Starting phenix.real_space_refine on Wed Jun 4 14:00:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcr_18333/06_2025/8qcr_18333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcr_18333/06_2025/8qcr_18333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qcr_18333/06_2025/8qcr_18333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcr_18333/06_2025/8qcr_18333.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcr_18333/06_2025/8qcr_18333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcr_18333/06_2025/8qcr_18333.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 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 3 5.16 5 C 966 2.51 5 N 285 2.21 5 O 291 1.98 5 H 1608 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3153 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Time building chain proxies: 3.10, per 1000 atoms: 0.98 Number of scatterers: 3153 At special positions: 0 Unit cell: (99.704, 70.864, 37.08, 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 3 16.00 O 291 8.00 N 285 7.00 C 966 6.00 H 1608 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: 0.80 Conformation dependent library (CDL) restraints added in 229.6 milliseconds 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 354 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 64.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 310 removed outlier: 6.614A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.715A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325 removed outlier: 6.754A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.313A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.513A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.529A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 362 removed outlier: 8.920A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP E 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 362 removed outlier: 8.920A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP E 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 368 through 374 removed outlier: 6.370A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 333 through 334 removed outlier: 6.871A pdb=" N GLY C 333 " --> pdb=" O GLY E 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 33 hydrogen bonds defined for protein. 99 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: 1.03 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 1605 1.12 - 1.29: 261 1.29 - 1.47: 487 1.47 - 1.64: 821 1.64 - 1.81: 3 Bond restraints: 3177 Sorted by residual: bond pdb=" N ILE C 308 " pdb=" H ILE C 308 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER A 324 " pdb=" H SER A 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY C 326 " pdb=" H GLY C 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL C 309 " pdb=" H VAL C 309 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN E 359 " pdb="HD21 ASN E 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 3172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 4867 2.43 - 4.87: 722 4.87 - 7.30: 203 7.30 - 9.74: 7 9.74 - 12.17: 3 Bond angle restraints: 5802 Sorted by residual: angle pdb=" CA ASP E 345 " pdb=" CB ASP E 345 " pdb=" CG ASP E 345 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.00e+00 1.00e+00 2.92e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 117.08 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CA GLY E 355 " pdb=" C GLY E 355 " pdb=" N SER E 356 " ideal model delta sigma weight residual 114.84 119.43 -4.59 1.06e+00 8.90e-01 1.87e+01 angle pdb=" CB HIS E 362 " pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 131.20 125.68 5.52 1.30e+00 5.92e-01 1.80e+01 ... (remaining 5797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.36: 1277 13.36 - 26.71: 88 26.71 - 40.07: 33 40.07 - 53.42: 22 53.42 - 66.78: 41 Dihedral angle restraints: 1461 sinusoidal: 840 harmonic: 621 Sorted by residual: dihedral pdb=" CA LYS E 321 " pdb=" C LYS E 321 " pdb=" N CYS E 322 " pdb=" CA CYS E 322 " ideal model delta harmonic sigma weight residual 180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA VAL C 350 " pdb=" C VAL C 350 " pdb=" N GLN C 351 " pdb=" CA GLN C 351 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL E 350 " pdb=" C VAL E 350 " pdb=" N GLN E 351 " pdb=" CA GLN E 351 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 1458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 115 0.052 - 0.104: 77 0.104 - 0.157: 27 0.157 - 0.209: 12 0.209 - 0.261: 3 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL E 337 " pdb=" N VAL E 337 " pdb=" C VAL E 337 " pdb=" CB VAL E 337 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 231 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 368 " -0.090 2.00e-02 2.50e+03 7.98e-02 9.55e+01 pdb=" CG ASN E 368 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 368 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN E 368 " 0.058 2.00e-02 2.50e+03 pdb="HD21 ASN E 368 " 0.074 2.00e-02 2.50e+03 pdb="HD22 ASN E 368 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 362 " 0.068 2.00e-02 2.50e+03 3.97e-02 3.55e+01 pdb=" CG HIS E 362 " -0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS E 362 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS E 362 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 HIS E 362 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS E 362 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 HIS E 362 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS E 362 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 HIS E 362 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 362 " 0.064 2.00e-02 2.50e+03 3.67e-02 3.03e+01 pdb=" CG HIS A 362 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS A 362 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS A 362 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS A 362 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 362 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 HIS A 362 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS A 362 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 HIS A 362 " 0.038 2.00e-02 2.50e+03 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 196 2.16 - 2.77: 5228 2.77 - 3.38: 8238 3.38 - 3.99: 10907 3.99 - 4.60: 15415 Nonbonded interactions: 39984 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.546 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.575 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.576 2.450 nonbonded pdb=" HG SER A 320 " pdb=" O GLY A 366 " model vdw 1.644 2.450 nonbonded pdb=" HG SER C 320 " pdb=" O GLY C 366 " model vdw 1.669 2.450 ... (remaining 39979 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' selection = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.680 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: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.580 Find NCS groups from input model: 0.070 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 0.035 1569 Z= 0.680 Angle : 1.777 5.847 2097 Z= 1.194 Chirality : 0.079 0.261 234 Planarity : 0.009 0.038 267 Dihedral : 9.596 42.499 606 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.50), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 330 PHE 0.042 0.021 PHE A 346 TYR 0.068 0.019 TYR C 310 ARG 0.002 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.06114 ( 33) hydrogen bonds : angle 7.15680 ( 99) covalent geometry : bond 0.01077 ( 1569) covalent geometry : angle 1.77711 ( 2097) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8115 (mttt) cc_final: 0.7912 (mtpt) REVERT: A 347 LYS cc_start: 0.8466 (mttt) cc_final: 0.7559 (pmtt) REVERT: A 369 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7992 (ttpt) REVERT: A 375 LYS cc_start: 0.7146 (tptm) cc_final: 0.6860 (tptt) REVERT: C 340 LYS cc_start: 0.7413 (mttt) cc_final: 0.7164 (ttmm) REVERT: C 345 ASP cc_start: 0.7491 (m-30) cc_final: 0.7001 (t70) REVERT: C 347 LYS cc_start: 0.8400 (mttt) cc_final: 0.8141 (mtpt) REVERT: C 349 ARG cc_start: 0.7573 (mtt180) cc_final: 0.6532 (mtt-85) REVERT: E 320 SER cc_start: 0.8567 (m) cc_final: 0.8255 (p) REVERT: E 321 LYS cc_start: 0.7395 (tttt) cc_final: 0.7089 (ttmp) REVERT: E 340 LYS cc_start: 0.7549 (mttt) cc_final: 0.7296 (ttmm) REVERT: E 369 LYS cc_start: 0.7591 (ttmt) cc_final: 0.7330 (ttpt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 2.8936 time to fit residues: 210.9136 Evaluate side-chains 49 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.119948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.111224 restraints weight = 6410.934| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.84 r_work: 0.3792 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1569 Z= 0.129 Angle : 0.608 4.034 2097 Z= 0.309 Chirality : 0.052 0.139 234 Planarity : 0.004 0.030 267 Dihedral : 6.192 17.053 207 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.26 % Allowed : 12.43 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.51), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.007 0.002 PHE E 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.02558 ( 33) hydrogen bonds : angle 4.83393 ( 99) covalent geometry : bond 0.00308 ( 1569) covalent geometry : angle 0.60824 ( 2097) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8692 (mttt) cc_final: 0.7856 (pmtt) REVERT: C 345 ASP cc_start: 0.7957 (m-30) cc_final: 0.7569 (t0) REVERT: C 349 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7026 (mtt-85) REVERT: C 375 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.5185 (tmmt) REVERT: E 340 LYS cc_start: 0.8220 (mttt) cc_final: 0.7970 (ttmm) REVERT: E 347 LYS cc_start: 0.8577 (mttt) cc_final: 0.8364 (mptp) outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 3.4263 time to fit residues: 187.0613 Evaluate side-chains 44 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 375 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.122250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.114267 restraints weight = 6233.139| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.69 r_work: 0.3815 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1569 Z= 0.103 Angle : 0.540 5.046 2097 Z= 0.266 Chirality : 0.053 0.140 234 Planarity : 0.003 0.020 267 Dihedral : 5.316 14.141 207 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.82 % Allowed : 16.95 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.52), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.005 0.001 PHE C 346 TYR 0.010 0.002 TYR E 310 ARG 0.003 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01672 ( 33) hydrogen bonds : angle 4.29468 ( 99) covalent geometry : bond 0.00248 ( 1569) covalent geometry : angle 0.54013 ( 2097) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8689 (mttt) cc_final: 0.7786 (pmtt) REVERT: C 345 ASP cc_start: 0.7902 (m-30) cc_final: 0.7641 (t0) REVERT: C 349 ARG cc_start: 0.8344 (mtt180) cc_final: 0.7209 (mtt-85) REVERT: C 375 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.5327 (tmmt) REVERT: E 349 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7389 (mtt180) outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 3.5191 time to fit residues: 163.5303 Evaluate side-chains 42 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN E 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.122014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.113538 restraints weight = 6440.612| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.80 r_work: 0.3821 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1569 Z= 0.090 Angle : 0.507 4.635 2097 Z= 0.247 Chirality : 0.052 0.127 234 Planarity : 0.002 0.017 267 Dihedral : 4.924 13.750 207 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.26 % Allowed : 18.64 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.53), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.005 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01354 ( 33) hydrogen bonds : angle 3.92451 ( 99) covalent geometry : bond 0.00222 ( 1569) covalent geometry : angle 0.50731 ( 2097) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 345 ASP cc_start: 0.7893 (m-30) cc_final: 0.7625 (t0) REVERT: C 349 ARG cc_start: 0.8340 (mtt180) cc_final: 0.7147 (mtt-85) REVERT: C 375 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.5398 (tmmt) REVERT: E 349 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7388 (mtt180) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 3.4132 time to fit residues: 141.5558 Evaluate side-chains 38 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.120969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.112444 restraints weight = 6398.372| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.78 r_work: 0.3798 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1569 Z= 0.116 Angle : 0.520 4.879 2097 Z= 0.251 Chirality : 0.051 0.125 234 Planarity : 0.002 0.017 267 Dihedral : 4.812 13.524 207 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.82 % Allowed : 19.21 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.54), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.005 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01356 ( 33) hydrogen bonds : angle 3.76280 ( 99) covalent geometry : bond 0.00265 ( 1569) covalent geometry : angle 0.52038 ( 2097) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 345 ASP cc_start: 0.7885 (m-30) cc_final: 0.7621 (t0) REVERT: C 349 ARG cc_start: 0.8350 (mtt180) cc_final: 0.7150 (mtt-85) REVERT: C 375 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.5469 (tmmt) REVERT: E 349 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7430 (mtt180) outliers start: 5 outliers final: 1 residues processed: 38 average time/residue: 3.4038 time to fit residues: 130.9062 Evaluate side-chains 37 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.120807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.112745 restraints weight = 6363.130| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.71 r_work: 0.3798 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1569 Z= 0.102 Angle : 0.507 4.782 2097 Z= 0.244 Chirality : 0.051 0.125 234 Planarity : 0.002 0.016 267 Dihedral : 4.666 12.731 207 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.26 % Allowed : 19.77 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.55), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.45 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01201 ( 33) hydrogen bonds : angle 3.59856 ( 99) covalent geometry : bond 0.00240 ( 1569) covalent geometry : angle 0.50659 ( 2097) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 345 ASP cc_start: 0.7885 (m-30) cc_final: 0.7664 (t70) REVERT: C 349 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7213 (mtt-85) REVERT: C 375 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.5523 (tmmt) REVERT: E 349 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7558 (mtt180) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 3.2652 time to fit residues: 122.2192 Evaluate side-chains 37 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.119631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.111534 restraints weight = 6159.850| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.71 r_work: 0.3787 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1569 Z= 0.122 Angle : 0.531 4.734 2097 Z= 0.255 Chirality : 0.051 0.124 234 Planarity : 0.003 0.019 267 Dihedral : 4.629 12.615 207 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.55), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.43 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01398 ( 33) hydrogen bonds : angle 3.61847 ( 99) covalent geometry : bond 0.00281 ( 1569) covalent geometry : angle 0.53122 ( 2097) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 345 ASP cc_start: 0.7865 (m-30) cc_final: 0.7664 (t70) REVERT: C 349 ARG cc_start: 0.8347 (mtt180) cc_final: 0.7233 (mtt-85) REVERT: C 375 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.5506 (tmmt) REVERT: E 349 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7646 (mtt180) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 3.2312 time to fit residues: 117.7589 Evaluate side-chains 37 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.117282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.109191 restraints weight = 6200.641| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.68 r_work: 0.3749 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1569 Z= 0.169 Angle : 0.544 5.317 2097 Z= 0.264 Chirality : 0.051 0.122 234 Planarity : 0.003 0.019 267 Dihedral : 4.783 13.278 207 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.69 % Allowed : 19.21 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.40 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 374 PHE 0.006 0.002 PHE E 346 TYR 0.012 0.003 TYR A 310 ARG 0.002 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01355 ( 33) hydrogen bonds : angle 3.66902 ( 99) covalent geometry : bond 0.00378 ( 1569) covalent geometry : angle 0.54413 ( 2097) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8716 (mttt) cc_final: 0.7717 (pmtt) REVERT: C 349 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7433 (mtt-85) REVERT: C 375 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.5675 (tmmt) REVERT: E 349 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7699 (mtp180) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 3.4269 time to fit residues: 124.8794 Evaluate side-chains 36 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.119910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.111548 restraints weight = 6407.890| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.80 r_work: 0.3781 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1569 Z= 0.095 Angle : 0.510 4.605 2097 Z= 0.245 Chirality : 0.052 0.125 234 Planarity : 0.003 0.023 267 Dihedral : 4.544 12.155 207 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.42 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 362 PHE 0.002 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.000 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01263 ( 33) hydrogen bonds : angle 3.56984 ( 99) covalent geometry : bond 0.00228 ( 1569) covalent geometry : angle 0.51019 ( 2097) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7409 (mtt-85) REVERT: E 321 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7946 (mtpt) REVERT: E 349 ARG cc_start: 0.8006 (mtm180) cc_final: 0.7664 (mtp180) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 3.3192 time to fit residues: 114.2747 Evaluate side-chains 30 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.118225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.110598 restraints weight = 6423.576| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.68 r_work: 0.3774 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1569 Z= 0.098 Angle : 0.529 6.352 2097 Z= 0.250 Chirality : 0.051 0.122 234 Planarity : 0.003 0.024 267 Dihedral : 4.491 12.195 207 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.69 % Allowed : 19.21 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.39 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.003 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.000 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01182 ( 33) hydrogen bonds : angle 3.53210 ( 99) covalent geometry : bond 0.00240 ( 1569) covalent geometry : angle 0.52885 ( 2097) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 396 Ramachandran restraints generated. 198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8302 (mtt180) cc_final: 0.7383 (mtt-85) REVERT: C 375 LYS cc_start: 0.8017 (mptt) cc_final: 0.7721 (mptt) REVERT: E 321 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7995 (mtpt) REVERT: E 349 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7582 (mtt180) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 3.1715 time to fit residues: 102.8233 Evaluate side-chains 33 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.117231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.109484 restraints weight = 6585.507| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.72 r_work: 0.3752 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1569 Z= 0.116 Angle : 0.514 4.862 2097 Z= 0.247 Chirality : 0.051 0.122 234 Planarity : 0.003 0.022 267 Dihedral : 4.540 12.107 207 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.13 % Allowed : 19.21 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.56), residues: 198 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE C 346 TYR 0.009 0.002 TYR E 310 ARG 0.000 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01227 ( 33) hydrogen bonds : angle 3.55159 ( 99) covalent geometry : bond 0.00270 ( 1569) covalent geometry : angle 0.51433 ( 2097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4328.06 seconds wall clock time: 73 minutes 54.10 seconds (4434.10 seconds total)