Starting phenix.real_space_refine on Wed Mar 12 03:05:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxq_45008/03_2025/9bxq_45008.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxq_45008/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxq_45008/03_2025/9bxq_45008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxq_45008/03_2025/9bxq_45008.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxq_45008/03_2025/9bxq_45008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxq_45008/03_2025/9bxq_45008.cif" } resolution = 3.1 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: E, D, G, F, H Time building chain proxies: 2.85, per 1000 atoms: 0.40 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: 1.65 Conformation dependent library (CDL) restraints added in 607.9 milliseconds 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: 0.64 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: 2.17 Time building geometry restraints manager: 2.05 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 1.410 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.430 ------------------------------------------------------------------------------- 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= 0.739 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 : 27.94 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 (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: -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 HIS 0.004 0.002 HIS G 330 PHE 0.019 0.010 PHE E 346 TYR 0.040 0.020 TYR G 310 ARG 0.001 0.000 ARG C 349 *********************** 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 : 0.636 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: symmetry clash REVERT: E 307 GLN cc_start: 0.7120 (mp10) cc_final: 0.6840 (mm110) REVERT: F 347 LYS cc_start: 0.7418 (ttmt) cc_final: 0.6750 (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: 0.7053 (mp-120) REVERT: G 342 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7044 (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: 0.7692 (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: 0.7385 (tt0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.4735 time to fit residues: 44.8214 Evaluate side-chains 53 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.191375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.163482 restraints weight = 11982.252| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.40 r_work: 0.4221 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4064 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3582 Z= 0.257 Angle : 0.720 5.506 4794 Z= 0.375 Chirality : 0.054 0.143 534 Planarity : 0.003 0.016 618 Dihedral : 8.115 39.103 480 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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 (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: -3.02 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.20), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS E 362 PHE 0.019 0.002 PHE D 378 TYR 0.004 0.001 TYR H 310 ARG 0.004 0.001 ARG C 349 *********************** 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 61 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.581 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: 0.6654 (mpt-90) cc_final: 0.6064 (mtt-85) REVERT: E 342 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6899 (mm-30) REVERT: F 342 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7181 (mm-30) REVERT: F 349 ARG cc_start: 0.7327 (ttm170) cc_final: 0.6998 (ttp-110) REVERT: G 306 VAL cc_start: 0.8566 (t) cc_final: 0.8317 (p) REVERT: G 307 GLN cc_start: 0.7631 (mp10) cc_final: 0.7398 (mp-120) REVERT: G 342 GLU cc_start: 0.7931 (mt-10) cc_final: 0.6820 (mp0) REVERT: H 307 GLN cc_start: 0.7598 (mp10) cc_final: 0.7341 (mp-120) REVERT: H 342 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7289 (mm-30) REVERT: H 347 LYS cc_start: 0.7874 (ttmt) cc_final: 0.7163 (tmtt) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.5185 time to fit residues: 36.4065 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 : 0.606 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.0020 chunk 39 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4615 r_free = 0.4615 target = 0.189244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.161759 restraints weight = 12130.407| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.41 r_work: 0.4206 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3582 Z= 0.161 Angle : 0.584 3.964 4794 Z= 0.300 Chirality : 0.051 0.149 534 Planarity : 0.002 0.018 618 Dihedral : 7.176 39.908 480 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % 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: -2.93 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.014 0.002 PHE D 378 TYR 0.005 0.001 TYR H 310 ARG 0.003 0.001 ARG C 349 *********************** 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 60 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.540 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: C 379 ARG cc_start: 0.6774 (mpt-90) cc_final: 0.6188 (mtt-85) REVERT: D 338 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7841 (mt-10) REVERT: E 342 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6980 (mm-30) REVERT: F 307 GLN cc_start: 0.7526 (mp10) cc_final: 0.7131 (mp-120) REVERT: F 349 ARG cc_start: 0.7441 (ttm170) cc_final: 0.7133 (ttp-110) REVERT: G 340 LYS cc_start: 0.8216 (mttt) cc_final: 0.7878 (mtpt) REVERT: G 342 GLU cc_start: 0.7967 (mt-10) cc_final: 0.6936 (mp0) REVERT: G 343 LYS cc_start: 0.8057 (mttt) cc_final: 0.7615 (ttmt) REVERT: H 307 GLN cc_start: 0.7709 (mp10) cc_final: 0.7427 (mp-120) REVERT: H 342 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7045 (mp0) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.6107 time to fit residues: 41.1305 Evaluate side-chains 51 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN ** 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 = 0.4573 r_free = 0.4573 target = 0.184316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.155678 restraints weight = 12008.430| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.39 r_work: 0.4237 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4069 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3582 Z= 0.207 Angle : 0.564 4.470 4794 Z= 0.293 Chirality : 0.050 0.140 534 Planarity : 0.002 0.023 618 Dihedral : 6.964 44.051 480 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 5.97 % 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 (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: -2.98 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 362 PHE 0.007 0.001 PHE H 378 TYR 0.015 0.002 TYR G 310 ARG 0.002 0.000 ARG C 379 *********************** 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 56 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.602 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: 0.6698 (mpt-90) cc_final: 0.6078 (mtt-85) REVERT: D 338 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7870 (mt-10) REVERT: E 317 LYS cc_start: 0.7703 (ptpt) cc_final: 0.7502 (pttt) REVERT: E 342 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6792 (mm-30) REVERT: F 307 GLN cc_start: 0.7505 (mp10) cc_final: 0.7037 (mm110) REVERT: F 349 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7155 (ttp-110) REVERT: G 307 GLN cc_start: 0.7666 (mp-120) cc_final: 0.7397 (mp-120) REVERT: G 340 LYS cc_start: 0.8414 (mttt) cc_final: 0.8007 (mtpt) REVERT: G 342 GLU cc_start: 0.8053 (mt-10) cc_final: 0.6991 (mp0) REVERT: H 307 GLN cc_start: 0.7808 (mp10) cc_final: 0.7513 (mp-120) REVERT: H 342 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7012 (mp0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.5792 time to fit residues: 36.7326 Evaluate side-chains 53 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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** G 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.182349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.153857 restraints weight = 12337.147| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.45 r_work: 0.4166 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3582 Z= 0.164 Angle : 0.529 4.191 4794 Z= 0.274 Chirality : 0.050 0.139 534 Planarity : 0.002 0.023 618 Dihedral : 6.649 45.442 480 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.84 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 362 PHE 0.007 0.001 PHE H 378 TYR 0.012 0.001 TYR G 310 ARG 0.001 0.000 ARG C 379 *********************** 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 56 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.616 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: C 379 ARG cc_start: 0.6751 (mpt-90) cc_final: 0.6003 (mtt-85) REVERT: D 338 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7854 (mt-10) REVERT: E 342 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6786 (mm-30) REVERT: E 349 ARG cc_start: 0.7180 (mtm180) cc_final: 0.6972 (mmm-85) REVERT: E 379 ARG cc_start: 0.6615 (mtt180) cc_final: 0.6010 (mtt90) REVERT: F 307 GLN cc_start: 0.7476 (mp10) cc_final: 0.7001 (mm110) REVERT: F 349 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7133 (ttp-110) REVERT: F 379 ARG cc_start: 0.6774 (mtt180) cc_final: 0.6216 (mtm180) REVERT: G 307 GLN cc_start: 0.7643 (mp10) cc_final: 0.7299 (mp-120) REVERT: G 340 LYS cc_start: 0.8402 (mttt) cc_final: 0.7977 (mtpt) REVERT: G 342 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7001 (mp0) REVERT: H 307 GLN cc_start: 0.7801 (mp10) cc_final: 0.7487 (mp-120) REVERT: H 342 GLU cc_start: 0.7691 (mt-10) cc_final: 0.6951 (mp0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.6320 time to fit residues: 39.9724 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 : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.0570 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4564 r_free = 0.4564 target = 0.184963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.156417 restraints weight = 12492.143| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.47 r_work: 0.4115 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5393 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= 0.256 Angle : 0.558 4.153 4794 Z= 0.291 Chirality : 0.050 0.140 534 Planarity : 0.002 0.023 618 Dihedral : 6.620 44.829 480 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.01 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 362 PHE 0.006 0.001 PHE H 378 TYR 0.010 0.001 TYR G 310 ARG 0.001 0.000 ARG D 379 *********************** 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 50 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6695 (mpt-90) cc_final: 0.5411 (mtp85) REVERT: D 338 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7935 (mt-10) REVERT: E 342 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6734 (mm-30) REVERT: E 379 ARG cc_start: 0.6795 (mtt180) cc_final: 0.6261 (mtt90) REVERT: F 307 GLN cc_start: 0.7543 (mp10) cc_final: 0.7073 (mm110) REVERT: F 349 ARG cc_start: 0.7589 (ttm170) cc_final: 0.7147 (ttp-110) REVERT: F 379 ARG cc_start: 0.6998 (mtt180) cc_final: 0.6470 (mtm180) REVERT: G 307 GLN cc_start: 0.7705 (mp10) cc_final: 0.7399 (mp-120) REVERT: G 342 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7003 (mp0) REVERT: H 342 GLU cc_start: 0.7772 (mt-10) cc_final: 0.6990 (mp0) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.5582 time to fit residues: 31.3666 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 : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.187725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.160060 restraints weight = 12325.720| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.44 r_work: 0.4164 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3582 Z= 0.145 Angle : 0.506 3.896 4794 Z= 0.262 Chirality : 0.050 0.138 534 Planarity : 0.002 0.022 618 Dihedral : 6.359 44.270 480 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -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 HIS 0.004 0.001 HIS F 362 PHE 0.007 0.001 PHE H 378 TYR 0.012 0.001 TYR G 310 ARG 0.001 0.000 ARG C 379 *********************** 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 45 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.582 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: 0.6774 (mpt-90) cc_final: 0.5415 (mtp85) REVERT: D 338 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7932 (mt-10) REVERT: E 342 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6727 (mm-30) REVERT: E 379 ARG cc_start: 0.6795 (mtt180) cc_final: 0.6161 (mtm180) REVERT: F 307 GLN cc_start: 0.7504 (mp10) cc_final: 0.7072 (mm110) REVERT: F 349 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7116 (ttp-110) REVERT: F 379 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6475 (mtm180) REVERT: G 307 GLN cc_start: 0.7587 (mp10) cc_final: 0.7242 (mp-120) REVERT: G 342 GLU cc_start: 0.8108 (mt-10) cc_final: 0.6991 (mp0) REVERT: H 342 GLU cc_start: 0.7744 (mt-10) cc_final: 0.6976 (mp0) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.6157 time to fit residues: 31.3974 Evaluate side-chains 45 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 14 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.186358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.158437 restraints weight = 12487.884| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.43 r_work: 0.4144 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3582 Z= 0.190 Angle : 0.506 3.836 4794 Z= 0.264 Chirality : 0.049 0.138 534 Planarity : 0.002 0.022 618 Dihedral : 6.332 41.690 480 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.50 % Allowed : 6.72 % Favored : 92.79 % 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: -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 HIS 0.004 0.001 HIS F 362 PHE 0.006 0.001 PHE H 378 TYR 0.010 0.001 TYR G 310 ARG 0.001 0.000 ARG C 379 *********************** 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 49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.661 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: 0.6809 (mpt-90) cc_final: 0.5490 (mtp85) REVERT: D 338 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7970 (mt-10) REVERT: E 342 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6840 (mm-30) REVERT: E 379 ARG cc_start: 0.6862 (mtt180) cc_final: 0.6325 (mtt90) REVERT: F 307 GLN cc_start: 0.7578 (mp10) cc_final: 0.7118 (mm110) REVERT: F 349 ARG cc_start: 0.7519 (ttm170) cc_final: 0.7071 (ttp-110) REVERT: F 379 ARG cc_start: 0.7116 (mtt180) cc_final: 0.6563 (mtm180) REVERT: G 307 GLN cc_start: 0.7604 (mp10) cc_final: 0.7235 (mp-120) REVERT: G 342 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7010 (mp0) REVERT: G 343 LYS cc_start: 0.8301 (mttt) cc_final: 0.7737 (ttmt) REVERT: H 342 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7013 (mp0) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.6157 time to fit residues: 34.1965 Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 GLU 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 39 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.186679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.157990 restraints weight = 12334.823| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.44 r_work: 0.4227 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4062 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3582 Z= 0.150 Angle : 0.485 3.834 4794 Z= 0.252 Chirality : 0.049 0.135 534 Planarity : 0.002 0.023 618 Dihedral : 5.926 39.695 480 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 6.97 % 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 (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: -2.79 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.006 0.001 PHE H 378 TYR 0.008 0.001 TYR G 310 ARG 0.001 0.000 ARG F 349 *********************** 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 48 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.667 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: 0.6909 (mpt-90) cc_final: 0.5524 (mtp85) REVERT: C 380 GLU cc_start: 0.4858 (tm-30) cc_final: 0.4648 (tm-30) REVERT: D 329 HIS cc_start: 0.7646 (m-70) cc_final: 0.7365 (m170) REVERT: D 338 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7956 (mt-10) REVERT: E 342 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6969 (mm-30) REVERT: E 379 ARG cc_start: 0.6854 (mtt180) cc_final: 0.6263 (mtm180) REVERT: F 307 GLN cc_start: 0.7637 (mp10) cc_final: 0.7190 (mm110) REVERT: F 349 ARG cc_start: 0.7509 (ttm170) cc_final: 0.7091 (ttp-110) REVERT: F 379 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6544 (mtm180) REVERT: G 307 GLN cc_start: 0.7619 (mp10) cc_final: 0.7259 (mp-120) REVERT: G 342 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7066 (mp0) REVERT: G 343 LYS cc_start: 0.8317 (mttt) cc_final: 0.7798 (ttmt) REVERT: H 342 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7069 (mp0) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.6144 time to fit residues: 33.9563 Evaluate side-chains 48 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 50.0000 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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** H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.185023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.155994 restraints weight = 12431.782| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.44 r_work: 0.4198 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5976 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= 0.198 Angle : 0.499 3.758 4794 Z= 0.261 Chirality : 0.049 0.136 534 Planarity : 0.002 0.021 618 Dihedral : 5.947 36.547 480 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.50 % Allowed : 6.47 % 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 (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: -2.85 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 362 PHE 0.006 0.001 PHE G 378 TYR 0.009 0.001 TYR G 310 ARG 0.001 0.000 ARG C 349 ********************** 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 51 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.591 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: 0.6903 (mpt-90) cc_final: 0.5619 (mtp85) REVERT: C 380 GLU cc_start: 0.4860 (tm-30) cc_final: 0.4599 (tm-30) REVERT: D 329 HIS cc_start: 0.7662 (m-70) cc_final: 0.7348 (m170) REVERT: D 338 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7987 (mt-10) REVERT: E 342 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6931 (mm-30) REVERT: E 379 ARG cc_start: 0.6914 (mtt180) cc_final: 0.6386 (mtt90) REVERT: F 307 GLN cc_start: 0.7626 (mp10) cc_final: 0.7246 (mm110) REVERT: F 349 ARG cc_start: 0.7563 (ttm170) cc_final: 0.7137 (ttp-110) REVERT: F 379 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6618 (mtm180) REVERT: G 307 GLN cc_start: 0.7639 (mp10) cc_final: 0.7271 (mp-120) REVERT: G 342 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7026 (mp0) REVERT: G 343 LYS cc_start: 0.8338 (mttt) cc_final: 0.7796 (ttmt) REVERT: H 342 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7073 (mp0) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.5497 time to fit residues: 32.0318 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 : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.185920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.156983 restraints weight = 12304.849| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 2.42 r_work: 0.4204 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.6061 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= 0.183 Angle : 0.495 3.812 4794 Z= 0.257 Chirality : 0.049 0.134 534 Planarity : 0.002 0.019 618 Dihedral : 5.845 33.642 480 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % 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: -2.83 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 362 PHE 0.006 0.001 PHE H 378 TYR 0.008 0.001 TYR G 310 ARG 0.001 0.000 ARG F 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4739.49 seconds wall clock time: 81 minutes 6.80 seconds (4866.80 seconds total)