Starting phenix.real_space_refine on Tue Mar 3 11:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql3_14062/03_2026/7ql3_14062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql3_14062/03_2026/7ql3_14062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql3_14062/03_2026/7ql3_14062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql3_14062/03_2026/7ql3_14062.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql3_14062/03_2026/7ql3_14062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql3_14062/03_2026/7ql3_14062.cif" } resolution = 3.32 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3246 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 0.75, per 1000 atoms: 0.23 Number of scatterers: 3246 At special positions: 0 Unit cell: (95.79, 111.6, 35.34, 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 606 8.00 N 588 7.00 C 2046 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: 0.22 Conformation dependent library (CDL) restraints added in 133.7 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 310 removed outlier: 6.734A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.758A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 3.525A pdb=" N LEU A 325 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.623A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.521A pdb=" N GLN A 336 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL B 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.682A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 361 removed outlier: 6.581A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 371 Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 377 removed outlier: 6.599A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.609A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.707A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 3.582A pdb=" N LEU D 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.694A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 339 removed outlier: 6.528A pdb=" N GLN D 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL E 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.591A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 359 through 361 removed outlier: 6.580A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 368 through 371 removed outlier: 6.623A pdb=" N ASN D 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ILE F 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 374 through 377 removed outlier: 6.658A pdb=" N HIS D 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR F 377 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 57 hydrogen bonds defined for protein. 171 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: 0.30 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 879 1.33 - 1.45: 446 1.45 - 1.57: 1969 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3300 Sorted by residual: bond pdb=" CA LYS C 331 " pdb=" C LYS C 331 " ideal model delta sigma weight residual 1.532 1.550 -0.018 6.50e-03 2.37e+04 7.90e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.30e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.68e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.30e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.21e+00 ... (remaining 3295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 3767 2.85 - 5.70: 618 5.70 - 8.55: 26 8.55 - 11.40: 4 11.40 - 14.25: 1 Bond angle restraints: 4416 Sorted by residual: angle pdb=" N GLY A 323 " pdb=" CA GLY A 323 " pdb=" C GLY A 323 " ideal model delta sigma weight residual 111.14 125.39 -14.25 1.80e+00 3.09e-01 6.27e+01 angle pdb=" N SER D 356 " pdb=" CA SER D 356 " pdb=" C SER D 356 " ideal model delta sigma weight residual 111.03 117.92 -6.89 1.11e+00 8.12e-01 3.85e+01 angle pdb=" N SER A 356 " pdb=" CA SER A 356 " pdb=" C SER A 356 " ideal model delta sigma weight residual 111.03 117.88 -6.85 1.11e+00 8.12e-01 3.81e+01 angle pdb=" N SER A 324 " pdb=" CA SER A 324 " pdb=" C SER A 324 " ideal model delta sigma weight residual 108.02 97.08 10.94 1.78e+00 3.16e-01 3.78e+01 angle pdb=" N GLY D 323 " pdb=" CA GLY D 323 " pdb=" C GLY D 323 " ideal model delta sigma weight residual 110.56 120.42 -9.86 1.66e+00 3.63e-01 3.53e+01 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 1791 14.12 - 28.25: 167 28.25 - 42.37: 34 42.37 - 56.50: 6 56.50 - 70.62: 6 Dihedral angle restraints: 2004 sinusoidal: 834 harmonic: 1170 Sorted by residual: dihedral pdb=" CA GLY A 323 " pdb=" C GLY A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta harmonic sigma weight residual 180.00 149.74 30.26 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA CYS A 322 " pdb=" C CYS A 322 " pdb=" N GLY A 323 " pdb=" CA GLY A 323 " ideal model delta harmonic sigma weight residual -180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA CYS C 322 " pdb=" C CYS C 322 " pdb=" N GLY C 323 " pdb=" CA GLY C 323 " ideal model delta harmonic sigma weight residual 180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 275 0.080 - 0.160: 166 0.160 - 0.240: 36 0.240 - 0.320: 11 0.320 - 0.400: 10 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA GLN A 351 " pdb=" N GLN A 351 " pdb=" C GLN A 351 " pdb=" CB GLN A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN D 351 " pdb=" N GLN D 351 " pdb=" C GLN D 351 " pdb=" CB GLN D 351 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+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 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 495 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.129 2.00e-02 2.50e+03 6.75e-02 9.11e+01 pdb=" CG TYR C 310 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.122 2.00e-02 2.50e+03 6.55e-02 8.59e+01 pdb=" CG TYR F 310 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.105 2.00e-02 2.50e+03 5.57e-02 6.20e+01 pdb=" CG TYR D 310 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.080 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1389 2.97 - 3.45: 2648 3.45 - 3.94: 4714 3.94 - 4.42: 4640 4.42 - 4.90: 9852 Nonbonded interactions: 23243 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.489 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.502 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.524 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.526 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.530 3.040 ... (remaining 23238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.970 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 0.035 3300 Z= 0.750 Angle : 2.010 14.251 4416 Z= 1.337 Chirality : 0.111 0.400 498 Planarity : 0.011 0.067 558 Dihedral : 12.269 70.619 1260 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 2.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.47 (0.31), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 349 TYR 0.129 0.041 TYR C 310 PHE 0.037 0.011 PHE B 346 HIS 0.009 0.002 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.01145 ( 3300) covalent geometry : angle 2.01014 ( 4416) hydrogen bonds : bond 0.13391 ( 57) hydrogen bonds : angle 7.09551 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.141 Fit side-chains REVERT: B 352 SER cc_start: 0.9293 (t) cc_final: 0.8913 (m) REVERT: E 352 SER cc_start: 0.9144 (t) cc_final: 0.8810 (m) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1019 time to fit residues: 8.8224 Evaluate side-chains 50 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 330 HIS B 374 HIS C 374 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS E 330 HIS E 374 HIS F 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.139928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.130445 restraints weight = 3770.629| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.02 r_work: 0.4078 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3300 Z= 0.192 Angle : 0.867 8.058 4416 Z= 0.437 Chirality : 0.055 0.151 498 Planarity : 0.005 0.038 558 Dihedral : 7.091 20.866 432 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.08 % Allowed : 8.87 % Favored : 90.05 % 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: -2.80 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.022 0.005 TYR C 310 PHE 0.012 0.002 PHE F 346 HIS 0.007 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 3300) covalent geometry : angle 0.86725 ( 4416) hydrogen bonds : bond 0.03319 ( 57) hydrogen bonds : angle 6.02869 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.109 Fit side-chains REVERT: B 343 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8236 (mttt) REVERT: B 352 SER cc_start: 0.9113 (t) cc_final: 0.8634 (m) REVERT: B 375 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8570 (ttmt) REVERT: C 343 LYS cc_start: 0.8501 (tttt) cc_final: 0.8252 (mttp) REVERT: D 343 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8385 (mtmm) REVERT: D 348 ASP cc_start: 0.8692 (t0) cc_final: 0.8416 (t0) REVERT: E 343 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8338 (mtpt) REVERT: E 375 LYS cc_start: 0.8373 (mttt) cc_final: 0.8172 (ttmt) REVERT: F 343 LYS cc_start: 0.8435 (tttt) cc_final: 0.8182 (mtmt) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.1046 time to fit residues: 6.1666 Evaluate side-chains 46 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 overall best weight: 5.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS D 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.135023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.125620 restraints weight = 3874.642| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.03 r_work: 0.4028 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3300 Z= 0.241 Angle : 0.805 7.116 4416 Z= 0.412 Chirality : 0.055 0.155 498 Planarity : 0.006 0.051 558 Dihedral : 6.679 19.238 432 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.69 % Allowed : 9.68 % Favored : 87.63 % 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: -2.68 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.024 0.006 TYR C 310 PHE 0.015 0.003 PHE F 346 HIS 0.010 0.002 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 3300) covalent geometry : angle 0.80501 ( 4416) hydrogen bonds : bond 0.02905 ( 57) hydrogen bonds : angle 5.06587 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.135 Fit side-chains REVERT: B 352 SER cc_start: 0.9076 (t) cc_final: 0.8778 (m) REVERT: C 352 SER cc_start: 0.9185 (t) cc_final: 0.8882 (m) REVERT: D 343 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8256 (mtmt) REVERT: E 343 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8316 (mttp) outliers start: 10 outliers final: 4 residues processed: 44 average time/residue: 0.0951 time to fit residues: 4.8186 Evaluate side-chains 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.140120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.130555 restraints weight = 3939.232| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.12 r_work: 0.4065 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3300 Z= 0.158 Angle : 0.683 7.268 4416 Z= 0.343 Chirality : 0.050 0.134 498 Planarity : 0.006 0.048 558 Dihedral : 5.963 17.214 432 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.42 % Allowed : 11.56 % Favored : 86.02 % 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: -2.72 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.016 0.004 TYR C 310 PHE 0.008 0.002 PHE D 346 HIS 0.006 0.002 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3300) covalent geometry : angle 0.68287 ( 4416) hydrogen bonds : bond 0.01990 ( 57) hydrogen bonds : angle 4.57088 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.124 Fit side-chains REVERT: B 352 SER cc_start: 0.8945 (t) cc_final: 0.8674 (m) REVERT: C 352 SER cc_start: 0.9087 (t) cc_final: 0.8819 (m) REVERT: D 343 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8285 (mtmt) REVERT: F 352 SER cc_start: 0.9066 (t) cc_final: 0.8803 (m) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.0758 time to fit residues: 3.8937 Evaluate side-chains 44 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.130574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.121729 restraints weight = 3955.339| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.97 r_work: 0.3970 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3300 Z= 0.286 Angle : 0.796 7.539 4416 Z= 0.414 Chirality : 0.055 0.147 498 Planarity : 0.007 0.054 558 Dihedral : 6.437 17.527 432 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.96 % Allowed : 12.90 % Favored : 84.14 % 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: -2.71 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.026 0.006 TYR C 310 PHE 0.015 0.003 PHE F 346 HIS 0.009 0.002 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 3300) covalent geometry : angle 0.79570 ( 4416) hydrogen bonds : bond 0.02916 ( 57) hydrogen bonds : angle 4.50358 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 352 SER cc_start: 0.9028 (t) cc_final: 0.8793 (m) REVERT: C 352 SER cc_start: 0.9182 (t) cc_final: 0.8973 (m) REVERT: C 375 LYS cc_start: 0.8178 (mttt) cc_final: 0.7849 (tttp) REVERT: D 343 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8083 (mttp) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.0830 time to fit residues: 5.3452 Evaluate side-chains 49 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN F 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.134017 restraints weight = 3893.894| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.15 r_work: 0.4120 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3300 Z= 0.100 Angle : 0.616 6.166 4416 Z= 0.307 Chirality : 0.047 0.122 498 Planarity : 0.006 0.053 558 Dihedral : 5.229 15.278 432 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.88 % Allowed : 16.13 % Favored : 81.99 % 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: -2.68 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.006 0.001 TYR C 310 PHE 0.004 0.001 PHE A 378 HIS 0.003 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3300) covalent geometry : angle 0.61642 ( 4416) hydrogen bonds : bond 0.01397 ( 57) hydrogen bonds : angle 4.37199 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.130 Fit side-chains REVERT: B 352 SER cc_start: 0.8783 (t) cc_final: 0.8510 (m) REVERT: C 375 LYS cc_start: 0.8169 (mttt) cc_final: 0.7764 (tttp) REVERT: D 343 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8107 (mttp) REVERT: D 352 SER cc_start: 0.8789 (t) cc_final: 0.8570 (m) REVERT: F 375 LYS cc_start: 0.8069 (mttt) cc_final: 0.7713 (tttm) outliers start: 7 outliers final: 1 residues processed: 50 average time/residue: 0.0711 time to fit residues: 4.3401 Evaluate side-chains 46 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 HIS ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.128305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.119257 restraints weight = 4057.188| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.01 r_work: 0.3927 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 3300 Z= 0.319 Angle : 0.818 9.583 4416 Z= 0.422 Chirality : 0.056 0.153 498 Planarity : 0.007 0.062 558 Dihedral : 6.281 17.146 432 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.34 % Allowed : 16.67 % Favored : 81.99 % 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: -2.75 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.028 0.007 TYR C 310 PHE 0.016 0.003 PHE F 346 HIS 0.009 0.002 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 3300) covalent geometry : angle 0.81841 ( 4416) hydrogen bonds : bond 0.03136 ( 57) hydrogen bonds : angle 4.54932 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.136 Fit side-chains REVERT: A 317 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7529 (mttt) REVERT: A 340 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7661 (mptt) REVERT: A 375 LYS cc_start: 0.8006 (mttt) cc_final: 0.7509 (tttm) REVERT: C 375 LYS cc_start: 0.8256 (mttt) cc_final: 0.7931 (tttm) REVERT: D 343 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8060 (mttp) REVERT: F 375 LYS cc_start: 0.8282 (mttt) cc_final: 0.7927 (tttm) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.1025 time to fit residues: 5.5696 Evaluate side-chains 43 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.133883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.124276 restraints weight = 4140.811| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.22 r_work: 0.3978 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3300 Z= 0.177 Angle : 0.729 8.807 4416 Z= 0.364 Chirality : 0.051 0.143 498 Planarity : 0.007 0.060 558 Dihedral : 5.706 15.399 432 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.15 % Allowed : 15.86 % Favored : 81.99 % 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: -2.79 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.015 0.003 TYR C 310 PHE 0.007 0.002 PHE F 346 HIS 0.005 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3300) covalent geometry : angle 0.72940 ( 4416) hydrogen bonds : bond 0.02130 ( 57) hydrogen bonds : angle 4.44693 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.136 Fit side-chains REVERT: C 375 LYS cc_start: 0.8193 (mttt) cc_final: 0.7878 (tttp) REVERT: D 343 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8039 (mttp) REVERT: F 375 LYS cc_start: 0.8217 (mttt) cc_final: 0.7840 (tttm) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.0701 time to fit residues: 3.9706 Evaluate side-chains 45 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.0170 chunk 0 optimal weight: 0.8980 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.147099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.137309 restraints weight = 4034.907| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.17 r_work: 0.4075 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3300 Z= 0.105 Angle : 0.687 8.493 4416 Z= 0.327 Chirality : 0.049 0.128 498 Planarity : 0.006 0.055 558 Dihedral : 4.946 13.823 432 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.81 % Allowed : 16.67 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.68 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 349 TYR 0.007 0.001 TYR D 310 PHE 0.004 0.001 PHE A 378 HIS 0.002 0.000 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3300) covalent geometry : angle 0.68675 ( 4416) hydrogen bonds : bond 0.01390 ( 57) hydrogen bonds : angle 4.13178 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.138 Fit side-chains REVERT: A 331 LYS cc_start: 0.8398 (mttt) cc_final: 0.8191 (mttt) REVERT: C 375 LYS cc_start: 0.8279 (mttt) cc_final: 0.7855 (tttp) REVERT: D 343 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8027 (mttp) REVERT: F 375 LYS cc_start: 0.8152 (mttt) cc_final: 0.7723 (tttm) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.0821 time to fit residues: 4.1666 Evaluate side-chains 42 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 0.0170 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 overall best weight: 3.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.135974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.126249 restraints weight = 4050.695| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.20 r_work: 0.4009 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3300 Z= 0.162 Angle : 0.744 9.894 4416 Z= 0.359 Chirality : 0.051 0.140 498 Planarity : 0.007 0.060 558 Dihedral : 5.243 14.598 432 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.08 % Allowed : 16.40 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.66 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 349 TYR 0.015 0.003 TYR C 310 PHE 0.007 0.002 PHE F 346 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3300) covalent geometry : angle 0.74436 ( 4416) hydrogen bonds : bond 0.01998 ( 57) hydrogen bonds : angle 4.15447 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.077 Fit side-chains REVERT: C 375 LYS cc_start: 0.8298 (mttt) cc_final: 0.7943 (tttp) REVERT: D 343 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8044 (mttp) REVERT: F 375 LYS cc_start: 0.8218 (mttt) cc_final: 0.7835 (tttm) outliers start: 4 outliers final: 4 residues processed: 40 average time/residue: 0.0721 time to fit residues: 3.4726 Evaluate side-chains 41 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.134367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.124673 restraints weight = 4103.943| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.23 r_work: 0.3985 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3300 Z= 0.182 Angle : 0.756 9.602 4416 Z= 0.369 Chirality : 0.052 0.139 498 Planarity : 0.007 0.063 558 Dihedral : 5.401 15.194 432 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.61 % Allowed : 16.13 % Favored : 82.26 % 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: -2.71 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.017 0.004 TYR C 310 PHE 0.007 0.002 PHE F 346 HIS 0.005 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 3300) covalent geometry : angle 0.75593 ( 4416) hydrogen bonds : bond 0.02150 ( 57) hydrogen bonds : angle 4.18343 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 853.49 seconds wall clock time: 15 minutes 21.70 seconds (921.70 seconds total)