Starting phenix.real_space_refine on Thu Nov 14 19:18:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxi_45005/11_2024/9bxi_45005.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxi_45005/11_2024/9bxi_45005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxi_45005/11_2024/9bxi_45005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxi_45005/11_2024/9bxi_45005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxi_45005/11_2024/9bxi_45005.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxi_45005/11_2024/9bxi_45005.cif" } resolution = 2.7 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= 0.003 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 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7182 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, F Time building chain proxies: 2.98, per 1000 atoms: 0.41 Number of scatterers: 7182 At special positions: 0 Unit cell: (81.732, 159.294, 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: 1.83 Conformation dependent library (CDL) restraints added in 672.1 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 18 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.506A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.422A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.807A pdb=" N SER A 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER C 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.468A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 375 Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.498A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LYS F 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.423A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340 Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.824A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER D 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.488A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS F 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 375 92 hydrogen bonds defined for protein. 276 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: 2.34 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3648 1.12 - 1.29: 600 1.29 - 1.46: 1045 1.46 - 1.63: 1937 1.63 - 1.80: 6 Bond restraints: 7236 Sorted by residual: bond pdb=" N SER D 305 " pdb=" H SER D 305 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N SER F 305 " pdb=" H SER F 305 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N SER B 305 " pdb=" H SER B 305 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LYS B 331 " pdb=" H LYS B 331 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LYS F 331 " pdb=" H LYS F 331 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 7231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11365 2.50 - 5.00: 1325 5.00 - 7.49: 474 7.49 - 9.99: 18 9.99 - 12.49: 6 Bond angle restraints: 13188 Sorted by residual: angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 118.79 -4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 118.76 -4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 118.76 -4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 118.74 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 118.73 -4.93 1.00e+00 1.00e+00 2.43e+01 ... (remaining 13183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.99: 2982 13.99 - 27.97: 144 27.97 - 41.96: 72 41.96 - 55.94: 54 55.94 - 69.93: 72 Dihedral angle restraints: 3324 sinusoidal: 1902 harmonic: 1422 Sorted by residual: dihedral pdb=" CA GLN B 351 " pdb=" C GLN B 351 " pdb=" N SER B 352 " pdb=" CA SER B 352 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA GLN D 351 " pdb=" C GLN D 351 " pdb=" N SER D 352 " pdb=" CA SER D 352 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA GLN A 351 " pdb=" C GLN A 351 " pdb=" N SER A 352 " pdb=" CA SER A 352 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3321 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.053: 281 0.053 - 0.105: 163 0.105 - 0.157: 72 0.157 - 0.209: 12 0.209 - 0.261: 6 Chirality restraints: 534 Sorted by residual: 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 1.70e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 531 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 360 " -0.020 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" N THR A 361 " 0.064 2.00e-02 2.50e+03 pdb=" CA THR A 361 " -0.018 2.00e-02 2.50e+03 pdb=" H THR A 361 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 360 " 0.020 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" N THR D 361 " -0.064 2.00e-02 2.50e+03 pdb=" CA THR D 361 " 0.018 2.00e-02 2.50e+03 pdb=" H THR D 361 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 360 " 0.020 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" N THR B 361 " -0.064 2.00e-02 2.50e+03 pdb=" CA THR B 361 " 0.018 2.00e-02 2.50e+03 pdb=" H THR B 361 " 0.025 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 0.59 - 1.40: 61 1.40 - 2.20: 778 2.20 - 3.00: 18727 3.00 - 3.80: 28293 3.80 - 4.60: 44416 Warning: very small nonbonded interaction distances. Nonbonded interactions: 92275 Sorted by model distance: nonbonded pdb=" NZ LYS B 370 " pdb=" HG SER D 316 " model vdw 0.594 2.600 nonbonded pdb=" NZ LYS C 370 " pdb=" HG SER E 316 " model vdw 0.603 2.600 nonbonded pdb=" NZ LYS D 370 " pdb=" HG SER F 316 " model vdw 0.607 2.600 nonbonded pdb=" NZ LYS A 370 " pdb=" HG SER C 316 " model vdw 0.632 2.600 nonbonded pdb=" HZ1 LYS A 370 " pdb=" HG SER C 316 " model vdw 0.734 2.100 ... (remaining 92270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.050 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.610 Find NCS groups from input model: 0.170 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 : 0.010 0.041 3582 Z= 0.676 Angle : 1.608 5.507 4794 Z= 1.016 Chirality : 0.078 0.261 534 Planarity : 0.006 0.017 618 Dihedral : 10.278 69.928 1380 Min Nonbonded Distance : 1.231 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 362 PHE 0.017 0.006 PHE E 346 TYR 0.011 0.005 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** 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 144 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8337 (mttt) cc_final: 0.7745 (pttt) REVERT: B 340 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8153 (mttt) REVERT: B 342 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7090 (mp0) REVERT: B 343 LYS cc_start: 0.8341 (mttt) cc_final: 0.7935 (mtpt) REVERT: C 343 LYS cc_start: 0.8212 (mttt) cc_final: 0.7972 (mtpt) REVERT: C 375 LYS cc_start: 0.8166 (tttt) cc_final: 0.7320 (ttmm) REVERT: D 338 GLU cc_start: 0.8457 (tt0) cc_final: 0.8228 (tt0) REVERT: D 343 LYS cc_start: 0.8247 (mttt) cc_final: 0.7924 (mtpm) REVERT: D 379 ARG cc_start: 0.6120 (mtt180) cc_final: 0.5746 (mmm160) REVERT: E 343 LYS cc_start: 0.8149 (mttt) cc_final: 0.7803 (mtpp) REVERT: F 340 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8003 (ttmm) REVERT: F 343 LYS cc_start: 0.8199 (mttt) cc_final: 0.7610 (tptt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 2.6228 time to fit residues: 387.5132 Evaluate side-chains 95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3582 Z= 0.177 Angle : 0.581 3.603 4794 Z= 0.303 Chirality : 0.050 0.127 534 Planarity : 0.004 0.034 618 Dihedral : 6.233 19.266 480 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.49 % Allowed : 12.94 % Favored : 85.57 % 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: -2.28 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 330 PHE 0.011 0.002 PHE A 378 TYR 0.010 0.002 TYR C 310 ARG 0.002 0.000 ARG F 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 106 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8504 (tt0) cc_final: 0.8287 (tt0) REVERT: A 340 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8219 (tmtm) REVERT: A 342 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7902 (mm-30) REVERT: B 311 LYS cc_start: 0.8348 (mttt) cc_final: 0.7743 (pttt) REVERT: B 340 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8291 (mttt) REVERT: B 342 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6959 (mp0) REVERT: B 343 LYS cc_start: 0.8499 (mttt) cc_final: 0.8057 (mtpt) REVERT: C 340 LYS cc_start: 0.8326 (ttmm) cc_final: 0.7966 (mttt) REVERT: C 342 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7625 (mt-10) REVERT: C 343 LYS cc_start: 0.8278 (mttt) cc_final: 0.8047 (mtpt) REVERT: C 375 LYS cc_start: 0.8054 (tttt) cc_final: 0.7204 (ttmm) REVERT: D 340 LYS cc_start: 0.8312 (ttmm) cc_final: 0.7741 (mmtm) REVERT: D 343 LYS cc_start: 0.8311 (mttt) cc_final: 0.8003 (mtpm) REVERT: E 340 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7713 (ttpp) REVERT: E 343 LYS cc_start: 0.8213 (mttt) cc_final: 0.7893 (mtpp) REVERT: F 311 LYS cc_start: 0.8353 (mttt) cc_final: 0.7647 (mttm) REVERT: F 340 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8052 (ttmm) REVERT: F 343 LYS cc_start: 0.8238 (mttt) cc_final: 0.7719 (tptt) REVERT: F 372 GLU cc_start: 0.8644 (tt0) cc_final: 0.8403 (tt0) outliers start: 6 outliers final: 4 residues processed: 103 average time/residue: 2.9832 time to fit residues: 314.6438 Evaluate side-chains 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN D 368 ASN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3582 Z= 0.325 Angle : 0.602 4.719 4794 Z= 0.314 Chirality : 0.050 0.135 534 Planarity : 0.004 0.040 618 Dihedral : 6.326 19.535 480 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.49 % Allowed : 16.92 % Favored : 80.60 % 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: -2.34 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 330 PHE 0.009 0.001 PHE D 378 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.001 ARG B 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 101 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7982 (mm-30) REVERT: A 375 LYS cc_start: 0.8585 (tttt) cc_final: 0.8026 (ttmm) REVERT: B 327 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7753 (m-40) REVERT: B 338 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: B 340 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8316 (mttt) REVERT: B 342 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7126 (mp0) REVERT: B 343 LYS cc_start: 0.8550 (mttt) cc_final: 0.8096 (mtpt) REVERT: B 375 LYS cc_start: 0.8505 (tttt) cc_final: 0.7791 (ttmm) REVERT: C 340 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8105 (mttt) REVERT: C 342 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7676 (mt-10) REVERT: C 343 LYS cc_start: 0.8366 (mttt) cc_final: 0.8124 (mtpt) REVERT: C 375 LYS cc_start: 0.8229 (tttt) cc_final: 0.7409 (ttmm) REVERT: D 340 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7640 (mmtm) REVERT: D 343 LYS cc_start: 0.8320 (mttt) cc_final: 0.8004 (mtpm) REVERT: E 340 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7756 (ttpp) REVERT: E 343 LYS cc_start: 0.8272 (mttt) cc_final: 0.7946 (mtpp) REVERT: F 311 LYS cc_start: 0.8413 (mttt) cc_final: 0.7656 (mttm) REVERT: F 343 LYS cc_start: 0.8310 (mttt) cc_final: 0.7698 (tptt) REVERT: F 372 GLU cc_start: 0.8747 (tt0) cc_final: 0.8543 (tt0) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 3.0244 time to fit residues: 291.1806 Evaluate side-chains 96 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3582 Z= 0.239 Angle : 0.536 3.880 4794 Z= 0.279 Chirality : 0.049 0.126 534 Planarity : 0.004 0.045 618 Dihedral : 5.902 17.294 480 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.99 % Allowed : 18.16 % Favored : 79.85 % 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: -2.32 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.009 0.001 PHE D 378 TYR 0.010 0.002 TYR D 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 101 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8655 (tttt) cc_final: 0.8106 (ttmm) REVERT: B 311 LYS cc_start: 0.8395 (mttt) cc_final: 0.7806 (pttt) REVERT: B 327 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7811 (m-40) REVERT: B 338 GLU cc_start: 0.8651 (tt0) cc_final: 0.8391 (tm-30) REVERT: B 340 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8278 (mttt) REVERT: B 343 LYS cc_start: 0.8535 (mttt) cc_final: 0.8119 (mtpt) REVERT: B 375 LYS cc_start: 0.8531 (tttt) cc_final: 0.7825 (ttmm) REVERT: C 340 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8083 (mttt) REVERT: C 343 LYS cc_start: 0.8373 (mttt) cc_final: 0.7860 (mtpt) REVERT: C 375 LYS cc_start: 0.8280 (tttt) cc_final: 0.7452 (ttmm) REVERT: D 340 LYS cc_start: 0.8322 (ttmm) cc_final: 0.7990 (mttt) REVERT: D 343 LYS cc_start: 0.8323 (mttt) cc_final: 0.7883 (mtpp) REVERT: E 340 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7770 (ttpp) REVERT: E 343 LYS cc_start: 0.8304 (mttt) cc_final: 0.7931 (mtpp) REVERT: F 311 LYS cc_start: 0.8416 (mttt) cc_final: 0.7653 (mttm) REVERT: F 343 LYS cc_start: 0.8294 (mttt) cc_final: 0.7698 (tptt) REVERT: F 372 GLU cc_start: 0.8740 (tt0) cc_final: 0.8532 (tt0) outliers start: 8 outliers final: 3 residues processed: 96 average time/residue: 3.0218 time to fit residues: 297.4052 Evaluate side-chains 96 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3582 Z= 0.169 Angle : 0.499 4.436 4794 Z= 0.257 Chirality : 0.049 0.129 534 Planarity : 0.004 0.043 618 Dihedral : 5.477 14.785 480 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.23 % Allowed : 18.91 % Favored : 77.86 % 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: -2.29 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.008 0.001 PHE D 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 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 104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.8004 (m-40) REVERT: A 338 GLU cc_start: 0.8483 (tt0) cc_final: 0.8229 (tm-30) REVERT: A 342 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 311 LYS cc_start: 0.8387 (mttt) cc_final: 0.7819 (pttt) REVERT: B 327 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7740 (m-40) REVERT: B 338 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: B 340 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8263 (mttt) REVERT: B 343 LYS cc_start: 0.8510 (mttt) cc_final: 0.8101 (mtpt) REVERT: B 375 LYS cc_start: 0.8538 (tttt) cc_final: 0.7863 (ttmm) REVERT: C 340 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8082 (mttt) REVERT: C 342 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: C 343 LYS cc_start: 0.8363 (mttt) cc_final: 0.7857 (mtpt) REVERT: C 375 LYS cc_start: 0.8282 (tttt) cc_final: 0.7464 (ttmm) REVERT: D 340 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7995 (mttt) REVERT: D 343 LYS cc_start: 0.8330 (mttt) cc_final: 0.7886 (mtpp) REVERT: E 340 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7745 (ttpp) REVERT: E 343 LYS cc_start: 0.8337 (mttt) cc_final: 0.7963 (mtpp) REVERT: F 311 LYS cc_start: 0.8408 (mttt) cc_final: 0.7670 (mttm) REVERT: F 343 LYS cc_start: 0.8303 (mttt) cc_final: 0.7700 (tptt) outliers start: 13 outliers final: 4 residues processed: 95 average time/residue: 3.0534 time to fit residues: 297.1462 Evaluate side-chains 99 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4783 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= 0.135 Angle : 0.476 4.651 4794 Z= 0.244 Chirality : 0.049 0.125 534 Planarity : 0.004 0.041 618 Dihedral : 5.022 13.674 480 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.24 % Allowed : 19.90 % Favored : 77.86 % 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: -2.31 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.006 0.001 PHE D 378 TYR 0.007 0.001 TYR D 310 ARG 0.002 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 100 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: A 338 GLU cc_start: 0.8449 (tt0) cc_final: 0.8233 (tm-30) REVERT: A 342 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 311 LYS cc_start: 0.8371 (mttt) cc_final: 0.7830 (pttt) REVERT: B 327 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7747 (m-40) REVERT: B 338 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: B 340 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8252 (mttt) REVERT: B 343 LYS cc_start: 0.8511 (mttt) cc_final: 0.8122 (mtpt) REVERT: B 375 LYS cc_start: 0.8554 (tttt) cc_final: 0.7881 (ttmm) REVERT: C 340 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8088 (mttt) REVERT: C 342 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: C 343 LYS cc_start: 0.8382 (mttt) cc_final: 0.7891 (mtpt) REVERT: C 375 LYS cc_start: 0.8284 (tttt) cc_final: 0.7488 (ttmm) REVERT: D 340 LYS cc_start: 0.8286 (ttmm) cc_final: 0.8003 (mttt) REVERT: D 343 LYS cc_start: 0.8340 (mttt) cc_final: 0.8000 (mtpm) REVERT: E 340 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7779 (ttpp) REVERT: E 343 LYS cc_start: 0.8348 (mttt) cc_final: 0.7974 (mtpp) REVERT: E 379 ARG cc_start: 0.7454 (mmm160) cc_final: 0.7164 (mmm-85) REVERT: F 311 LYS cc_start: 0.8396 (mttt) cc_final: 0.7655 (mttm) REVERT: F 343 LYS cc_start: 0.8314 (mttt) cc_final: 0.7740 (tptt) outliers start: 9 outliers final: 2 residues processed: 94 average time/residue: 2.9668 time to fit residues: 285.7032 Evaluate side-chains 94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3582 Z= 0.218 Angle : 0.509 5.211 4794 Z= 0.261 Chirality : 0.049 0.122 534 Planarity : 0.004 0.041 618 Dihedral : 5.382 16.429 480 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.49 % Allowed : 18.41 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.007 0.001 PHE D 378 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG E 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 103 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8027 (m-40) REVERT: A 338 GLU cc_start: 0.8473 (tt0) cc_final: 0.8253 (tm-30) REVERT: A 375 LYS cc_start: 0.8659 (tttt) cc_final: 0.8128 (ttmm) REVERT: B 311 LYS cc_start: 0.8387 (mttt) cc_final: 0.7835 (pttt) REVERT: B 327 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7605 (m-40) REVERT: B 338 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8369 (tm-30) REVERT: B 340 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8266 (mttt) REVERT: B 343 LYS cc_start: 0.8518 (mttt) cc_final: 0.8125 (mtpt) REVERT: B 375 LYS cc_start: 0.8578 (tttt) cc_final: 0.7905 (ttmm) REVERT: C 340 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8075 (mttt) REVERT: C 343 LYS cc_start: 0.8363 (mttt) cc_final: 0.7873 (mtpt) REVERT: C 375 LYS cc_start: 0.8288 (tttt) cc_final: 0.7490 (ttmm) REVERT: D 340 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8026 (mttt) REVERT: D 343 LYS cc_start: 0.8344 (mttt) cc_final: 0.8007 (mtpm) REVERT: E 340 LYS cc_start: 0.8273 (ttmm) cc_final: 0.7783 (ttpp) REVERT: E 343 LYS cc_start: 0.8357 (mttt) cc_final: 0.7963 (mtpp) REVERT: E 379 ARG cc_start: 0.7481 (mmm160) cc_final: 0.7194 (mmm-85) REVERT: F 311 LYS cc_start: 0.8417 (mttt) cc_final: 0.7676 (mttm) REVERT: F 343 LYS cc_start: 0.8311 (mttt) cc_final: 0.7721 (tptt) outliers start: 10 outliers final: 3 residues processed: 95 average time/residue: 2.2869 time to fit residues: 222.6570 Evaluate side-chains 97 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.0270 chunk 34 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3582 Z= 0.130 Angle : 0.475 5.082 4794 Z= 0.242 Chirality : 0.049 0.126 534 Planarity : 0.004 0.039 618 Dihedral : 4.719 13.230 480 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.24 % Allowed : 20.15 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.006 0.001 PHE D 378 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** 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 95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8361 (mttt) cc_final: 0.7846 (pttt) REVERT: B 327 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7523 (m-40) REVERT: B 338 GLU cc_start: 0.8582 (tt0) cc_final: 0.8380 (tm-30) REVERT: B 340 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8261 (mttt) REVERT: B 343 LYS cc_start: 0.8561 (mttt) cc_final: 0.8170 (mtpt) REVERT: B 347 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7689 (mtpt) REVERT: B 375 LYS cc_start: 0.8565 (tttt) cc_final: 0.7883 (ttmm) REVERT: C 340 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8070 (mttt) REVERT: C 343 LYS cc_start: 0.8376 (mttt) cc_final: 0.7897 (mtpt) REVERT: C 375 LYS cc_start: 0.8304 (tttt) cc_final: 0.7525 (ttmm) REVERT: D 340 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7995 (mttt) REVERT: D 343 LYS cc_start: 0.8344 (mttt) cc_final: 0.8007 (mtpm) REVERT: E 340 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7786 (ttpp) REVERT: E 343 LYS cc_start: 0.8376 (mttt) cc_final: 0.7989 (mtpp) REVERT: E 379 ARG cc_start: 0.7441 (mmm160) cc_final: 0.7167 (mmm-85) REVERT: F 311 LYS cc_start: 0.8390 (mttt) cc_final: 0.7637 (mttm) REVERT: F 343 LYS cc_start: 0.8344 (mttt) cc_final: 0.7764 (tptt) outliers start: 5 outliers final: 1 residues processed: 93 average time/residue: 3.3352 time to fit residues: 317.1822 Evaluate side-chains 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3582 Z= 0.174 Angle : 0.488 5.688 4794 Z= 0.249 Chirality : 0.049 0.127 534 Planarity : 0.004 0.038 618 Dihedral : 4.933 13.954 480 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.00 % Allowed : 20.90 % Favored : 78.11 % 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: -2.23 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.006 0.001 PHE D 378 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG C 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 94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8694 (tttt) cc_final: 0.8168 (ttmm) REVERT: B 311 LYS cc_start: 0.8340 (mttt) cc_final: 0.7825 (pttt) REVERT: B 327 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: B 338 GLU cc_start: 0.8595 (tt0) cc_final: 0.8386 (tm-30) REVERT: B 340 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8267 (mttt) REVERT: B 343 LYS cc_start: 0.8595 (mttt) cc_final: 0.8197 (mtpt) REVERT: B 347 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7709 (mtpt) REVERT: B 375 LYS cc_start: 0.8586 (tttt) cc_final: 0.7908 (ttmm) REVERT: C 340 LYS cc_start: 0.8356 (ttmm) cc_final: 0.8071 (mttt) REVERT: C 343 LYS cc_start: 0.8389 (mttt) cc_final: 0.7915 (mtpt) REVERT: D 340 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8010 (mttt) REVERT: D 343 LYS cc_start: 0.8343 (mttt) cc_final: 0.7998 (mtpm) REVERT: E 340 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7778 (ttpp) REVERT: E 343 LYS cc_start: 0.8370 (mttt) cc_final: 0.7983 (mtpp) REVERT: E 379 ARG cc_start: 0.7405 (mmm160) cc_final: 0.7138 (mmm-85) REVERT: F 311 LYS cc_start: 0.8407 (mttt) cc_final: 0.7662 (mttm) REVERT: F 343 LYS cc_start: 0.8347 (mttt) cc_final: 0.7763 (tptt) outliers start: 4 outliers final: 1 residues processed: 93 average time/residue: 3.1751 time to fit residues: 302.0045 Evaluate side-chains 94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3582 Z= 0.145 Angle : 0.479 6.111 4794 Z= 0.244 Chirality : 0.049 0.126 534 Planarity : 0.004 0.037 618 Dihedral : 4.682 13.542 480 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.24 % Allowed : 20.90 % Favored : 77.86 % 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: -2.26 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.006 0.001 PHE D 378 TYR 0.007 0.001 TYR D 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 94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8210 (tmtm) REVERT: B 311 LYS cc_start: 0.8309 (mttt) cc_final: 0.7822 (pttt) REVERT: B 340 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8259 (mttt) REVERT: B 343 LYS cc_start: 0.8593 (mttt) cc_final: 0.8193 (mtpt) REVERT: B 347 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7681 (mtpt) REVERT: C 306 VAL cc_start: 0.7845 (m) cc_final: 0.7637 (p) REVERT: C 340 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8056 (mttt) REVERT: C 343 LYS cc_start: 0.8390 (mttt) cc_final: 0.7912 (mtpt) REVERT: D 340 LYS cc_start: 0.8259 (ttmm) cc_final: 0.8002 (mttt) REVERT: D 343 LYS cc_start: 0.8344 (mttt) cc_final: 0.7999 (mtpm) REVERT: E 340 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7768 (ttpp) REVERT: E 343 LYS cc_start: 0.8342 (mttt) cc_final: 0.7967 (mtpp) REVERT: E 349 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7852 (mtm180) REVERT: E 379 ARG cc_start: 0.7377 (mmm160) cc_final: 0.6348 (mmp-170) REVERT: F 311 LYS cc_start: 0.8405 (mttt) cc_final: 0.7661 (mttm) REVERT: F 343 LYS cc_start: 0.8323 (mttt) cc_final: 0.7767 (tptt) outliers start: 5 outliers final: 2 residues processed: 93 average time/residue: 3.2257 time to fit residues: 307.0601 Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.163623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.129041 restraints weight = 10781.746| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.74 r_work: 0.3801 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.209 3582 Z= 0.349 Angle : 1.172 59.184 4794 Z= 0.727 Chirality : 0.048 0.124 534 Planarity : 0.004 0.037 618 Dihedral : 4.697 13.589 480 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.50 % Allowed : 21.64 % Favored : 77.86 % 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: -2.25 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.006 0.001 PHE D 378 TYR 0.007 0.001 TYR D 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5565.10 seconds wall clock time: 102 minutes 59.72 seconds (6179.72 seconds total)