Starting phenix.real_space_refine on Tue Jan 14 18:32:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxq_45008/01_2025/9bxq_45008.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxq_45008/01_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_45008/01_2025/9bxq_45008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxq_45008/01_2025/9bxq_45008.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxq_45008/01_2025/9bxq_45008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxq_45008/01_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 2.84, 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: 1.75 Conformation dependent library (CDL) restraints added in 660.7 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: 0.58 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: 1.94 Time building geometry restraints manager: 2.10 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: 1.480 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: 0.130 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- 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 : 0.572 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: 0.4986 time to fit residues: 47.0385 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 : 0.634 ------------------------------------------------------------------------------- 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: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.4652 r_free = 0.4652 target = 0.192283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.164753 restraints weight = 11988.762| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.40 r_work: 0.4233 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3582 Z= 0.253 Angle : 0.713 5.644 4794 Z= 0.370 Chirality : 0.053 0.142 534 Planarity : 0.003 0.017 618 Dihedral : 8.162 41.615 480 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.75 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: -2.99 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.20), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 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 : 0.632 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: 0.6666 (mpt-90) cc_final: 0.6097 (mtt-85) REVERT: E 342 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6988 (mm-30) REVERT: F 342 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7348 (mm-30) REVERT: F 349 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6970 (ttp-110) REVERT: G 306 VAL cc_start: 0.8563 (t) cc_final: 0.8316 (p) REVERT: G 307 GLN cc_start: 0.7625 (mp10) cc_final: 0.7395 (mp-120) REVERT: G 342 GLU cc_start: 0.7893 (mt-10) cc_final: 0.6812 (mp0) REVERT: H 342 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6830 (mp0) REVERT: H 347 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7181 (tmtt) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.5713 time to fit residues: 39.9965 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 : 0.592 ------------------------------------------------------------------------------- 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: 0.6980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ** 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 = 0.4625 r_free = 0.4625 target = 0.190196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.163410 restraints weight = 12142.623| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.37 r_work: 0.4224 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.154 Angle : 0.577 3.994 4794 Z= 0.296 Chirality : 0.051 0.144 534 Planarity : 0.002 0.016 618 Dihedral : 7.243 41.205 480 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.25 % Allowed : 4.48 % 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: -2.91 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.015 0.002 PHE D 378 TYR 0.006 0.001 TYR H 310 ARG 0.002 0.000 ARG C 379 *********************** 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 58 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.586 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: 0.6775 (mpt-90) cc_final: 0.6207 (mtt-85) REVERT: D 338 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7764 (mt-10) REVERT: E 342 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7008 (mm-30) REVERT: F 307 GLN cc_start: 0.7452 (mp10) cc_final: 0.7053 (mp-120) REVERT: F 349 ARG cc_start: 0.7375 (ttm170) cc_final: 0.7077 (ttp-110) REVERT: G 340 LYS cc_start: 0.8160 (mttt) cc_final: 0.7802 (mtpt) REVERT: G 342 GLU cc_start: 0.7885 (mt-10) cc_final: 0.6909 (mp0) REVERT: H 342 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6961 (mp0) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.6136 time to fit residues: 39.7911 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 : 0.624 ------------------------------------------------------------------------------- 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: 50.0000 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 chunk 5 optimal weight: 50.0000 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 330 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 = 0.4584 r_free = 0.4584 target = 0.187950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.159065 restraints weight = 11706.474| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.33 r_work: 0.4130 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3582 Z= 0.308 Angle : 0.635 4.476 4794 Z= 0.331 Chirality : 0.051 0.142 534 Planarity : 0.003 0.026 618 Dihedral : 7.377 45.777 480 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % 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: -3.14 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 362 PHE 0.014 0.001 PHE D 378 TYR 0.017 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 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: C 379 ARG cc_start: 0.6741 (mpt-90) cc_final: 0.6043 (mtt-85) REVERT: D 338 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7775 (mt-10) REVERT: E 342 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6759 (mm-30) REVERT: E 379 ARG cc_start: 0.6665 (mtt180) cc_final: 0.6174 (mtt90) REVERT: F 307 GLN cc_start: 0.7553 (mp10) cc_final: 0.7103 (mm110) REVERT: F 349 ARG cc_start: 0.7558 (ttm170) cc_final: 0.7132 (ttp-110) REVERT: F 379 ARG cc_start: 0.6684 (mtt180) cc_final: 0.6159 (mtm180) REVERT: G 307 GLN cc_start: 0.7736 (mp10) cc_final: 0.7017 (mp-120) REVERT: G 340 LYS cc_start: 0.8484 (mttt) cc_final: 0.8083 (mtpt) REVERT: G 342 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7029 (mp0) REVERT: H 307 GLN cc_start: 0.7953 (mp10) cc_final: 0.7658 (mp-120) REVERT: H 342 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6983 (mp0) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.6928 time to fit residues: 46.4410 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 : 0.560 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.6980 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.0470 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 50.0000 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS E 307 GLN F 327 ASN F 374 HIS ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 HIS H 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.182448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.154447 restraints weight = 12375.554| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.45 r_work: 0.4179 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.142 Angle : 0.525 3.811 4794 Z= 0.273 Chirality : 0.050 0.138 534 Planarity : 0.002 0.022 618 Dihedral : 6.895 48.000 480 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: -2.88 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 362 PHE 0.013 0.001 PHE D 378 TYR 0.011 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 53 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.567 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: 0.6786 (mpt-90) cc_final: 0.6047 (mtt-85) REVERT: D 338 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7794 (mt-10) REVERT: E 342 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6768 (mm-30) REVERT: E 379 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6056 (mtt90) REVERT: F 307 GLN cc_start: 0.7510 (mp10) cc_final: 0.7039 (mm110) REVERT: F 349 ARG cc_start: 0.7565 (ttm170) cc_final: 0.7149 (ttp-110) REVERT: G 307 GLN cc_start: 0.7570 (mp10) cc_final: 0.7301 (mp-120) REVERT: G 342 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7001 (mp0) REVERT: H 342 GLU cc_start: 0.7706 (mt-10) cc_final: 0.6981 (mp0) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.6330 time to fit residues: 38.2342 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 : 0.558 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.4502 r_free = 0.4502 target = 0.177825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.148426 restraints weight = 12627.258| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.46 r_work: 0.4088 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3582 Z= 0.299 Angle : 0.577 4.343 4794 Z= 0.303 Chirality : 0.051 0.142 534 Planarity : 0.003 0.022 618 Dihedral : 7.058 48.455 480 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.53 % 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: -3.05 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 362 PHE 0.011 0.001 PHE D 378 TYR 0.012 0.002 TYR G 310 ARG 0.001 0.000 ARG C 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 49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6737 (mpt-90) cc_final: 0.5387 (mtp85) REVERT: D 338 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7863 (mt-10) REVERT: E 342 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6769 (mm-30) REVERT: E 349 ARG cc_start: 0.7167 (mtm180) cc_final: 0.6946 (mmm-85) REVERT: E 379 ARG cc_start: 0.6837 (mtt180) cc_final: 0.6278 (mtt90) REVERT: F 307 GLN cc_start: 0.7498 (mp10) cc_final: 0.7072 (mm110) REVERT: F 349 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7142 (ttp-110) REVERT: F 379 ARG cc_start: 0.7022 (mtt180) cc_final: 0.6473 (mtm180) REVERT: G 307 GLN cc_start: 0.7686 (mp10) cc_final: 0.7366 (mp-120) REVERT: G 342 GLU cc_start: 0.8117 (mt-10) cc_final: 0.6933 (mp0) REVERT: G 343 LYS cc_start: 0.8329 (mttt) cc_final: 0.7732 (ttmt) REVERT: H 342 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7000 (mp0) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.6520 time to fit residues: 36.3380 Evaluate side-chains 44 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 369 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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 = 0.4606 r_free = 0.4606 target = 0.188348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.160596 restraints weight = 12334.236| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.45 r_work: 0.4173 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4000 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.134 Angle : 0.506 3.821 4794 Z= 0.262 Chirality : 0.050 0.137 534 Planarity : 0.002 0.021 618 Dihedral : 6.723 52.589 480 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.35 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 (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: -2.89 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.012 0.001 PHE D 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: 1 poor density : 44 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6849 (mpt-90) cc_final: 0.5524 (mtp85) REVERT: D 329 HIS cc_start: 0.7521 (m-70) cc_final: 0.7293 (m170) REVERT: D 338 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7842 (mt-10) REVERT: E 307 GLN cc_start: 0.7441 (mp10) cc_final: 0.6774 (mm110) REVERT: E 342 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6769 (mm-30) REVERT: E 379 ARG cc_start: 0.6795 (mtt180) cc_final: 0.6265 (mtt90) REVERT: F 307 GLN cc_start: 0.7512 (mp10) cc_final: 0.7031 (mm110) REVERT: F 349 ARG cc_start: 0.7534 (ttm170) cc_final: 0.7097 (ttp-110) REVERT: F 379 ARG cc_start: 0.6959 (mtt180) cc_final: 0.6461 (mtm180) REVERT: G 307 GLN cc_start: 0.7567 (mp10) cc_final: 0.7211 (mp-120) REVERT: G 311 LYS cc_start: 0.8129 (pttm) cc_final: 0.7908 (pttm) REVERT: G 342 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7010 (mp0) REVERT: H 342 GLU cc_start: 0.7763 (mt-10) cc_final: 0.6993 (mp0) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.6037 time to fit residues: 31.0790 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 : 0.481 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.184876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.156122 restraints weight = 12452.112| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.48 r_work: 0.4119 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5885 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= 0.233 Angle : 0.533 3.890 4794 Z= 0.278 Chirality : 0.050 0.138 534 Planarity : 0.002 0.022 618 Dihedral : 6.784 54.652 480 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.25 % Allowed : 6.97 % 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: -3.00 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 362 PHE 0.010 0.001 PHE D 378 TYR 0.011 0.002 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 48 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7380 (mtpt) REVERT: C 379 ARG cc_start: 0.6811 (mpt-90) cc_final: 0.5442 (mtp85) REVERT: D 338 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7880 (mt-10) REVERT: E 342 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6817 (mm-30) REVERT: E 379 ARG cc_start: 0.6901 (mtt180) cc_final: 0.6356 (mtt90) REVERT: F 307 GLN cc_start: 0.7548 (mp10) cc_final: 0.7068 (mm110) REVERT: F 349 ARG cc_start: 0.7558 (ttm170) cc_final: 0.7099 (ttp-110) REVERT: F 379 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6550 (mtm180) REVERT: G 307 GLN cc_start: 0.7646 (mp10) cc_final: 0.7278 (mp-120) REVERT: G 342 GLU cc_start: 0.8146 (mt-10) cc_final: 0.6972 (mp0) REVERT: G 343 LYS cc_start: 0.8320 (mttt) cc_final: 0.7734 (ttmt) REVERT: H 342 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7052 (mp0) REVERT: H 379 ARG cc_start: 0.6755 (mtt180) cc_final: 0.5288 (ptt-90) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.6118 time to fit residues: 33.4833 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 : 0.593 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 40.0000 chunk 28 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.4599 r_free = 0.4599 target = 0.187660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.159254 restraints weight = 12292.217| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.43 r_work: 0.4217 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.133 Angle : 0.485 3.749 4794 Z= 0.251 Chirality : 0.050 0.136 534 Planarity : 0.002 0.022 618 Dihedral : 6.290 46.480 480 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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 (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: -2.82 (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 0.003 0.001 HIS F 362 PHE 0.009 0.001 PHE D 378 TYR 0.007 0.001 TYR G 310 ARG 0.005 0.000 ARG E 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 46 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.587 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: 0.7786 (mtpt) cc_final: 0.7537 (mtpt) REVERT: C 379 ARG cc_start: 0.6882 (mpt-90) cc_final: 0.5565 (mtp85) REVERT: D 329 HIS cc_start: 0.7640 (m-70) cc_final: 0.7371 (m170) REVERT: D 338 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7849 (mt-10) REVERT: E 307 GLN cc_start: 0.7530 (mp10) cc_final: 0.6951 (mp10) REVERT: E 342 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7017 (mm-30) REVERT: E 379 ARG cc_start: 0.6863 (mtt180) cc_final: 0.6338 (mtt90) REVERT: F 307 GLN cc_start: 0.7591 (mp10) cc_final: 0.7155 (mm110) REVERT: F 349 ARG cc_start: 0.7507 (ttm170) cc_final: 0.7093 (ttp-110) REVERT: F 379 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6504 (mtm180) REVERT: G 307 GLN cc_start: 0.7632 (mp10) cc_final: 0.7264 (mp-120) REVERT: G 342 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7064 (mp0) REVERT: G 343 LYS cc_start: 0.8293 (mttt) cc_final: 0.7760 (ttmt) REVERT: H 342 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7065 (mp0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.5925 time to fit residues: 31.2168 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 : 0.569 ------------------------------------------------------------------------------- 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: 3.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.187369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.158376 restraints weight = 12398.680| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.47 r_work: 0.4214 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3582 Z= 0.160 Angle : 0.493 4.169 4794 Z= 0.256 Chirality : 0.049 0.135 534 Planarity : 0.002 0.021 618 Dihedral : 5.983 44.635 480 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.49 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 (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: -2.82 (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 0.003 0.001 HIS F 362 PHE 0.010 0.001 PHE D 378 TYR 0.008 0.001 TYR G 310 ARG 0.002 0.000 ARG E 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 46 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7513 (mtpt) REVERT: C 379 ARG cc_start: 0.6829 (mpt-90) cc_final: 0.5499 (mtp85) REVERT: D 329 HIS cc_start: 0.7654 (m-70) cc_final: 0.7385 (m170) REVERT: D 338 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7865 (mt-10) REVERT: E 342 GLU cc_start: 0.7674 (mt-10) cc_final: 0.6986 (mm-30) REVERT: E 379 ARG cc_start: 0.6896 (mtt180) cc_final: 0.6352 (mtt90) REVERT: F 307 GLN cc_start: 0.7582 (mp10) cc_final: 0.7143 (mm110) REVERT: F 349 ARG cc_start: 0.7471 (ttm170) cc_final: 0.7089 (ttp-110) REVERT: F 379 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6583 (mtm180) REVERT: G 307 GLN cc_start: 0.7601 (mp10) cc_final: 0.7228 (mp-120) REVERT: G 342 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7042 (mp0) REVERT: G 343 LYS cc_start: 0.8334 (mttt) cc_final: 0.7785 (ttmt) REVERT: H 342 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7086 (mp0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.5476 time to fit residues: 28.8584 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 : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4561 r_free = 0.4561 target = 0.183775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.154424 restraints weight = 12288.537| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.42 r_work: 0.4114 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3582 Z= 0.255 Angle : 0.544 4.066 4794 Z= 0.284 Chirality : 0.050 0.136 534 Planarity : 0.003 0.033 618 Dihedral : 6.183 40.030 480 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.25 % Allowed : 7.46 % 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 (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: -2.97 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 362 PHE 0.009 0.001 PHE D 378 TYR 0.010 0.002 TYR G 310 ARG 0.003 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4741.63 seconds wall clock time: 86 minutes 55.55 seconds (5215.55 seconds total)