight = 23365.551| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.87 r_work: 0.4184 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4098 r_free = 0.4098 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3300 Z= 0.168 Angle : 0.873 12.478 4416 Z= 0.476 Chirality : 0.049 0.128 498 Planarity : 0.003 0.021 558 Dihedral : 6.251 18.161 432 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.81 % Allowed : 15.32 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.015 0.003 TYR A 310 PHE 0.010 0.002 PHE F 346 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3300) covalent geometry : angle 0.87329 ( 4416) hydrogen bonds : bond 0.03292 ( 79) hydrogen bonds : angle 5.40323 ( 237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7806 (mttm) cc_final: 0.7586 (mttm) REVERT: C 370 LYS cc_start: 0.8045 (tttt) cc_final: 0.6745 (mttt) REVERT: B 345 ASP cc_start: 0.7747 (m-30) cc_final: 0.7484 (t0) REVERT: E 342 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7870 (tt0) REVERT: E 348 ASP cc_start: 0.8381 (t0) cc_final: 0.8139 (t70) REVERT: E 353 LYS cc_start: 0.8950 (tttt) cc_final: 0.8748 (tttp) REVERT: F 370 LYS cc_start: 0.8238 (tttt) cc_final: 0.6832 (mttt) outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 1.4063 time to fit residues: 92.1047 Evaluate side-chains 57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN D 327 ASN E 327 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.157531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.143449 restraints weight = 25602.571| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 3.04 r_work: 0.4203 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4207 r_free = 0.4207 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4207 r_free = 0.4207 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3300 Z= 0.126 Angle : 0.775 12.126 4416 Z= 0.434 Chirality : 0.049 0.128 498 Planarity : 0.002 0.013 558 Dihedral : 5.667 16.103 432 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.34 % Allowed : 16.94 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.34), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.011 0.002 TYR A 310 PHE 0.005 0.001 PHE D 346 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3300) covalent geometry : angle 0.77546 ( 4416) hydrogen bonds : bond 0.02440 ( 79) hydrogen bonds : angle 4.76301 ( 237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.7642 (mtp180) cc_final: 0.5911 (mmp-170) REVERT: C 370 LYS cc_start: 0.7870 (tttt) cc_final: 0.6581 (mttt) REVERT: B 345 ASP cc_start: 0.7692 (m-30) cc_final: 0.7430 (t0) REVERT: E 349 ARG cc_start: 0.7845 (mtp180) cc_final: 0.6698 (pmt-80) REVERT: E 353 LYS cc_start: 0.8907 (tttt) cc_final: 0.8704 (tttp) REVERT: F 317 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7811 (mttm) REVERT: F 349 ARG cc_start: 0.7602 (mtp180) cc_final: 0.5642 (mmp-170) REVERT: F 370 LYS cc_start: 0.7873 (tttt) cc_final: 0.6653 (mttt) outliers start: 5 outliers final: 0 residues processed: 62 average time/residue: 1.5374 time to fit residues: 97.3094 Evaluate side-chains 58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.0570 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.0040 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 374 HIS ** 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 = 0.4462 r_free = 0.4462 target = 0.156031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.143357 restraints weight = 20592.933| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 2.61 r_work: 0.4262 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4172 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4175 r_free = 0.4175 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4175 r_free = 0.4175 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3300 Z= 0.085 Angle : 0.731 12.008 4416 Z= 0.417 Chirality : 0.050 0.131 498 Planarity : 0.002 0.022 558 Dihedral : 5.061 14.131 432 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.81 % Allowed : 18.01 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 349 TYR 0.010 0.002 TYR F 310 PHE 0.002 0.000 PHE B 346 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 3300) covalent geometry : angle 0.73072 ( 4416) hydrogen bonds : bond 0.01991 ( 79) hydrogen bonds : angle 4.40839 ( 237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7278 (ttm-80) cc_final: 0.7058 (ttm110) REVERT: D 348 ASP cc_start: 0.8163 (t0) cc_final: 0.7632 (t70) REVERT: C 349 ARG cc_start: 0.7650 (mtp180) cc_final: 0.5895 (mmp-170) REVERT: F 317 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7793 (mttm) REVERT: F 349 ARG cc_start: 0.7661 (mtp180) cc_final: 0.5654 (mmp-170) REVERT: F 370 LYS cc_start: 0.8050 (tttt) cc_final: 0.6806 (mttt) outliers start: 3 outliers final: 0 residues processed: 57 average time/residue: 1.6473 time to fit residues: 95.9491 Evaluate side-chains 50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** 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 = 0.4502 r_free = 0.4502 target = 0.158744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.145489 restraints weight = 23489.104| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.89 r_work: 0.4254 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4160 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4164 r_free = 0.4164 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4164 r_free = 0.4164 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3300 Z= 0.116 Angle : 0.712 12.084 4416 Z= 0.411 Chirality : 0.049 0.124 498 Planarity : 0.002 0.014 558 Dihedral : 5.007 14.220 432 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.81 % Allowed : 18.82 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.009 0.002 TYR A 310 PHE 0.006 0.001 PHE C 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3300) covalent geometry : angle 0.71246 ( 4416) hydrogen bonds : bond 0.01963 ( 79) hydrogen bonds : angle 4.23538 ( 237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7311 (ttm-80) cc_final: 0.7050 (ttm110) REVERT: D 348 ASP cc_start: 0.8270 (t0) cc_final: 0.7757 (t70) REVERT: C 349 ARG cc_start: 0.7709 (mtp180) cc_final: 0.5875 (mmp-170) REVERT: C 370 LYS cc_start: 0.8067 (tttt) cc_final: 0.6773 (mttt) REVERT: E 349 ARG cc_start: 0.7864 (mtp180) cc_final: 0.6691 (pmt-80) REVERT: F 317 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7795 (mttm) REVERT: F 349 ARG cc_start: 0.7659 (mtp180) cc_final: 0.5616 (mmp-170) REVERT: F 370 LYS cc_start: 0.8109 (tttt) cc_final: 0.6823 (mttt) outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 1.5364 time to fit residues: 87.9404 Evaluate side-chains 53 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.166488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.152823 restraints weight = 21792.958| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 2.89 r_work: 0.4340 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4249 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4255 r_free = 0.4255 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4255 r_free = 0.4255 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3300 Z= 0.082 Angle : 0.706 12.087 4416 Z= 0.407 Chirality : 0.049 0.136 498 Planarity : 0.002 0.015 558 Dihedral : 4.678 13.487 432 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.81 % Allowed : 19.89 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.009 0.002 TYR F 310 PHE 0.004 0.000 PHE A 378 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 3300) covalent geometry : angle 0.70563 ( 4416) hydrogen bonds : bond 0.01766 ( 79) hydrogen bonds : angle 4.10578 ( 237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7846 (mt) cc_final: 0.7395 (mt) REVERT: A 349 ARG cc_start: 0.7273 (ttm-80) cc_final: 0.7019 (ttm110) REVERT: D 348 ASP cc_start: 0.8195 (t0) cc_final: 0.7707 (t70) REVERT: C 349 ARG cc_start: 0.7681 (mtp180) cc_final: 0.5822 (mmp-170) REVERT: C 370 LYS cc_start: 0.8073 (tttt) cc_final: 0.6724 (mttt) REVERT: B 353 LYS cc_start: 0.8734 (tttt) cc_final: 0.8529 (tttp) REVERT: F 317 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7783 (mttm) REVERT: F 349 ARG cc_start: 0.7643 (mtp180) cc_final: 0.5624 (mmp-170) outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 1.5036 time to fit residues: 83.0024 Evaluate side-chains 51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** 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 = 0.4536 r_free = 0.4536 target = 0.163281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.150082 restraints weight = 18970.011| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.61 r_work: 0.4145 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4044 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3300 Z= 0.148 Angle : 0.734 12.079 4416 Z= 0.417 Chirality : 0.048 0.128 498 Planarity : 0.003 0.039 558 Dihedral : 4.971 13.976 432 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.54 % Allowed : 20.70 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 349 TYR 0.011 0.002 TYR A 310 PHE 0.007 0.001 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3300) covalent geometry : angle 0.73430 ( 4416) hydrogen bonds : bond 0.01961 ( 79) hydrogen bonds : angle 4.06021 ( 237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7383 (ttm-80) cc_final: 0.7099 (ttm110) REVERT: D 348 ASP cc_start: 0.8267 (t0) cc_final: 0.7849 (t70) REVERT: D 353 LYS cc_start: 0.8941 (tttt) cc_final: 0.8718 (tttp) REVERT: C 349 ARG cc_start: 0.7772 (mtp180) cc_final: 0.6033 (mmm160) REVERT: C 370 LYS cc_start: 0.8037 (tttt) cc_final: 0.6781 (mttt) REVERT: B 353 LYS cc_start: 0.8767 (tttt) cc_final: 0.8505 (tttp) REVERT: F 317 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7917 (mttm) REVERT: F 349 ARG cc_start: 0.7779 (mtp180) cc_final: 0.5778 (mmp-170) REVERT: F 370 LYS cc_start: 0.8035 (tttt) cc_final: 0.6809 (mttt) outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 1.2918 time to fit residues: 74.0720 Evaluate side-chains 53 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** 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 = 0.4501 r_free = 0.4501 target = 0.160915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.147997 restraints weight = 17360.828| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 2.46 r_work: 0.4272 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4186 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3300 Z= 0.177 Angle : 0.760 12.061 4416 Z= 0.428 Chirality : 0.048 0.133 498 Planarity : 0.003 0.032 558 Dihedral : 5.273 14.513 432 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.08 % Allowed : 21.77 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 349 TYR 0.011 0.002 TYR A 310 PHE 0.009 0.002 PHE A 346 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3300) covalent geometry : angle 0.76027 ( 4416) hydrogen bonds : bond 0.02114 ( 79) hydrogen bonds : angle 4.04294 ( 237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.8054 (m110) cc_final: 0.7801 (m-40) REVERT: D 348 ASP cc_start: 0.8292 (t0) cc_final: 0.7993 (t70) REVERT: D 353 LYS cc_start: 0.8961 (tttt) cc_final: 0.8731 (tttp) REVERT: C 370 LYS cc_start: 0.8109 (tttt) cc_final: 0.6771 (mttt) REVERT: B 348 ASP cc_start: 0.7945 (t0) cc_final: 0.7629 (t70) REVERT: B 353 LYS cc_start: 0.8729 (tttt) cc_final: 0.8454 (tttp) REVERT: F 317 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7822 (mttm) REVERT: F 348 ASP cc_start: 0.8150 (t0) cc_final: 0.7918 (t0) REVERT: F 349 ARG cc_start: 0.7687 (mtp180) cc_final: 0.5788 (mmp-170) REVERT: F 370 LYS cc_start: 0.8081 (tttt) cc_final: 0.6793 (mttt) outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 1.3311 time to fit residues: 75.0627 Evaluate side-chains 56 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.156293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.143115 restraints weight = 21172.967| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.68 r_work: 0.4238 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4148 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4103 r_free = 0.4103 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4103 r_free = 0.4103 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3300 Z= 0.190 Angle : 0.740 12.020 4416 Z= 0.426 Chirality : 0.048 0.133 498 Planarity : 0.003 0.031 558 Dihedral : 5.408 15.015 432 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.54 % Allowed : 21.77 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 349 TYR 0.011 0.002 TYR A 310 PHE 0.009 0.002 PHE A 346 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3300) covalent geometry : angle 0.74024 ( 4416) hydrogen bonds : bond 0.02233 ( 79) hydrogen bonds : angle 4.08756 ( 237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.8151 (m110) cc_final: 0.7914 (m-40) REVERT: D 348 ASP cc_start: 0.8315 (t0) cc_final: 0.8050 (t70) REVERT: D 353 LYS cc_start: 0.8992 (tttt) cc_final: 0.8770 (tttp) REVERT: C 370 LYS cc_start: 0.8129 (tttt) cc_final: 0.6796 (mttt) REVERT: C 372 GLU cc_start: 0.7847 (tt0) cc_final: 0.7640 (tt0) REVERT: B 353 LYS cc_start: 0.8758 (tttt) cc_final: 0.8495 (tttp) REVERT: E 353 LYS cc_start: 0.8966 (tttt) cc_final: 0.8749 (tttp) REVERT: F 317 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7931 (mttm) REVERT: F 348 ASP cc_start: 0.8143 (t0) cc_final: 0.7925 (t0) REVERT: F 349 ARG cc_start: 0.7750 (mtp180) cc_final: 0.5877 (mmp-170) REVERT: F 370 LYS cc_start: 0.8175 (tttt) cc_final: 0.6888 (mttt) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 1.4129 time to fit residues: 79.4651 Evaluate side-chains 55 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.160999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.147364 restraints weight = 22178.506| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.78 r_work: 0.4258 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3300 Z= 0.137 Angle : 0.716 12.016 4416 Z= 0.415 Chirality : 0.048 0.129 498 Planarity : 0.003 0.034 558 Dihedral : 5.210 14.751 432 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.54 % Allowed : 21.77 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 349 TYR 0.010 0.002 TYR A 310 PHE 0.006 0.001 PHE A 346 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3300) covalent geometry : angle 0.71642 ( 4416) hydrogen bonds : bond 0.02042 ( 79) hydrogen bonds : angle 4.03273 ( 237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.8114 (m110) cc_final: 0.7854 (m-40) REVERT: D 348 ASP cc_start: 0.8290 (t0) cc_final: 0.7938 (t70) REVERT: C 370 LYS cc_start: 0.8131 (tttt) cc_final: 0.6769 (pttt) REVERT: B 348 ASP cc_start: 0.8010 (t0) cc_final: 0.7730 (t70) REVERT: B 353 LYS cc_start: 0.8745 (tttt) cc_final: 0.8508 (tttp) REVERT: F 317 LYS cc_start: 0.8397 (mtpp) cc_final: 0.7946 (mttm) REVERT: F 349 ARG cc_start: 0.7750 (mtp180) cc_final: 0.5871 (mmp-170) REVERT: F 370 LYS cc_start: 0.8205 (tttt) cc_final: 0.6911 (mttt) REVERT: F 372 GLU cc_start: 0.7677 (tt0) cc_final: 0.7462 (tt0) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 1.3566 time to fit residues: 72.3240 Evaluate side-chains 52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.164386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.151046 restraints weight = 20340.550| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 2.72 r_work: 0.4320 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4232 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4063 r_free = 0.4063 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3300 Z= 0.087 Angle : 0.699 12.080 4416 Z= 0.407 Chirality : 0.049 0.126 498 Planarity : 0.002 0.036 558 Dihedral : 4.870 14.425 432 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.27 % Allowed : 21.77 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 349 TYR 0.008 0.002 TYR F 310 PHE 0.004 0.001 PHE A 346 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 3300) covalent geometry : angle 0.69858 ( 4416) hydrogen bonds : bond 0.01800 ( 79) hydrogen bonds : angle 3.96213 ( 237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3103.57 seconds wall clock time: 53 minutes 20.33 seconds (3200.33 seconds total)