Starting phenix.real_space_refine on Thu Nov 14 02:46:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/11_2024/8cax_16535.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/11_2024/8cax_16535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/11_2024/8cax_16535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/11_2024/8cax_16535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/11_2024/8cax_16535.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cax_16535/11_2024/8cax_16535.cif" } resolution = 3.7 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 3444 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.05, per 1000 atoms: 0.60 Number of scatterers: 3444 At special positions: 0 Unit cell: (130.192, 119.48, 37.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 642 8.00 N 636 7.00 C 2160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 384.0 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 308 removed outlier: 6.833A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.927A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 321 through 325 removed outlier: 8.973A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N SER A 324 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER F 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU E 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.439A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 346 removed outlier: 6.125A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS A 343 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS E 343 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.351A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 357 removed outlier: 6.131A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.833A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.927A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.728A pdb=" N SER D 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU C 325 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AB3, first strand: chain 'C' and resid 342 through 346 removed outlier: 6.838A pdb=" N LYS C 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB5, first strand: chain 'C' and resid 354 through 357 36 hydrogen bonds defined for protein. 108 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: 0.69 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 990 1.34 - 1.46: 739 1.46 - 1.58: 1763 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.311 0.043 1.10e-02 8.26e+03 1.50e+01 bond pdb=" CG HIS F 330 " pdb=" CD2 HIS F 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.49e+01 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.48e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.45e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 4091 2.25 - 4.50: 481 4.50 - 6.76: 90 6.76 - 9.01: 12 9.01 - 11.26: 6 Bond angle restraints: 4680 Sorted by residual: angle pdb=" C HIS C 362 " pdb=" CA HIS C 362 " pdb=" CB HIS C 362 " ideal model delta sigma weight residual 109.84 121.10 -11.26 1.63e+00 3.76e-01 4.77e+01 angle pdb=" C HIS D 362 " pdb=" CA HIS D 362 " pdb=" CB HIS D 362 " ideal model delta sigma weight residual 109.84 121.09 -11.25 1.63e+00 3.76e-01 4.76e+01 angle pdb=" C HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta sigma weight residual 109.84 121.09 -11.25 1.63e+00 3.76e-01 4.76e+01 angle pdb=" C HIS B 362 " pdb=" CA HIS B 362 " pdb=" CB HIS B 362 " ideal model delta sigma weight residual 109.84 121.07 -11.23 1.63e+00 3.76e-01 4.75e+01 angle pdb=" C HIS A 362 " pdb=" CA HIS A 362 " pdb=" CB HIS A 362 " ideal model delta sigma weight residual 109.84 121.07 -11.23 1.63e+00 3.76e-01 4.75e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 1619 11.41 - 22.81: 350 22.81 - 34.21: 113 34.21 - 45.62: 42 45.62 - 57.02: 12 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 326 " pdb=" C GLY B 326 " pdb=" N ASN B 327 " pdb=" CA ASN B 327 " ideal model delta harmonic sigma weight residual 180.00 143.47 36.53 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA GLY E 326 " pdb=" C GLY E 326 " pdb=" N ASN E 327 " pdb=" CA ASN E 327 " ideal model delta harmonic sigma weight residual 180.00 143.49 36.51 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA GLY D 326 " pdb=" C GLY D 326 " pdb=" N ASN D 327 " pdb=" CA ASN D 327 " ideal model delta harmonic sigma weight residual 180.00 143.50 36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 193 0.045 - 0.089: 137 0.089 - 0.134: 99 0.134 - 0.179: 87 0.179 - 0.223: 12 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA HIS B 362 " pdb=" N HIS B 362 " pdb=" C HIS B 362 " pdb=" CB HIS B 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HIS E 362 " pdb=" N HIS E 362 " pdb=" C HIS E 362 " pdb=" CB HIS E 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HIS D 362 " pdb=" N HIS D 362 " pdb=" C HIS D 362 " pdb=" CB HIS D 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.024 2.00e-02 2.50e+03 1.57e-02 4.95e+00 pdb=" CG TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.024 2.00e-02 2.50e+03 1.57e-02 4.91e+00 pdb=" CG TYR B 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.024 2.00e-02 2.50e+03 1.56e-02 4.89e+00 pdb=" CG TYR A 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.003 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 648 2.80 - 3.32: 3342 3.32 - 3.85: 5056 3.85 - 4.37: 6045 4.37 - 4.90: 11475 Nonbonded interactions: 26566 Sorted by model distance: nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.271 3.120 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.271 3.120 nonbonded pdb=" OG SER F 316 " pdb=" NZ LYS F 370 " model vdw 2.271 3.120 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.271 3.120 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.271 3.120 ... (remaining 26561 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 group one per residue 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: 1.200 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.120 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.009 0.043 3498 Z= 0.598 Angle : 1.646 11.259 4680 Z= 1.069 Chirality : 0.092 0.223 528 Planarity : 0.009 0.040 594 Dihedral : 14.826 57.023 1344 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.55 % Allowed : 7.58 % Favored : 87.88 % Cbeta Deviations : 1.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -3.97 (0.25), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.19), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.005 HIS E 330 PHE 0.015 0.003 PHE D 378 TYR 0.036 0.010 TYR E 310 ARG 0.004 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.9051 (tttt) cc_final: 0.8834 (tttp) REVERT: B 310 TYR cc_start: 0.8145 (t80) cc_final: 0.7858 (t80) REVERT: B 346 PHE cc_start: 0.8797 (m-80) cc_final: 0.7886 (p90) REVERT: B 369 LYS cc_start: 0.8704 (mttt) cc_final: 0.8488 (ttmt) REVERT: C 310 TYR cc_start: 0.8172 (t80) cc_final: 0.7787 (t80) REVERT: C 345 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8053 (t0) REVERT: C 346 PHE cc_start: 0.8834 (m-80) cc_final: 0.8070 (p90) REVERT: D 349 ARG cc_start: 0.8905 (mtt180) cc_final: 0.8204 (pmt-80) REVERT: D 372 GLU cc_start: 0.8531 (tt0) cc_final: 0.8157 (mp0) REVERT: D 375 LYS cc_start: 0.9126 (tttt) cc_final: 0.8838 (tttp) REVERT: E 308 ILE cc_start: 0.9394 (mt) cc_final: 0.9117 (mp) REVERT: E 310 TYR cc_start: 0.8050 (t80) cc_final: 0.7797 (t80) REVERT: E 369 LYS cc_start: 0.8715 (mttt) cc_final: 0.8504 (ttpt) REVERT: E 372 GLU cc_start: 0.8734 (tt0) cc_final: 0.8312 (mp0) REVERT: E 375 LYS cc_start: 0.9018 (tttt) cc_final: 0.8741 (tttm) REVERT: E 378 PHE cc_start: 0.8799 (t80) cc_final: 0.8491 (t80) REVERT: F 343 LYS cc_start: 0.9041 (mttm) cc_final: 0.8508 (tmmt) REVERT: F 349 ARG cc_start: 0.8745 (mtt180) cc_final: 0.7988 (ptt-90) outliers start: 18 outliers final: 6 residues processed: 189 average time/residue: 0.2163 time to fit residues: 46.4365 Evaluate side-chains 110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0010 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 368 ASN B 374 HIS C 362 HIS D 330 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.233 Angle : 0.727 6.477 4680 Z= 0.373 Chirality : 0.050 0.134 528 Planarity : 0.006 0.050 594 Dihedral : 7.133 45.235 476 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.79 % Allowed : 19.70 % Favored : 76.52 % 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: -3.49 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.020 0.002 PHE E 346 TYR 0.014 0.002 TYR D 310 ARG 0.003 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.9531 (tptm) cc_final: 0.9128 (mmtm) REVERT: B 336 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8394 (tp40) REVERT: B 346 PHE cc_start: 0.8958 (m-80) cc_final: 0.7820 (p90) REVERT: B 358 ASP cc_start: 0.8685 (m-30) cc_final: 0.8463 (t0) REVERT: B 369 LYS cc_start: 0.8551 (mttt) cc_final: 0.8321 (ttmt) REVERT: C 310 TYR cc_start: 0.7778 (t80) cc_final: 0.7236 (t80) REVERT: C 336 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8065 (tp40) REVERT: C 346 PHE cc_start: 0.8839 (m-80) cc_final: 0.7824 (p90) REVERT: D 372 GLU cc_start: 0.8483 (tt0) cc_final: 0.8004 (mp0) REVERT: D 376 LEU cc_start: 0.8633 (tp) cc_final: 0.8337 (tt) REVERT: E 310 TYR cc_start: 0.7927 (t80) cc_final: 0.7387 (t80) REVERT: E 369 LYS cc_start: 0.8595 (mttt) cc_final: 0.8386 (ttpt) REVERT: E 372 GLU cc_start: 0.8710 (tt0) cc_final: 0.8330 (mp0) outliers start: 15 outliers final: 11 residues processed: 136 average time/residue: 0.1788 time to fit residues: 28.8335 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS F 336 GLN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3498 Z= 0.369 Angle : 0.806 10.557 4680 Z= 0.396 Chirality : 0.051 0.135 528 Planarity : 0.006 0.045 594 Dihedral : 6.674 45.948 468 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.79 % Allowed : 21.46 % Favored : 74.75 % 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: -3.24 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS C 330 PHE 0.014 0.001 PHE E 378 TYR 0.016 0.004 TYR A 310 ARG 0.003 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8274 (tp40) REVERT: B 345 ASP cc_start: 0.8867 (t0) cc_final: 0.8588 (t0) REVERT: B 346 PHE cc_start: 0.9007 (m-80) cc_final: 0.7895 (p90) REVERT: C 310 TYR cc_start: 0.7803 (t80) cc_final: 0.7298 (t80) REVERT: C 336 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8045 (tp40) REVERT: C 346 PHE cc_start: 0.8855 (m-80) cc_final: 0.7987 (p90) REVERT: D 372 GLU cc_start: 0.8660 (tt0) cc_final: 0.8171 (mp0) REVERT: E 372 GLU cc_start: 0.8780 (tt0) cc_final: 0.8425 (mp0) REVERT: E 376 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8430 (mt) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.1248 time to fit residues: 18.0932 Evaluate side-chains 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 368 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3498 Z= 0.161 Angle : 0.750 14.214 4680 Z= 0.336 Chirality : 0.049 0.129 528 Planarity : 0.004 0.047 594 Dihedral : 6.233 51.229 468 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.53 % Allowed : 23.99 % Favored : 73.48 % 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: -2.80 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.020 0.001 PHE D 378 TYR 0.014 0.002 TYR B 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8318 (mp0) REVERT: B 310 TYR cc_start: 0.7197 (t80) cc_final: 0.6718 (p90) REVERT: B 336 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8268 (tp40) REVERT: B 345 ASP cc_start: 0.8784 (t0) cc_final: 0.8566 (t0) REVERT: B 346 PHE cc_start: 0.8974 (m-80) cc_final: 0.7775 (p90) REVERT: C 310 TYR cc_start: 0.7619 (t80) cc_final: 0.7180 (t80) REVERT: C 336 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8057 (tp40) REVERT: C 346 PHE cc_start: 0.8846 (m-80) cc_final: 0.7938 (p90) REVERT: D 372 GLU cc_start: 0.8510 (tt0) cc_final: 0.8216 (mp0) REVERT: E 372 GLU cc_start: 0.8631 (tt0) cc_final: 0.8343 (mp0) outliers start: 10 outliers final: 9 residues processed: 112 average time/residue: 0.1280 time to fit residues: 18.1323 Evaluate side-chains 104 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 overall best weight: 7.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 374 HIS D 359 ASN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 3498 Z= 0.389 Angle : 0.831 14.692 4680 Z= 0.398 Chirality : 0.050 0.156 528 Planarity : 0.005 0.043 594 Dihedral : 6.683 48.778 468 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.28 % Allowed : 27.27 % Favored : 69.44 % 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: -2.92 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.023 0.002 PHE E 378 TYR 0.013 0.004 TYR E 310 ARG 0.005 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 310 TYR cc_start: 0.7449 (t80) cc_final: 0.6831 (p90) REVERT: B 336 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8293 (tp40) REVERT: B 345 ASP cc_start: 0.8796 (t0) cc_final: 0.8499 (t0) REVERT: B 346 PHE cc_start: 0.9036 (m-80) cc_final: 0.8020 (p90) REVERT: C 310 TYR cc_start: 0.7817 (t80) cc_final: 0.7482 (t80) REVERT: C 336 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8056 (tp40) REVERT: C 346 PHE cc_start: 0.8841 (m-80) cc_final: 0.8050 (p90) REVERT: D 311 LYS cc_start: 0.3462 (OUTLIER) cc_final: 0.3120 (pptt) REVERT: D 372 GLU cc_start: 0.8705 (tt0) cc_final: 0.8306 (mp0) REVERT: E 372 GLU cc_start: 0.8771 (tt0) cc_final: 0.8470 (mp0) REVERT: E 376 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8386 (mt) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.1127 time to fit residues: 15.8713 Evaluate side-chains 99 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL 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: 8.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3498 Z= 0.233 Angle : 0.829 15.202 4680 Z= 0.372 Chirality : 0.051 0.139 528 Planarity : 0.005 0.041 594 Dihedral : 6.418 51.113 468 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.79 % Allowed : 26.77 % Favored : 69.44 % 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: -2.69 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.011 0.001 PHE D 378 TYR 0.010 0.003 TYR B 310 ARG 0.002 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 310 TYR cc_start: 0.7135 (t80) cc_final: 0.6736 (p90) REVERT: B 336 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8319 (tp-100) REVERT: B 345 ASP cc_start: 0.8853 (t0) cc_final: 0.8521 (t0) REVERT: B 346 PHE cc_start: 0.9053 (m-80) cc_final: 0.7905 (p90) REVERT: C 310 TYR cc_start: 0.7596 (t80) cc_final: 0.7275 (t80) REVERT: C 336 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8030 (tp40) REVERT: C 346 PHE cc_start: 0.8833 (m-80) cc_final: 0.8036 (p90) REVERT: D 311 LYS cc_start: 0.3663 (OUTLIER) cc_final: 0.3338 (pptt) REVERT: D 372 GLU cc_start: 0.8657 (tt0) cc_final: 0.8373 (mp0) REVERT: E 372 GLU cc_start: 0.8698 (tt0) cc_final: 0.8418 (mp0) REVERT: E 376 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8260 (mt) REVERT: F 310 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: F 336 GLN cc_start: 0.8820 (tm130) cc_final: 0.8231 (pm20) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.1238 time to fit residues: 17.9550 Evaluate side-chains 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS F 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3498 Z= 0.224 Angle : 0.810 16.091 4680 Z= 0.367 Chirality : 0.050 0.138 528 Planarity : 0.005 0.039 594 Dihedral : 6.349 53.794 468 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.04 % Allowed : 26.26 % Favored : 69.70 % 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: -2.59 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.021 0.002 PHE E 378 TYR 0.010 0.003 TYR B 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8296 (mp0) REVERT: B 310 TYR cc_start: 0.7132 (t80) cc_final: 0.6704 (p90) REVERT: B 336 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8335 (tp-100) REVERT: B 345 ASP cc_start: 0.8873 (t0) cc_final: 0.8488 (t0) REVERT: B 346 PHE cc_start: 0.9038 (m-80) cc_final: 0.7877 (p90) REVERT: C 310 TYR cc_start: 0.7512 (t80) cc_final: 0.7169 (t80) REVERT: C 336 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8079 (tp40) REVERT: C 346 PHE cc_start: 0.8835 (m-80) cc_final: 0.8037 (p90) REVERT: D 311 LYS cc_start: 0.3646 (OUTLIER) cc_final: 0.3353 (pptt) REVERT: D 372 GLU cc_start: 0.8676 (tt0) cc_final: 0.8363 (mp0) REVERT: E 372 GLU cc_start: 0.8667 (tt0) cc_final: 0.8310 (mp0) REVERT: E 376 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8252 (mt) REVERT: F 310 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: F 311 LYS cc_start: 0.4256 (OUTLIER) cc_final: 0.3726 (pptt) REVERT: F 336 GLN cc_start: 0.8801 (tm130) cc_final: 0.8245 (pm20) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.1133 time to fit residues: 15.5180 Evaluate side-chains 110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS E 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3498 Z= 0.151 Angle : 0.824 16.863 4680 Z= 0.355 Chirality : 0.050 0.154 528 Planarity : 0.004 0.036 594 Dihedral : 6.150 57.897 468 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.03 % Allowed : 27.78 % Favored : 69.19 % 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 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.004 0.001 PHE B 346 TYR 0.010 0.001 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8264 (mp0) REVERT: B 310 TYR cc_start: 0.6809 (t80) cc_final: 0.6556 (p90) REVERT: B 345 ASP cc_start: 0.8865 (t0) cc_final: 0.8442 (t0) REVERT: B 346 PHE cc_start: 0.9032 (m-80) cc_final: 0.7796 (p90) REVERT: C 310 TYR cc_start: 0.7287 (t80) cc_final: 0.6941 (t80) REVERT: C 331 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8547 (tttt) REVERT: C 336 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8149 (tp40) REVERT: C 346 PHE cc_start: 0.8801 (m-80) cc_final: 0.7980 (p90) REVERT: E 372 GLU cc_start: 0.8601 (tt0) cc_final: 0.8248 (mp0) REVERT: F 336 GLN cc_start: 0.8790 (tm130) cc_final: 0.8237 (pm20) outliers start: 12 outliers final: 10 residues processed: 110 average time/residue: 0.1185 time to fit residues: 16.7866 Evaluate side-chains 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3498 Z= 0.171 Angle : 0.784 13.446 4680 Z= 0.351 Chirality : 0.049 0.131 528 Planarity : 0.004 0.034 594 Dihedral : 6.124 59.332 468 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.78 % Allowed : 27.27 % Favored : 69.95 % 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: -2.10 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.022 0.002 PHE E 378 TYR 0.007 0.002 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.9015 (m-40) cc_final: 0.8510 (m110) REVERT: A 372 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8265 (mp0) REVERT: B 345 ASP cc_start: 0.8878 (t0) cc_final: 0.8508 (t0) REVERT: B 346 PHE cc_start: 0.9013 (m-80) cc_final: 0.7808 (p90) REVERT: C 310 TYR cc_start: 0.7294 (t80) cc_final: 0.7009 (t80) REVERT: C 336 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8188 (tp40) REVERT: C 346 PHE cc_start: 0.8817 (m-80) cc_final: 0.7936 (p90) REVERT: E 372 GLU cc_start: 0.8556 (tt0) cc_final: 0.8168 (mp0) REVERT: F 314 ASP cc_start: 0.7838 (t0) cc_final: 0.7573 (t0) REVERT: F 336 GLN cc_start: 0.8783 (tm130) cc_final: 0.8241 (pm20) REVERT: F 372 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8276 (mp0) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.1159 time to fit residues: 15.8828 Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 0.2980 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3498 Z= 0.272 Angle : 0.857 14.862 4680 Z= 0.388 Chirality : 0.049 0.135 528 Planarity : 0.004 0.033 594 Dihedral : 6.408 56.618 468 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.54 % Allowed : 28.28 % Favored : 68.18 % 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: -2.18 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.007 0.001 PHE A 346 TYR 0.011 0.003 TYR B 310 ARG 0.003 0.001 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.9023 (m-40) cc_final: 0.8543 (m110) REVERT: A 372 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8360 (mp0) REVERT: A 378 PHE cc_start: 0.8449 (t80) cc_final: 0.8039 (t80) REVERT: B 345 ASP cc_start: 0.8842 (t0) cc_final: 0.8479 (t0) REVERT: B 346 PHE cc_start: 0.9049 (m-80) cc_final: 0.7944 (p90) REVERT: C 310 TYR cc_start: 0.7513 (t80) cc_final: 0.7174 (t80) REVERT: C 336 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8125 (tp40) REVERT: C 346 PHE cc_start: 0.8800 (m-80) cc_final: 0.7973 (p90) REVERT: E 372 GLU cc_start: 0.8633 (tt0) cc_final: 0.8311 (mp0) REVERT: F 310 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: F 311 LYS cc_start: 0.4052 (OUTLIER) cc_final: 0.3578 (pptt) REVERT: F 336 GLN cc_start: 0.8826 (tm130) cc_final: 0.8281 (pm20) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.1198 time to fit residues: 15.5883 Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.116707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.098563 restraints weight = 8488.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.100582 restraints weight = 4342.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.102028 restraints weight = 2844.603| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.7206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3498 Z= 0.355 Angle : 0.895 13.591 4680 Z= 0.416 Chirality : 0.051 0.155 528 Planarity : 0.006 0.038 594 Dihedral : 6.684 52.677 468 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.54 % Allowed : 27.78 % Favored : 68.69 % 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: -2.49 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.026 0.002 PHE E 378 TYR 0.010 0.003 TYR A 310 ARG 0.008 0.001 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1136.06 seconds wall clock time: 21 minutes 50.58 seconds (1310.58 seconds total)