Starting phenix.real_space_refine on Wed Sep 17 08:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxq_45008/09_2025/9bxq_45008.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxq_45008/09_2025/9bxq_45008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bxq_45008/09_2025/9bxq_45008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxq_45008/09_2025/9bxq_45008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bxq_45008/09_2025/9bxq_45008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxq_45008/09_2025/9bxq_45008.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 2202 2.51 5 N 648 2.21 5 O 672 1.98 5 H 3654 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7182 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: D, E, F, G, H Time building chain proxies: 1.10, per 1000 atoms: 0.15 Number of scatterers: 7182 At special positions: 0 Unit cell: (139.278, 107.586, 37.53, 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 672 8.00 N 648 7.00 C 2202 6.00 H 3654 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: 0.53 Conformation dependent library (CDL) restraints added in 322.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.766A pdb=" N SER C 305 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ILE E 308 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER E 305 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ILE G 308 " --> pdb=" O SER E 305 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN E 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N TYR G 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL E 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.745A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.545A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS E 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.474A pdb=" N GLN C 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N VAL E 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU C 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN E 336 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL G 339 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU E 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 343 through 344 removed outlier: 6.541A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS E 343 " --> pdb=" O LEU G 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 359 through 360 Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 373 Processing sheet with id=AA8, first strand: chain 'D' and resid 305 through 310 removed outlier: 6.604A pdb=" N SER D 305 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ILE F 308 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN D 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR F 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER F 305 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ILE H 308 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN F 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N TYR H 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL F 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.596A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL F 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.424A pdb=" N LYS D 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS F 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.441A pdb=" N GLN D 336 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL F 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU D 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN F 336 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL H 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU F 338 " --> pdb=" O VAL H 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 343 through 344 removed outlier: 6.513A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS F 343 " --> pdb=" O LEU H 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 359 through 360 Processing sheet with id=AB5, first strand: chain 'D' and resid 369 through 373 20 hydrogen bonds defined for protein. 60 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: 1.31 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 3648 1.13 - 1.30: 600 1.30 - 1.47: 1153 1.47 - 1.64: 1829 1.64 - 1.81: 6 Bond restraints: 7236 Sorted by residual: bond pdb=" N ILE F 328 " pdb=" H ILE F 328 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N ILE F 371 " pdb=" H ILE F 371 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N HIS F 362 " pdb=" H HIS F 362 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N ASN F 368 " pdb=" H ASN F 368 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N ILE D 328 " pdb=" H ILE D 328 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 7231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 11079 2.47 - 4.94: 1617 4.94 - 7.41: 432 7.41 - 9.89: 54 9.89 - 12.36: 6 Bond angle restraints: 13188 Sorted by residual: angle pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" C LYS E 347 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.09e+00 8.42e-01 1.85e+01 angle pdb=" N LYS C 347 " pdb=" CA LYS C 347 " pdb=" C LYS C 347 " ideal model delta sigma weight residual 111.36 116.03 -4.67 1.09e+00 8.42e-01 1.83e+01 angle pdb=" N LYS G 347 " pdb=" CA LYS G 347 " pdb=" C LYS G 347 " ideal model delta sigma weight residual 111.36 116.00 -4.64 1.09e+00 8.42e-01 1.82e+01 angle pdb=" N LYS F 347 " pdb=" CA LYS F 347 " pdb=" C LYS F 347 " ideal model delta sigma weight residual 111.36 115.99 -4.63 1.09e+00 8.42e-01 1.80e+01 angle pdb=" N LYS D 347 " pdb=" CA LYS D 347 " pdb=" C LYS D 347 " ideal model delta sigma weight residual 111.36 115.99 -4.63 1.09e+00 8.42e-01 1.80e+01 ... (remaining 13183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 2964 15.69 - 31.37: 186 31.37 - 47.06: 60 47.06 - 62.75: 90 62.75 - 78.43: 24 Dihedral angle restraints: 3324 sinusoidal: 1902 harmonic: 1422 Sorted by residual: dihedral pdb=" CA LEU F 325 " pdb=" C LEU F 325 " pdb=" N GLY F 326 " pdb=" CA GLY F 326 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA LEU D 325 " pdb=" C LEU D 325 " pdb=" N GLY D 326 " pdb=" CA GLY D 326 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU E 325 " pdb=" C LEU E 325 " pdb=" N GLY E 326 " pdb=" CA GLY E 326 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 254 0.053 - 0.105: 143 0.105 - 0.158: 101 0.158 - 0.210: 30 0.210 - 0.263: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ARG D 349 " pdb=" N ARG D 349 " pdb=" C ARG D 349 " pdb=" CB ARG D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ARG C 349 " pdb=" N ARG C 349 " pdb=" C ARG C 349 " pdb=" CB ARG C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 531 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 346 " -0.025 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" N LYS D 347 " 0.078 2.00e-02 2.50e+03 pdb=" CA LYS D 347 " -0.023 2.00e-02 2.50e+03 pdb=" H LYS D 347 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 346 " -0.025 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" N LYS F 347 " 0.078 2.00e-02 2.50e+03 pdb=" CA LYS F 347 " -0.023 2.00e-02 2.50e+03 pdb=" H LYS F 347 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 346 " 0.025 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" N LYS E 347 " -0.078 2.00e-02 2.50e+03 pdb=" CA LYS E 347 " 0.023 2.00e-02 2.50e+03 pdb=" H LYS E 347 " 0.031 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 0.62 - 1.42: 40 1.42 - 2.21: 889 2.21 - 3.01: 19337 3.01 - 3.80: 28770 3.80 - 4.60: 44149 Warning: very small nonbonded interaction distances. Nonbonded interactions: 93185 Sorted by model distance: nonbonded pdb=" OXT GLU D 380 " pdb=" HB2 GLU F 380 " model vdw 0.624 2.620 nonbonded pdb=" OXT GLU E 380 " pdb=" HB2 GLU G 380 " model vdw 0.671 2.620 nonbonded pdb=" OXT GLU F 380 " pdb=" HB2 GLU H 380 " model vdw 0.695 2.620 nonbonded pdb=" OXT GLU C 380 " pdb=" HB2 GLU E 380 " model vdw 0.742 2.620 nonbonded pdb=" OE2 GLU C 338 " pdb=" HZ1 LYS D 331 " model vdw 0.770 2.450 ... (remaining 93180 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.480 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.840 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 0.032 3582 Z= 0.691 Angle : 1.842 5.673 4794 Z= 1.186 Chirality : 0.088 0.263 534 Planarity : 0.008 0.034 618 Dihedral : 10.866 78.433 1380 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.37 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.040 0.020 TYR G 310 PHE 0.019 0.010 PHE E 346 HIS 0.004 0.002 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.01092 ( 3582) covalent geometry : angle 1.84249 ( 4794) hydrogen bonds : bond 0.16544 ( 20) hydrogen bonds : angle 7.52626 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.212 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 307 GLN cc_start: 0.7120 (mp10) cc_final: 0.6838 (mm110) REVERT: F 347 LYS cc_start: 0.7418 (ttmt) cc_final: 0.6749 (tmtt) REVERT: F 349 ARG cc_start: 0.7301 (ttm170) cc_final: 0.7061 (ttm110) REVERT: F 372 GLU cc_start: 0.7770 (tt0) cc_final: 0.7494 (tt0) REVERT: G 307 GLN cc_start: 0.7450 (mp10) cc_final: 0.7054 (mp-120) REVERT: G 342 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7045 (mm-30) REVERT: G 347 LYS cc_start: 0.7590 (ttmt) cc_final: 0.6806 (tmtt) REVERT: G 372 GLU cc_start: 0.7654 (tt0) cc_final: 0.7185 (tt0) REVERT: G 378 PHE cc_start: 0.7903 (t80) cc_final: 0.7693 (t80) REVERT: G 379 ARG cc_start: 0.6336 (mtt180) cc_final: 0.5210 (ptt-90) REVERT: H 307 GLN cc_start: 0.7520 (mp10) cc_final: 0.7210 (mp-120) REVERT: H 311 LYS cc_start: 0.7750 (mttt) cc_final: 0.7440 (ptmm) REVERT: H 342 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6505 (mp0) REVERT: H 347 LYS cc_start: 0.7348 (ttmt) cc_final: 0.6661 (tmtt) REVERT: H 349 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7351 (ttm110) REVERT: H 372 GLU cc_start: 0.7826 (tt0) cc_final: 0.7386 (tt0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2321 time to fit residues: 21.8858 Evaluate side-chains 52 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 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 362 HIS D 362 HIS F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.191107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.163136 restraints weight = 11911.247| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.42 r_work: 0.4212 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3582 Z= 0.153 Angle : 0.716 4.706 4794 Z= 0.376 Chirality : 0.053 0.137 534 Planarity : 0.003 0.016 618 Dihedral : 7.982 34.485 480 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.25 % Allowed : 2.99 % Favored : 96.77 % 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: -3.00 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.20), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 349 TYR 0.003 0.001 TYR H 310 PHE 0.019 0.002 PHE D 378 HIS 0.010 0.002 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3582) covalent geometry : angle 0.71639 ( 4794) hydrogen bonds : bond 0.04066 ( 20) hydrogen bonds : angle 5.46396 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6555 (mpt-90) cc_final: 0.5984 (mtt-85) REVERT: E 342 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6872 (mm-30) REVERT: F 342 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7114 (mm-30) REVERT: F 349 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6991 (ttp-110) REVERT: G 306 VAL cc_start: 0.8526 (t) cc_final: 0.8283 (p) REVERT: G 307 GLN cc_start: 0.7665 (mp10) cc_final: 0.7418 (mp-120) REVERT: G 342 GLU cc_start: 0.7895 (mt-10) cc_final: 0.6704 (mp0) REVERT: G 347 LYS cc_start: 0.7829 (ttmt) cc_final: 0.6949 (tmtt) REVERT: H 342 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7293 (mm-30) REVERT: H 347 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7133 (tmtt) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.2195 time to fit residues: 15.1520 Evaluate side-chains 49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 40.0000 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN F 374 HIS ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.189295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.162034 restraints weight = 12243.962| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.43 r_work: 0.4249 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4088 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3582 Z= 0.103 Angle : 0.569 3.909 4794 Z= 0.293 Chirality : 0.051 0.155 534 Planarity : 0.002 0.016 618 Dihedral : 7.124 41.657 480 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.25 % Allowed : 4.98 % Favored : 94.78 % 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: -2.89 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.006 0.001 TYR E 310 PHE 0.014 0.002 PHE D 378 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3582) covalent geometry : angle 0.56909 ( 4794) hydrogen bonds : bond 0.02988 ( 20) hydrogen bonds : angle 4.74812 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.195 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: C 379 ARG cc_start: 0.6732 (mpt-90) cc_final: 0.6181 (mtt-85) REVERT: D 338 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7771 (mt-10) REVERT: E 342 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6856 (mm-30) REVERT: F 349 ARG cc_start: 0.7437 (ttm170) cc_final: 0.7113 (ttp-110) REVERT: G 342 GLU cc_start: 0.7908 (mt-10) cc_final: 0.6850 (mp0) REVERT: H 342 GLU cc_start: 0.7762 (mt-10) cc_final: 0.6983 (mp0) outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.2948 time to fit residues: 18.5567 Evaluate side-chains 46 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 306 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN G 307 GLN ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 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 = 0.4571 r_free = 0.4571 target = 0.183973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.155609 restraints weight = 12116.398| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.39 r_work: 0.4168 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4002 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3582 Z= 0.131 Angle : 0.554 3.574 4794 Z= 0.288 Chirality : 0.050 0.140 534 Planarity : 0.002 0.022 618 Dihedral : 6.782 43.659 480 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % 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: -2.93 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.006 0.001 TYR H 310 PHE 0.009 0.001 PHE D 378 HIS 0.007 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3582) covalent geometry : angle 0.55432 ( 4794) hydrogen bonds : bond 0.02964 ( 20) hydrogen bonds : angle 4.62906 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6748 (mpt-90) cc_final: 0.6093 (mtt-85) REVERT: D 338 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7795 (mt-10) REVERT: E 342 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6814 (mm-30) REVERT: F 307 GLN cc_start: 0.7470 (mp10) cc_final: 0.7014 (mm110) REVERT: F 349 ARG cc_start: 0.7517 (ttm170) cc_final: 0.7130 (ttp-110) REVERT: G 307 GLN cc_start: 0.7645 (mp10) cc_final: 0.7307 (mp-120) REVERT: G 342 GLU cc_start: 0.8020 (mt-10) cc_final: 0.6955 (mp0) REVERT: H 342 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7021 (mp0) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2733 time to fit residues: 16.7277 Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS ** G 330 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 = 0.4534 r_free = 0.4534 target = 0.180573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.151134 restraints weight = 12257.192| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.43 r_work: 0.4173 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3582 Z= 0.159 Angle : 0.555 4.235 4794 Z= 0.291 Chirality : 0.050 0.144 534 Planarity : 0.002 0.022 618 Dihedral : 6.646 43.958 480 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.25 % Allowed : 6.47 % Favored : 93.28 % 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: -2.90 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.008 0.001 TYR H 310 PHE 0.008 0.001 PHE H 378 HIS 0.007 0.002 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3582) covalent geometry : angle 0.55487 ( 4794) hydrogen bonds : bond 0.03171 ( 20) hydrogen bonds : angle 4.69660 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6772 (mpt-90) cc_final: 0.6061 (mtt-85) REVERT: D 338 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7913 (mt-10) REVERT: E 342 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6772 (mm-30) REVERT: E 349 ARG cc_start: 0.7183 (mtm180) cc_final: 0.6965 (mmm-85) REVERT: E 379 ARG cc_start: 0.6776 (mtt180) cc_final: 0.6264 (mtt90) REVERT: F 307 GLN cc_start: 0.7603 (mp10) cc_final: 0.7123 (mm110) REVERT: F 349 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7152 (ttp-110) REVERT: F 379 ARG cc_start: 0.6912 (mtt180) cc_final: 0.6390 (mtm180) REVERT: G 307 GLN cc_start: 0.7712 (mp10) cc_final: 0.7394 (mp-120) REVERT: G 342 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7026 (mp0) REVERT: H 307 GLN cc_start: 0.7760 (mp10) cc_final: 0.7378 (mp-120) REVERT: H 342 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7002 (mp0) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2816 time to fit residues: 16.2531 Evaluate side-chains 46 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.183777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.155443 restraints weight = 12444.536| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.43 r_work: 0.4174 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3582 Z= 0.086 Angle : 0.496 3.523 4794 Z= 0.258 Chirality : 0.050 0.137 534 Planarity : 0.002 0.021 618 Dihedral : 6.243 43.191 480 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.25 % Allowed : 6.72 % Favored : 93.03 % 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: -2.84 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.008 0.001 TYR H 310 PHE 0.007 0.001 PHE H 378 HIS 0.004 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 3582) covalent geometry : angle 0.49603 ( 4794) hydrogen bonds : bond 0.02574 ( 20) hydrogen bonds : angle 4.12834 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6808 (mpt-90) cc_final: 0.5514 (mtp85) REVERT: D 338 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7881 (mt-10) REVERT: E 307 GLN cc_start: 0.7429 (mp10) cc_final: 0.6801 (mm110) REVERT: E 342 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6748 (mm-30) REVERT: E 379 ARG cc_start: 0.6752 (mtt180) cc_final: 0.6245 (mtt90) REVERT: F 307 GLN cc_start: 0.7577 (mp10) cc_final: 0.7114 (mm110) REVERT: F 349 ARG cc_start: 0.7525 (ttm170) cc_final: 0.7100 (ttp-110) REVERT: F 379 ARG cc_start: 0.6967 (mtt180) cc_final: 0.6453 (mtm180) REVERT: G 307 GLN cc_start: 0.7689 (mp10) cc_final: 0.7389 (mp-120) REVERT: G 342 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7033 (mp0) REVERT: H 342 GLU cc_start: 0.7733 (mt-10) cc_final: 0.6996 (mp0) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.2682 time to fit residues: 14.4130 Evaluate side-chains 46 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.0170 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 overall best weight: 1.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 330 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 = 0.4596 r_free = 0.4596 target = 0.187379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.159043 restraints weight = 12371.718| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.43 r_work: 0.4157 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3582 Z= 0.119 Angle : 0.497 3.570 4794 Z= 0.259 Chirality : 0.050 0.143 534 Planarity : 0.002 0.021 618 Dihedral : 6.103 39.889 480 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.25 % Allowed : 7.21 % Favored : 92.54 % 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: -2.83 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.007 0.001 TYR H 310 PHE 0.006 0.001 PHE H 378 HIS 0.004 0.001 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3582) covalent geometry : angle 0.49710 ( 4794) hydrogen bonds : bond 0.02799 ( 20) hydrogen bonds : angle 4.25170 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6857 (mpt-90) cc_final: 0.5537 (mtp85) REVERT: D 338 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7945 (mt-10) REVERT: E 307 GLN cc_start: 0.7467 (mp10) cc_final: 0.6822 (mm110) REVERT: E 342 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6816 (mm-30) REVERT: E 379 ARG cc_start: 0.6847 (mtt180) cc_final: 0.6320 (mtt90) REVERT: F 307 GLN cc_start: 0.7636 (mp10) cc_final: 0.7148 (mm110) REVERT: F 349 ARG cc_start: 0.7508 (ttm170) cc_final: 0.7074 (ttp-110) REVERT: F 379 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6490 (mtm180) REVERT: G 307 GLN cc_start: 0.7745 (mp10) cc_final: 0.7413 (mp-120) REVERT: G 342 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7022 (mp0) REVERT: G 343 LYS cc_start: 0.8338 (mttt) cc_final: 0.7775 (ttmt) REVERT: H 307 GLN cc_start: 0.7745 (mp10) cc_final: 0.7343 (mp-120) REVERT: H 342 GLU cc_start: 0.7743 (mt-10) cc_final: 0.6991 (mp0) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.2988 time to fit residues: 16.2131 Evaluate side-chains 45 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 330 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 = 0.4565 r_free = 0.4565 target = 0.183335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.154430 restraints weight = 12364.630| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.34 r_work: 0.4163 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3582 Z= 0.135 Angle : 0.515 3.751 4794 Z= 0.268 Chirality : 0.050 0.139 534 Planarity : 0.002 0.022 618 Dihedral : 6.039 36.725 480 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.25 % Allowed : 7.21 % Favored : 92.54 % 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: -2.86 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.007 0.001 TYR H 310 PHE 0.006 0.001 PHE H 378 HIS 0.005 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3582) covalent geometry : angle 0.51467 ( 4794) hydrogen bonds : bond 0.02816 ( 20) hydrogen bonds : angle 4.26749 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7541 (mtpt) REVERT: C 379 ARG cc_start: 0.6905 (mpt-90) cc_final: 0.5591 (mtp85) REVERT: C 380 GLU cc_start: 0.4825 (tm-30) cc_final: 0.4510 (tm-30) REVERT: D 338 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7955 (mt-10) REVERT: E 307 GLN cc_start: 0.7538 (mp10) cc_final: 0.6904 (mm110) REVERT: E 342 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6900 (mm-30) REVERT: E 379 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6358 (mtt90) REVERT: F 307 GLN cc_start: 0.7723 (mp10) cc_final: 0.7304 (mm110) REVERT: F 349 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7144 (ttp-110) REVERT: F 379 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6583 (mtm180) REVERT: G 307 GLN cc_start: 0.7756 (mp10) cc_final: 0.7418 (mp-120) REVERT: G 342 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7085 (mp0) REVERT: G 343 LYS cc_start: 0.8322 (mttt) cc_final: 0.7822 (ttmt) REVERT: H 307 GLN cc_start: 0.7801 (mp10) cc_final: 0.7410 (mp-120) REVERT: H 342 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7034 (mp0) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.3006 time to fit residues: 16.9840 Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.0040 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN ** G 330 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 = 0.4604 r_free = 0.4604 target = 0.187275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.159037 restraints weight = 12272.576| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.35 r_work: 0.4234 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4065 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3582 Z= 0.071 Angle : 0.463 4.393 4794 Z= 0.239 Chirality : 0.049 0.135 534 Planarity : 0.002 0.021 618 Dihedral : 5.649 36.266 480 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % 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: -2.64 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.005 0.001 TYR H 310 PHE 0.007 0.001 PHE H 378 HIS 0.002 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00172 ( 3582) covalent geometry : angle 0.46338 ( 4794) hydrogen bonds : bond 0.02372 ( 20) hydrogen bonds : angle 3.85202 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6924 (mpt-90) cc_final: 0.5646 (mtp85) REVERT: C 380 GLU cc_start: 0.4895 (tm-30) cc_final: 0.4622 (tm-30) REVERT: D 329 HIS cc_start: 0.7593 (m-70) cc_final: 0.7208 (m-70) REVERT: D 338 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7937 (mt-10) REVERT: E 307 GLN cc_start: 0.7487 (mp10) cc_final: 0.6864 (mm110) REVERT: E 342 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6917 (mm-30) REVERT: E 379 ARG cc_start: 0.6811 (mtt180) cc_final: 0.6289 (mtt90) REVERT: F 307 GLN cc_start: 0.7759 (mp10) cc_final: 0.7329 (mm110) REVERT: F 349 ARG cc_start: 0.7499 (ttm170) cc_final: 0.7111 (ttp-110) REVERT: F 379 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6497 (mtm180) REVERT: G 307 GLN cc_start: 0.7607 (mp-120) cc_final: 0.7277 (mp-120) REVERT: G 342 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7092 (mp0) REVERT: H 342 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7061 (mp0) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2720 time to fit residues: 13.7367 Evaluate side-chains 43 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN ** G 330 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 = 0.4588 r_free = 0.4588 target = 0.185734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.157255 restraints weight = 12324.709| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.32 r_work: 0.4207 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4032 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3582 Z= 0.102 Angle : 0.476 4.058 4794 Z= 0.247 Chirality : 0.049 0.139 534 Planarity : 0.002 0.020 618 Dihedral : 5.634 32.908 480 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % 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: -2.72 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.006 0.001 TYR H 310 PHE 0.005 0.001 PHE H 378 HIS 0.004 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 3582) covalent geometry : angle 0.47642 ( 4794) hydrogen bonds : bond 0.02486 ( 20) hydrogen bonds : angle 3.95045 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7484 (mtpt) REVERT: C 379 ARG cc_start: 0.6906 (mpt-90) cc_final: 0.5601 (mtp85) REVERT: C 380 GLU cc_start: 0.4971 (tm-30) cc_final: 0.4646 (tm-30) REVERT: D 329 HIS cc_start: 0.7642 (m-70) cc_final: 0.7267 (m-70) REVERT: D 338 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7907 (mt-10) REVERT: E 307 GLN cc_start: 0.7539 (mp10) cc_final: 0.6914 (mm110) REVERT: E 342 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6918 (mm-30) REVERT: E 379 ARG cc_start: 0.6916 (mtt180) cc_final: 0.6414 (mtt90) REVERT: F 307 GLN cc_start: 0.7823 (mp10) cc_final: 0.7353 (mm110) REVERT: F 349 ARG cc_start: 0.7460 (ttm170) cc_final: 0.7084 (ttp-110) REVERT: F 379 ARG cc_start: 0.7141 (mtt180) cc_final: 0.6576 (mtm180) REVERT: G 307 GLN cc_start: 0.7728 (mp10) cc_final: 0.7348 (mp-120) REVERT: G 342 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7072 (mp0) REVERT: G 343 LYS cc_start: 0.8283 (mttt) cc_final: 0.7754 (ttmt) REVERT: H 307 GLN cc_start: 0.7780 (mp10) cc_final: 0.7385 (mp-120) REVERT: H 342 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7066 (mp0) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2825 time to fit residues: 15.1222 Evaluate side-chains 46 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 0.0970 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.0770 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 330 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 = 0.4582 r_free = 0.4582 target = 0.184941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.156392 restraints weight = 12277.778| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.32 r_work: 0.4204 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3582 Z= 0.108 Angle : 0.481 4.138 4794 Z= 0.249 Chirality : 0.049 0.136 534 Planarity : 0.002 0.019 618 Dihedral : 5.584 30.148 480 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % 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: -2.71 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.005 0.001 TYR H 310 PHE 0.006 0.001 PHE H 378 HIS 0.004 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3582) covalent geometry : angle 0.48146 ( 4794) hydrogen bonds : bond 0.02545 ( 20) hydrogen bonds : angle 4.03011 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.06 seconds wall clock time: 47 minutes 38.75 seconds (2858.75 seconds total)