Starting phenix.real_space_refine on Thu Sep 10 19:48:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pva_71887/09_2026/9pva_71887_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pva_71887/09_2026/9pva_71887.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 { model { file = "/net/cci-nas-00/data/ceres_data/9pva_71887/09_2026/9pva_71887_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pva_71887/09_2026/9pva_71887_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pva_71887/09_2026/9pva_71887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pva_71887/09_2026/9pva_71887.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 936 2.51 5 N 246 2.21 5 O 255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1443 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 202 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 195 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 0.41, per 1000 atoms: 0.28 Number of scatterers: 1443 At special positions: 0 Unit cell: (92.4852, 51.6584, 39.9936, 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 255 8.00 N 246 7.00 C 936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS B 322 " distance=2.21 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS E 322 " distance=2.18 Simple disulfide: pdb=" SG CYS G 322 " - pdb=" SG CYS H 322 " distance=2.31 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: 0.06 Conformation dependent library (CDL) restraints added in 82.4 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 342 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 309 removed outlier: 5.507A pdb=" N VAL A 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL D 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL D 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL G 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 308 " --> pdb=" O VAL G 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 316 removed outlier: 7.348A pdb=" N LEU A 315 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER G 316 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 329 removed outlier: 7.195A pdb=" N SER A 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N ASN D 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY A 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N HIS D 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS D 322 " --> pdb=" O GLY G 323 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N LEU G 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N SER D 324 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ASN G 327 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY D 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N HIS G 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE D 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 310 removed outlier: 6.267A pdb=" N VAL B 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL E 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.735A pdb=" N VAL B 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL E 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.533A pdb=" N LYS B 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE E 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR B 319 " --> pdb=" O PHE E 320 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N CYS E 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS B 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS E 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N PHE H 320 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR E 319 " --> pdb=" O PHE H 320 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS H 322 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LYS E 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 325 through 329 removed outlier: 7.253A pdb=" N GLY E 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE H 328 " --> pdb=" O ASN E 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.197A pdb=" N VAL C 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL F 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL F 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL I 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE F 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 5 hydrogen bonds defined for protein. 15 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: 0.09 Time building geometry restraints manager: 0.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 432 1.35 - 1.46: 314 1.46 - 1.58: 718 1.58 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 1470 Sorted by residual: bond pdb=" CB ASN A 327 " pdb=" CG ASN A 327 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.89e+00 bond pdb=" CB ASN D 327 " pdb=" CG ASN D 327 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.83e+00 bond pdb=" CB ASN G 327 " pdb=" CG ASN G 327 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.82e+00 bond pdb=" CA ASN G 327 " pdb=" CB ASN G 327 " ideal model delta sigma weight residual 1.535 1.572 -0.036 2.09e-02 2.29e+03 3.05e+00 bond pdb=" CA ASN D 327 " pdb=" CB ASN D 327 " ideal model delta sigma weight residual 1.535 1.572 -0.036 2.09e-02 2.29e+03 3.03e+00 ... (remaining 1465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 1796 1.66 - 3.31: 130 3.31 - 4.97: 39 4.97 - 6.62: 12 6.62 - 8.28: 6 Bond angle restraints: 1983 Sorted by residual: angle pdb=" CA ASN D 327 " pdb=" CB ASN D 327 " pdb=" CG ASN D 327 " ideal model delta sigma weight residual 112.60 116.56 -3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" CA ASN A 327 " pdb=" CB ASN A 327 " pdb=" CG ASN A 327 " ideal model delta sigma weight residual 112.60 116.53 -3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA ASN G 327 " pdb=" CB ASN G 327 " pdb=" CG ASN G 327 " ideal model delta sigma weight residual 112.60 116.50 -3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" C TYR A 310 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " ideal model delta sigma weight residual 121.80 130.08 -8.28 2.44e+00 1.68e-01 1.15e+01 angle pdb=" C TYR G 310 " pdb=" N LYS G 311 " pdb=" CA LYS G 311 " ideal model delta sigma weight residual 121.80 130.06 -8.26 2.44e+00 1.68e-01 1.15e+01 ... (remaining 1978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.75: 663 11.75 - 23.50: 149 23.50 - 35.25: 34 35.25 - 47.00: 24 47.00 - 58.75: 9 Dihedral angle restraints: 879 sinusoidal: 351 harmonic: 528 Sorted by residual: dihedral pdb=" CA TYR D 310 " pdb=" C TYR D 310 " pdb=" N LYS D 311 " pdb=" CA LYS D 311 " ideal model delta harmonic sigma weight residual 180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR G 310 " pdb=" C TYR G 310 " pdb=" N LYS G 311 " pdb=" CA LYS G 311 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR A 310 " pdb=" C TYR A 310 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " ideal model delta harmonic sigma weight residual 180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 876 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.036: 116 0.036 - 0.071: 51 0.071 - 0.107: 37 0.107 - 0.142: 27 0.142 - 0.177: 6 Chirality restraints: 237 Sorted by residual: chirality pdb=" CA ILE A 328 " pdb=" N ILE A 328 " pdb=" C ILE A 328 " pdb=" CB ILE A 328 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ILE G 328 " pdb=" N ILE G 328 " pdb=" C ILE G 328 " pdb=" CB ILE G 328 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA ILE D 328 " pdb=" N ILE D 328 " pdb=" C ILE D 328 " pdb=" CB ILE D 328 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 234 not shown) Planarity restraints: 240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 311 " -0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO H 312 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 312 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 312 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 311 " -0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO B 312 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 312 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 312 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 311 " -0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO E 312 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO E 312 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 312 " -0.047 5.00e-02 4.00e+02 ... (remaining 237 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 434 2.88 - 3.39: 1138 3.39 - 3.89: 2166 3.89 - 4.40: 2082 4.40 - 4.90: 3553 Nonbonded interactions: 9373 Sorted by model distance: nonbonded pdb=" ND2 ASN A 327 " pdb=" OH TYR C 310 " model vdw 2.379 3.120 nonbonded pdb=" O SER A 324 " pdb=" OG SER D 324 " model vdw 2.430 3.040 nonbonded pdb=" O SER D 324 " pdb=" OG SER G 324 " model vdw 2.473 3.040 nonbonded pdb=" CG2 ILE B 328 " pdb=" CD1 ILE E 328 " model vdw 2.515 3.880 nonbonded pdb=" OD2 ASP E 314 " pdb=" OH TYR G 310 " model vdw 2.552 3.040 ... (remaining 9368 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 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 0.920 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.700 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.283 1473 Z= 0.541 Angle : 1.242 10.172 1989 Z= 0.653 Chirality : 0.067 0.177 237 Planarity : 0.011 0.085 240 Dihedral : 16.139 58.752 528 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.58 % Allowed : 23.98 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.54), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.006 TYR G 310 PHE 0.010 0.003 PHE E 320 HIS 0.002 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.26 ( 1470) covalent geometry : angle 1.18047 / 0.63 ( 1983) SS BOND : bond 0.21056 / 10.58 ( 3) SS BOND : angle 7.14957 / 4.04 ( 6) hydrogen bonds : bond 0.33281 / 16.73 ( 5) hydrogen bonds : angle 18.92935 / 11.49 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.038 Fit side-chains REVERT: A 311 LYS cc_start: 0.6027 (mttt) cc_final: 0.4495 (mmmt) REVERT: A 324 SER cc_start: 0.6743 (t) cc_final: 0.6485 (p) REVERT: B 311 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7344 (ptpp) REVERT: B 315 LEU cc_start: 0.7805 (tt) cc_final: 0.7284 (mp) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.0458 time to fit residues: 2.0253 Evaluate side-chains 27 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.294617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.267320 restraints weight = 1574.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.267320 restraints weight = 1668.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.267320 restraints weight = 1668.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.267320 restraints weight = 1668.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.267320 restraints weight = 1668.084| |-----------------------------------------------------------------------------| r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1473 Z= 0.194 Angle : 0.798 7.071 1989 Z= 0.416 Chirality : 0.056 0.156 237 Planarity : 0.009 0.067 240 Dihedral : 7.202 31.012 189 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 9.36 % Allowed : 20.47 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR D 310 PHE 0.027 0.004 PHE B 320 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 ( 1470) covalent geometry : angle 0.79750 / 0.42 ( 1983) SS BOND : bond 0.00666 / 0.34 ( 3) SS BOND : angle 0.97756 / 0.54 ( 6) hydrogen bonds : bond 0.05969 / 3.00 ( 5) hydrogen bonds : angle 13.25986 / 8.11 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 22 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7408 (mttt) cc_final: 0.5629 (mmtm) REVERT: B 311 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7519 (ptpp) REVERT: G 317 LYS cc_start: 0.8761 (mppt) cc_final: 0.8063 (mttt) outliers start: 16 outliers final: 7 residues processed: 32 average time/residue: 0.0531 time to fit residues: 1.8662 Evaluate side-chains 29 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.032 ------------------------------------------------------------------------------- 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 307 GLN Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 308 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.299813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.273301 restraints weight = 1574.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.273298 restraints weight = 1629.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.273298 restraints weight = 1630.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.273298 restraints weight = 1630.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.273298 restraints weight = 1630.155| |-----------------------------------------------------------------------------| r_work (final): 0.4973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1473 Z= 0.154 Angle : 0.711 7.584 1989 Z= 0.362 Chirality : 0.054 0.177 237 Planarity : 0.006 0.050 240 Dihedral : 6.633 30.575 189 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 9.94 % Allowed : 21.05 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.57), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR D 310 PHE 0.016 0.003 PHE B 320 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 1470) covalent geometry : angle 0.71160 / 0.36 ( 1983) SS BOND : bond 0.00391 / 0.20 ( 3) SS BOND : angle 0.55590 / 0.29 ( 6) hydrogen bonds : bond 0.04572 / 2.69 ( 5) hydrogen bonds : angle 11.99510 / 7.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 20 time to evaluate : 0.042 Fit side-chains REVERT: A 311 LYS cc_start: 0.7463 (mttt) cc_final: 0.5830 (mmtm) REVERT: B 311 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7486 (ptpp) REVERT: G 317 LYS cc_start: 0.8828 (mppt) cc_final: 0.8216 (mttp) outliers start: 17 outliers final: 12 residues processed: 31 average time/residue: 0.0858 time to fit residues: 2.9179 Evaluate side-chains 31 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 328 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.322284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.270881 restraints weight = 1681.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.270629 restraints weight = 1966.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.270629 restraints weight = 2115.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.270629 restraints weight = 2115.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.270629 restraints weight = 2115.441| |-----------------------------------------------------------------------------| r_work (final): 0.4951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1473 Z= 0.162 Angle : 0.738 7.793 1989 Z= 0.375 Chirality : 0.055 0.175 237 Planarity : 0.005 0.043 240 Dihedral : 6.520 29.312 189 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 8.77 % Allowed : 23.98 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.57), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR D 310 PHE 0.016 0.003 PHE B 320 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 1470) covalent geometry : angle 0.73860 / 0.38 ( 1983) SS BOND : bond 0.00428 / 0.22 ( 3) SS BOND : angle 0.46601 / 0.25 ( 6) hydrogen bonds : bond 0.04988 / 3.02 ( 5) hydrogen bonds : angle 11.12329 / 7.12 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.060 Fit side-chains REVERT: B 311 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7460 (ptpp) REVERT: E 308 ILE cc_start: 0.7183 (mp) cc_final: 0.6939 (mm) REVERT: G 317 LYS cc_start: 0.8828 (mppt) cc_final: 0.8200 (mttp) outliers start: 15 outliers final: 11 residues processed: 33 average time/residue: 0.1030 time to fit residues: 3.7183 Evaluate side-chains 31 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 328 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.326153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.5067 r_free = 0.5067 target = 0.273542 restraints weight = 1627.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.273334 restraints weight = 1862.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.273334 restraints weight = 2014.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.273334 restraints weight = 2014.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.273334 restraints weight = 2014.221| |-----------------------------------------------------------------------------| r_work (final): 0.4960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1473 Z= 0.124 Angle : 0.665 7.616 1989 Z= 0.335 Chirality : 0.055 0.165 237 Planarity : 0.004 0.044 240 Dihedral : 6.085 26.244 189 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 9.94 % Allowed : 24.56 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.57), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.002 TYR C 310 PHE 0.012 0.002 PHE B 320 HIS 0.003 0.001 HIS H 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 1470) covalent geometry : angle 0.66602 / 0.34 ( 1983) SS BOND : bond 0.00279 / 0.14 ( 3) SS BOND : angle 0.36160 / 0.19 ( 6) hydrogen bonds : bond 0.04612 / 2.83 ( 5) hydrogen bonds : angle 10.97491 / 7.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.064 Fit side-chains REVERT: B 311 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7504 (ptpp) REVERT: C 310 TYR cc_start: 0.5888 (t80) cc_final: 0.5651 (t80) REVERT: G 317 LYS cc_start: 0.8818 (mppt) cc_final: 0.8207 (mttp) outliers start: 17 outliers final: 9 residues processed: 35 average time/residue: 0.0653 time to fit residues: 2.5823 Evaluate side-chains 29 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.319150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.266382 restraints weight = 1600.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.266074 restraints weight = 1805.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.266045 restraints weight = 1935.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.265970 restraints weight = 1993.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.265970 restraints weight = 2056.721| |-----------------------------------------------------------------------------| r_work (final): 0.4934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1473 Z= 0.159 Angle : 0.742 7.502 1989 Z= 0.373 Chirality : 0.055 0.173 237 Planarity : 0.006 0.070 240 Dihedral : 6.343 29.643 189 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 9.36 % Allowed : 29.82 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.58), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR D 310 PHE 0.016 0.003 PHE B 320 HIS 0.003 0.001 HIS G 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 1470) covalent geometry : angle 0.74269 / 0.37 ( 1983) SS BOND : bond 0.00365 / 0.19 ( 3) SS BOND : angle 0.42773 / 0.22 ( 6) hydrogen bonds : bond 0.04800 / 2.95 ( 5) hydrogen bonds : angle 10.82705 / 7.05 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 17 time to evaluate : 0.067 Fit side-chains REVERT: B 311 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7505 (ptpp) REVERT: E 308 ILE cc_start: 0.7172 (mp) cc_final: 0.6939 (mm) REVERT: G 317 LYS cc_start: 0.8866 (mppt) cc_final: 0.8250 (mttp) outliers start: 16 outliers final: 12 residues processed: 30 average time/residue: 0.0590 time to fit residues: 2.0449 Evaluate side-chains 30 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 328 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.320588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.5059 r_free = 0.5059 target = 0.266368 restraints weight = 1582.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.266289 restraints weight = 1763.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.266276 restraints weight = 1841.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.266276 restraints weight = 1860.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.266276 restraints weight = 1860.618| |-----------------------------------------------------------------------------| r_work (final): 0.4946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1473 Z= 0.149 Angle : 0.717 7.098 1989 Z= 0.360 Chirality : 0.055 0.174 237 Planarity : 0.006 0.060 240 Dihedral : 6.235 28.890 189 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 9.94 % Allowed : 30.41 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.53 (0.57), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR F 310 PHE 0.014 0.003 PHE B 320 HIS 0.004 0.001 HIS G 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 1470) covalent geometry : angle 0.71763 / 0.36 ( 1983) SS BOND : bond 0.00327 / 0.17 ( 3) SS BOND : angle 0.41394 / 0.21 ( 6) hydrogen bonds : bond 0.04915 / 3.00 ( 5) hydrogen bonds : angle 10.81400 / 7.04 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 16 time to evaluate : 0.065 Fit side-chains REVERT: B 311 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7467 (ptpp) outliers start: 17 outliers final: 11 residues processed: 30 average time/residue: 0.0597 time to fit residues: 2.0709 Evaluate side-chains 28 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 16 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 328 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.330475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.5135 r_free = 0.5135 target = 0.280575 restraints weight = 1532.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.279839 restraints weight = 1866.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.279839 restraints weight = 2008.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.279839 restraints weight = 2007.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.279839 restraints weight = 2007.918| |-----------------------------------------------------------------------------| r_work (final): 0.5036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1473 Z= 0.105 Angle : 0.627 6.340 1989 Z= 0.311 Chirality : 0.054 0.169 237 Planarity : 0.005 0.052 240 Dihedral : 5.471 19.913 189 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 6.43 % Allowed : 31.58 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.34 (0.58), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR D 310 PHE 0.004 0.001 PHE B 320 HIS 0.004 0.001 HIS H 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 ( 1470) covalent geometry : angle 0.62814 / 0.31 ( 1983) SS BOND : bond 0.00184 / 0.10 ( 3) SS BOND : angle 0.23293 / 0.13 ( 6) hydrogen bonds : bond 0.04660 / 2.92 ( 5) hydrogen bonds : angle 10.45487 / 6.91 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.061 Fit side-chains REVERT: B 311 LYS cc_start: 0.7763 (mtmt) cc_final: 0.7378 (ptpp) outliers start: 11 outliers final: 7 residues processed: 31 average time/residue: 0.0551 time to fit residues: 1.9675 Evaluate side-chains 24 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.068 ------------------------------------------------------------------------------- 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 306 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.327650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 140)---------------| | r_work = 0.5124 r_free = 0.5124 target = 0.274703 restraints weight = 1555.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.274395 restraints weight = 1691.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.274395 restraints weight = 1831.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.274395 restraints weight = 1831.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.274395 restraints weight = 1831.149| |-----------------------------------------------------------------------------| r_work (final): 0.5010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1473 Z= 0.110 Angle : 0.659 5.861 1989 Z= 0.328 Chirality : 0.054 0.166 237 Planarity : 0.008 0.081 240 Dihedral : 5.667 23.891 189 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.26 % Allowed : 32.75 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.34 (0.58), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR F 310 PHE 0.010 0.002 PHE B 320 HIS 0.004 0.001 HIS H 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 1470) covalent geometry : angle 0.66024 / 0.33 ( 1983) SS BOND : bond 0.00218 / 0.11 ( 3) SS BOND : angle 0.30152 / 0.15 ( 6) hydrogen bonds : bond 0.04883 / 3.08 ( 5) hydrogen bonds : angle 10.29422 / 6.83 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.062 Fit side-chains REVERT: B 311 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7446 (ptpp) outliers start: 9 outliers final: 8 residues processed: 26 average time/residue: 0.0601 time to fit residues: 1.8084 Evaluate side-chains 25 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.062 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.327876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.5107 r_free = 0.5107 target = 0.275831 restraints weight = 1615.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.275256 restraints weight = 1898.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.275256 restraints weight = 2118.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.275256 restraints weight = 2118.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.275256 restraints weight = 2118.063| |-----------------------------------------------------------------------------| r_work (final): 0.5008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1473 Z= 0.117 Angle : 0.664 5.930 1989 Z= 0.333 Chirality : 0.054 0.156 237 Planarity : 0.008 0.080 240 Dihedral : 5.762 24.930 189 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.26 % Allowed : 33.33 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.59), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR F 310 PHE 0.010 0.002 PHE B 320 HIS 0.005 0.001 HIS H 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 1470) covalent geometry : angle 0.66478 / 0.33 ( 1983) SS BOND : bond 0.00217 / 0.11 ( 3) SS BOND : angle 0.28772 / 0.15 ( 6) hydrogen bonds : bond 0.06245 / 3.94 ( 5) hydrogen bonds : angle 10.29928 / 6.75 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.035 Fit side-chains REVERT: B 311 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7457 (ptpp) outliers start: 9 outliers final: 8 residues processed: 24 average time/residue: 0.0669 time to fit residues: 1.8167 Evaluate side-chains 24 residues out of total 171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.063 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.316966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.5029 r_free = 0.5029 target = 0.260520 restraints weight = 1603.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.260241 restraints weight = 1852.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.260241 restraints weight = 1991.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.260241 restraints weight = 1991.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.260241 restraints weight = 1991.814| |-----------------------------------------------------------------------------| r_work (final): 0.4917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 1473 Z= 0.198 Angle : 0.785 7.043 1989 Z= 0.399 Chirality : 0.056 0.163 237 Planarity : 0.008 0.080 240 Dihedral : 6.774 32.579 189 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 5.26 % Allowed : 33.33 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.57), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR F 310 PHE 0.022 0.004 PHE B 320 HIS 0.005 0.001 HIS G 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 1470) covalent geometry : angle 0.78572 / 0.40 ( 1983) SS BOND : bond 0.00357 / 0.19 ( 3) SS BOND : angle 0.50156 / 0.25 ( 6) hydrogen bonds : bond 0.06113 / 3.79 ( 5) hydrogen bonds : angle 10.96324 / 7.04 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 596.95 seconds wall clock time: 11 minutes 8.36 seconds (668.36 seconds total)