Starting phenix.real_space_refine on Tue Feb 3 16:45:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s4f_54563/02_2026/9s4f_54563.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s4f_54563/02_2026/9s4f_54563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s4f_54563/02_2026/9s4f_54563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s4f_54563/02_2026/9s4f_54563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s4f_54563/02_2026/9s4f_54563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s4f_54563/02_2026/9s4f_54563.map" } resolution = 4.2 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 10 5.16 5 C 3228 2.51 5 N 825 2.21 5 O 947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5012 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1062 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "B" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1116 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "C" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1461 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 167} Chain: "D" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 147} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.33, per 1000 atoms: 0.27 Number of scatterers: 5012 At special positions: 0 Unit cell: (96.2539, 87.3231, 103.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 10 16.00 O 947 8.00 N 825 7.00 C 3228 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 317.6 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1174 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 50.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.766A pdb=" N LYS A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.817A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.915A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.965A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 removed outlier: 3.527A pdb=" N PHE A 117 " --> pdb=" O PRO A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.933A pdb=" N ALA B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 77 Processing helix chain 'B' and resid 80 through 85 removed outlier: 4.253A pdb=" N THR B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.889A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 removed outlier: 7.407A pdb=" N LYS B 120 " --> pdb=" O HIS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.553A pdb=" N ILE C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 471 through 487 Proline residue: C 483 - end of helix Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 364 through 370 removed outlier: 3.524A pdb=" N TYR D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 482 Processing sheet with id=AA1, first strand: chain 'C' and resid 349 through 352 removed outlier: 3.909A pdb=" N TYR C 421 " --> pdb=" O ASP C 416 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP C 416 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 414 " --> pdb=" O TYR C 423 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG C 425 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU C 412 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.241A pdb=" N TYR C 453 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 437 " --> pdb=" O TYR C 453 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 455 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 435 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU C 442 " --> pdb=" O TRP C 396 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP C 396 " --> pdb=" O GLU C 442 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL C 401 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 350 through 352 removed outlier: 3.590A pdb=" N TYR D 423 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 414 " --> pdb=" O TYR D 423 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG D 425 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU D 412 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 354 through 357 removed outlier: 5.072A pdb=" N HIS D 448 " --> pdb=" O TYR D 443 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR D 443 " --> pdb=" O HIS D 448 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASP D 450 " --> pdb=" O ILE D 441 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE D 441 " --> pdb=" O ASP D 450 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP D 452 " --> pdb=" O SER D 439 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER D 439 " --> pdb=" O ASP D 452 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 454 " --> pdb=" O ILE D 437 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU D 442 " --> pdb=" O TRP D 396 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TRP D 396 " --> pdb=" O GLU D 442 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL D 401 " --> pdb=" O LEU D 408 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 735 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: 0.50 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 2138 1.39 - 1.56: 2989 1.56 - 1.72: 0 1.72 - 1.89: 17 1.89 - 2.05: 8 Bond restraints: 5152 Sorted by residual: bond pdb=" N HIS B 92 " pdb=" CA HIS B 92 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 5.99e+00 bond pdb=" N HIS A 87 " pdb=" CA HIS A 87 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.79e+00 bond pdb=" CG HIS B 92 " pdb=" CD2 HIS B 92 " ideal model delta sigma weight residual 1.354 1.334 0.020 1.10e-02 8.26e+03 3.28e+00 bond pdb=" N GLU C 328 " pdb=" CA GLU C 328 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N GLU D 328 " pdb=" CA GLU D 328 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 5147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 6883 1.50 - 3.00: 114 3.00 - 4.51: 29 4.51 - 6.01: 2 6.01 - 7.51: 1 Bond angle restraints: 7029 Sorted by residual: angle pdb=" C HIS B 92 " pdb=" CA HIS B 92 " pdb=" CB HIS B 92 " ideal model delta sigma weight residual 110.79 106.45 4.34 1.66e+00 3.63e-01 6.83e+00 angle pdb=" C PRO B 36 " pdb=" N TRP B 37 " pdb=" CA TRP B 37 " ideal model delta sigma weight residual 123.91 128.03 -4.12 1.66e+00 3.63e-01 6.17e+00 angle pdb=" CA HIS B 92 " pdb=" C HIS B 92 " pdb=" O HIS B 92 " ideal model delta sigma weight residual 120.55 118.31 2.24 1.06e+00 8.90e-01 4.48e+00 angle pdb=" N HIS B 92 " pdb=" CA HIS B 92 " pdb=" C HIS B 92 " ideal model delta sigma weight residual 111.28 113.52 -2.24 1.09e+00 8.42e-01 4.21e+00 angle pdb=" CA PHE B 122 " pdb=" C PHE B 122 " pdb=" N THR B 123 " ideal model delta sigma weight residual 114.76 116.77 -2.01 1.14e+00 7.69e-01 3.11e+00 ... (remaining 7024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2775 17.97 - 35.94: 209 35.94 - 53.90: 24 53.90 - 71.87: 11 71.87 - 89.84: 7 Dihedral angle restraints: 3026 sinusoidal: 1206 harmonic: 1820 Sorted by residual: dihedral pdb=" CA GLN C 364 " pdb=" C GLN C 364 " pdb=" N PHE C 365 " pdb=" CA PHE C 365 " ideal model delta harmonic sigma weight residual 180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CAD HEM A 201 " pdb=" CBD HEM A 201 " pdb=" CGD HEM A 201 " pdb=" O2D HEM A 201 " ideal model delta sinusoidal sigma weight residual -180.00 -90.16 -89.84 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2D HEM A 201 " pdb=" C3D HEM A 201 " pdb=" CAD HEM A 201 " pdb=" CBD HEM A 201 " ideal model delta sinusoidal sigma weight residual -180.00 -91.69 -88.31 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 3023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 451 0.027 - 0.054: 203 0.054 - 0.081: 47 0.081 - 0.108: 42 0.108 - 0.135: 15 Chirality restraints: 758 Sorted by residual: chirality pdb=" CA ILE C 352 " pdb=" N ILE C 352 " pdb=" C ILE C 352 " pdb=" CB ILE C 352 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE C 378 " pdb=" N ILE C 378 " pdb=" C ILE C 378 " pdb=" CB ILE C 378 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE C 437 " pdb=" N ILE C 437 " pdb=" C ILE C 437 " pdb=" CB ILE C 437 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 755 not shown) Planarity restraints: 896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 36 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C PRO B 36 " 0.030 2.00e-02 2.50e+03 pdb=" O PRO B 36 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP B 37 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 35 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 36 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 99 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 100 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.018 5.00e-02 4.00e+02 ... (remaining 893 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2092 2.92 - 3.41: 5366 3.41 - 3.91: 8011 3.91 - 4.40: 9105 4.40 - 4.90: 14444 Nonbonded interactions: 39018 Sorted by model distance: nonbonded pdb=" O ASN D 348 " pdb=" OD1 ASN D 348 " model vdw 2.425 3.040 nonbonded pdb=" OE2 GLU B 43 " pdb=" OG SER B 44 " model vdw 2.452 3.040 nonbonded pdb=" O ASN D 465 " pdb=" OD1 ASN D 465 " model vdw 2.459 3.040 nonbonded pdb=" O ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.464 3.040 nonbonded pdb=" O ASP C 353 " pdb=" OD1 ASP C 353 " model vdw 2.467 3.040 ... (remaining 39013 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 'C' and resid 328 through 484) selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.940 Find NCS groups from input model: 0.040 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.004 0.179 5154 Z= 0.136 Angle : 0.535 7.511 7029 Z= 0.283 Chirality : 0.039 0.135 758 Planarity : 0.003 0.037 896 Dihedral : 13.622 89.840 1852 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.21 (0.36), residues: 611 helix: 1.31 (0.33), residues: 270 sheet: -0.73 (0.49), residues: 121 loop : -0.71 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 425 TYR 0.009 0.001 TYR D 423 PHE 0.010 0.001 PHE A 117 TRP 0.007 0.001 TRP B 37 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5152) covalent geometry : angle 0.53547 ( 7029) hydrogen bonds : bond 0.17278 ( 261) hydrogen bonds : angle 7.50344 ( 735) Misc. bond : bond 0.16810 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8734 (m-30) cc_final: 0.8252 (m-30) REVERT: A 29 LEU cc_start: 0.9603 (tp) cc_final: 0.9274 (tp) REVERT: A 66 LEU cc_start: 0.9587 (mt) cc_final: 0.9349 (mt) REVERT: A 85 ASP cc_start: 0.8846 (t70) cc_final: 0.7959 (t0) REVERT: B 12 THR cc_start: 0.9101 (t) cc_final: 0.8775 (t) REVERT: B 84 THR cc_start: 0.8439 (p) cc_final: 0.7878 (p) REVERT: B 85 PHE cc_start: 0.8699 (m-80) cc_final: 0.8470 (m-10) REVERT: B 94 ASP cc_start: 0.8511 (t70) cc_final: 0.8026 (t70) REVERT: B 105 LEU cc_start: 0.8992 (tt) cc_final: 0.8454 (mt) REVERT: B 127 GLN cc_start: 0.8968 (tt0) cc_final: 0.8359 (tm-30) REVERT: C 349 TRP cc_start: 0.8275 (p-90) cc_final: 0.8018 (p-90) REVERT: C 362 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8371 (mp0) REVERT: C 365 PHE cc_start: 0.8068 (t80) cc_final: 0.7830 (t80) REVERT: D 390 LEU cc_start: 0.9170 (mt) cc_final: 0.8940 (mp) REVERT: D 435 VAL cc_start: 0.9084 (m) cc_final: 0.8852 (m) REVERT: D 443 TYR cc_start: 0.7890 (p90) cc_final: 0.7562 (p90) REVERT: D 478 GLN cc_start: 0.9330 (tt0) cc_final: 0.9126 (pt0) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1156 time to fit residues: 28.0614 Evaluate side-chains 123 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.042696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.032141 restraints weight = 37761.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.033238 restraints weight = 25909.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.034064 restraints weight = 19740.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.034708 restraints weight = 16038.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035176 restraints weight = 13626.324| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5154 Z= 0.145 Angle : 0.674 10.492 7029 Z= 0.335 Chirality : 0.045 0.197 758 Planarity : 0.005 0.060 896 Dihedral : 8.573 89.954 679 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.19 % Allowed : 3.57 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.06 (0.35), residues: 611 helix: 1.14 (0.32), residues: 277 sheet: -0.93 (0.47), residues: 123 loop : -0.96 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 425 TYR 0.013 0.001 TYR B 35 PHE 0.017 0.002 PHE B 103 TRP 0.037 0.003 TRP B 37 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5152) covalent geometry : angle 0.67435 ( 7029) hydrogen bonds : bond 0.03689 ( 261) hydrogen bonds : angle 5.42622 ( 735) Misc. bond : bond 0.01093 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8895 (m-30) cc_final: 0.8595 (m-30) REVERT: A 29 LEU cc_start: 0.9581 (tp) cc_final: 0.9311 (tp) REVERT: A 39 THR cc_start: 0.9662 (p) cc_final: 0.9236 (p) REVERT: A 85 ASP cc_start: 0.9494 (t70) cc_final: 0.8998 (t0) REVERT: A 94 ASP cc_start: 0.9491 (m-30) cc_final: 0.9134 (p0) REVERT: A 127 LYS cc_start: 0.9703 (mmmm) cc_final: 0.9260 (mmmm) REVERT: B 15 TRP cc_start: 0.9289 (t60) cc_final: 0.8962 (t60) REVERT: B 75 LEU cc_start: 0.9742 (tp) cc_final: 0.9396 (tp) REVERT: B 84 THR cc_start: 0.8423 (p) cc_final: 0.7661 (p) REVERT: B 85 PHE cc_start: 0.9689 (m-80) cc_final: 0.8979 (m-10) REVERT: B 108 ASN cc_start: 0.9584 (m110) cc_final: 0.9256 (m110) REVERT: C 349 TRP cc_start: 0.9386 (p-90) cc_final: 0.8856 (p-90) REVERT: C 363 ARG cc_start: 0.9207 (ttp-110) cc_final: 0.8812 (ptm-80) REVERT: C 425 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.8015 (mmm-85) REVERT: C 473 GLU cc_start: 0.9431 (tm-30) cc_final: 0.9231 (pp20) REVERT: D 355 GLN cc_start: 0.9465 (mm-40) cc_final: 0.9210 (tm-30) REVERT: D 356 MET cc_start: 0.8567 (mmp) cc_final: 0.8088 (mmm) REVERT: D 364 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8323 (tm-30) REVERT: D 421 TYR cc_start: 0.9356 (m-10) cc_final: 0.8897 (m-80) REVERT: D 443 TYR cc_start: 0.8972 (p90) cc_final: 0.8607 (p90) REVERT: D 460 GLN cc_start: 0.9223 (mp10) cc_final: 0.8999 (mp10) REVERT: D 478 GLN cc_start: 0.9518 (tt0) cc_final: 0.9193 (pt0) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.1025 time to fit residues: 18.3090 Evaluate side-chains 103 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.032070 restraints weight = 38177.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.033195 restraints weight = 25381.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.034049 restraints weight = 19020.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.034689 restraints weight = 15263.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035175 restraints weight = 12877.160| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5154 Z= 0.122 Angle : 0.622 8.199 7029 Z= 0.307 Chirality : 0.043 0.144 758 Planarity : 0.005 0.047 896 Dihedral : 7.880 86.019 679 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.18 (0.34), residues: 611 helix: 1.02 (0.32), residues: 275 sheet: -0.82 (0.47), residues: 121 loop : -1.09 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 425 TYR 0.014 0.001 TYR B 35 PHE 0.013 0.002 PHE A 98 TRP 0.022 0.002 TRP A 14 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5152) covalent geometry : angle 0.62191 ( 7029) hydrogen bonds : bond 0.03055 ( 261) hydrogen bonds : angle 4.95571 ( 735) Misc. bond : bond 0.00941 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8938 (m-30) cc_final: 0.8649 (m-30) REVERT: A 29 LEU cc_start: 0.9465 (tp) cc_final: 0.9137 (tp) REVERT: A 64 ASP cc_start: 0.9516 (t0) cc_final: 0.8946 (m-30) REVERT: A 78 ASN cc_start: 0.9758 (m-40) cc_final: 0.9281 (m110) REVERT: A 85 ASP cc_start: 0.9487 (t70) cc_final: 0.8954 (t0) REVERT: A 94 ASP cc_start: 0.9526 (m-30) cc_final: 0.9216 (p0) REVERT: A 98 PHE cc_start: 0.9254 (m-80) cc_final: 0.9013 (m-80) REVERT: A 127 LYS cc_start: 0.9709 (mmmm) cc_final: 0.9248 (mmmm) REVERT: B 15 TRP cc_start: 0.9283 (t-100) cc_final: 0.8939 (t60) REVERT: B 84 THR cc_start: 0.8503 (p) cc_final: 0.7944 (p) REVERT: B 85 PHE cc_start: 0.9686 (m-80) cc_final: 0.9053 (m-10) REVERT: B 108 ASN cc_start: 0.9611 (m110) cc_final: 0.9215 (m110) REVERT: B 131 GLN cc_start: 0.9706 (mm-40) cc_final: 0.9169 (mm-40) REVERT: B 139 ASN cc_start: 0.9606 (t0) cc_final: 0.9117 (m110) REVERT: C 349 TRP cc_start: 0.9229 (p-90) cc_final: 0.8840 (p-90) REVERT: C 355 GLN cc_start: 0.9458 (tt0) cc_final: 0.9042 (tp-100) REVERT: C 356 MET cc_start: 0.8729 (tpt) cc_final: 0.7851 (mmm) REVERT: C 363 ARG cc_start: 0.9226 (ttp-110) cc_final: 0.8664 (ptm-80) REVERT: C 365 PHE cc_start: 0.8839 (t80) cc_final: 0.8440 (t80) REVERT: C 425 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8230 (mmm-85) REVERT: C 472 GLU cc_start: 0.9568 (pp20) cc_final: 0.9362 (pm20) REVERT: D 356 MET cc_start: 0.8296 (mmp) cc_final: 0.7692 (mmm) REVERT: D 408 LEU cc_start: 0.9191 (tp) cc_final: 0.8970 (tp) REVERT: D 421 TYR cc_start: 0.9407 (m-10) cc_final: 0.8969 (m-10) REVERT: D 443 TYR cc_start: 0.8874 (p90) cc_final: 0.8355 (p90) REVERT: D 460 GLN cc_start: 0.9302 (mp10) cc_final: 0.9049 (mp10) REVERT: D 478 GLN cc_start: 0.9500 (tt0) cc_final: 0.9181 (pt0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0911 time to fit residues: 15.9190 Evaluate side-chains 97 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS C 448 HIS D 448 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.038889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.029314 restraints weight = 40308.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.030427 restraints weight = 25901.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.031236 restraints weight = 18978.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.031816 restraints weight = 15046.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.032298 restraints weight = 12634.464| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 5154 Z= 0.193 Angle : 0.659 5.730 7029 Z= 0.332 Chirality : 0.043 0.156 758 Planarity : 0.005 0.055 896 Dihedral : 8.263 88.582 679 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.34 (0.34), residues: 611 helix: 0.77 (0.32), residues: 278 sheet: -1.09 (0.45), residues: 124 loop : -0.85 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 425 TYR 0.011 0.002 TYR B 35 PHE 0.011 0.002 PHE A 98 TRP 0.023 0.002 TRP A 14 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 5152) covalent geometry : angle 0.65871 ( 7029) hydrogen bonds : bond 0.03040 ( 261) hydrogen bonds : angle 5.09791 ( 735) Misc. bond : bond 0.10123 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9651 (tp) cc_final: 0.9307 (tp) REVERT: A 64 ASP cc_start: 0.9554 (t0) cc_final: 0.8956 (m-30) REVERT: A 98 PHE cc_start: 0.9319 (m-80) cc_final: 0.9055 (m-80) REVERT: A 127 LYS cc_start: 0.9727 (mmmm) cc_final: 0.9333 (mmmm) REVERT: A 141 ARG cc_start: 0.8437 (mmp-170) cc_final: 0.8164 (mmm160) REVERT: B 15 TRP cc_start: 0.9500 (t-100) cc_final: 0.9061 (t60) REVERT: C 349 TRP cc_start: 0.9293 (p-90) cc_final: 0.8656 (p-90) REVERT: C 355 GLN cc_start: 0.9535 (tt0) cc_final: 0.9138 (tp-100) REVERT: C 356 MET cc_start: 0.9135 (tpt) cc_final: 0.8628 (tpp) REVERT: C 365 PHE cc_start: 0.8985 (t80) cc_final: 0.8446 (t80) REVERT: C 458 PHE cc_start: 0.9401 (m-10) cc_final: 0.8633 (m-10) REVERT: D 460 GLN cc_start: 0.9323 (mp10) cc_final: 0.9108 (mp10) REVERT: D 478 GLN cc_start: 0.9519 (tt0) cc_final: 0.9209 (mt0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0994 time to fit residues: 13.6778 Evaluate side-chains 85 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 0.0010 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 HIS ** D 355 GLN ** 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 = 0.2945 r_free = 0.2945 target = 0.039003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.029430 restraints weight = 40554.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.030507 restraints weight = 26237.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.031326 restraints weight = 19360.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.031905 restraints weight = 15345.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.032319 restraints weight = 12954.497| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 5154 Z= 0.137 Angle : 0.637 5.864 7029 Z= 0.320 Chirality : 0.043 0.172 758 Planarity : 0.005 0.058 896 Dihedral : 8.165 87.736 679 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.34 (0.34), residues: 611 helix: 0.65 (0.32), residues: 278 sheet: -1.01 (0.47), residues: 122 loop : -0.72 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 104 TYR 0.008 0.001 TYR C 415 PHE 0.014 0.002 PHE B 71 TRP 0.023 0.002 TRP A 14 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5152) covalent geometry : angle 0.63725 ( 7029) hydrogen bonds : bond 0.02832 ( 261) hydrogen bonds : angle 4.89323 ( 735) Misc. bond : bond 0.07870 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9648 (tp) cc_final: 0.9366 (tp) REVERT: A 64 ASP cc_start: 0.9555 (t0) cc_final: 0.9034 (m-30) REVERT: A 98 PHE cc_start: 0.9357 (m-80) cc_final: 0.9096 (m-80) REVERT: A 141 ARG cc_start: 0.8391 (mmp-170) cc_final: 0.8130 (mmm160) REVERT: B 15 TRP cc_start: 0.9507 (t-100) cc_final: 0.9108 (t60) REVERT: B 127 GLN cc_start: 0.9528 (tt0) cc_final: 0.9173 (tm-30) REVERT: C 349 TRP cc_start: 0.9275 (p-90) cc_final: 0.8612 (p-90) REVERT: C 355 GLN cc_start: 0.9545 (tt0) cc_final: 0.9139 (tp-100) REVERT: C 356 MET cc_start: 0.9240 (tpt) cc_final: 0.8497 (mmm) REVERT: C 365 PHE cc_start: 0.8832 (t80) cc_final: 0.8349 (t80) REVERT: C 425 ARG cc_start: 0.9252 (mmm-85) cc_final: 0.8933 (mmm-85) REVERT: D 356 MET cc_start: 0.8342 (mmm) cc_final: 0.8014 (mmp) REVERT: D 364 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8037 (tm-30) REVERT: D 408 LEU cc_start: 0.9248 (tp) cc_final: 0.8907 (tp) REVERT: D 460 GLN cc_start: 0.9321 (mp10) cc_final: 0.9084 (mp10) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0992 time to fit residues: 13.0724 Evaluate side-chains 88 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 45 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS C 448 HIS D 344 HIS ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.038444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.028880 restraints weight = 41381.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.029972 restraints weight = 26731.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.030787 restraints weight = 19704.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.031390 restraints weight = 15652.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.031832 restraints weight = 13128.501| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 5154 Z= 0.149 Angle : 0.647 5.686 7029 Z= 0.325 Chirality : 0.044 0.173 758 Planarity : 0.005 0.059 896 Dihedral : 7.846 84.193 679 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.24 (0.34), residues: 611 helix: 0.57 (0.31), residues: 277 sheet: -0.93 (0.49), residues: 121 loop : -0.43 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 104 TYR 0.007 0.001 TYR C 415 PHE 0.012 0.002 PHE B 71 TRP 0.027 0.002 TRP A 14 HIS 0.010 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5152) covalent geometry : angle 0.64653 ( 7029) hydrogen bonds : bond 0.02775 ( 261) hydrogen bonds : angle 4.97104 ( 735) Misc. bond : bond 0.09969 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9661 (tp) cc_final: 0.9368 (tp) REVERT: A 64 ASP cc_start: 0.9569 (t0) cc_final: 0.9083 (m-30) REVERT: A 98 PHE cc_start: 0.9369 (m-80) cc_final: 0.9078 (m-80) REVERT: A 141 ARG cc_start: 0.8377 (mmp-170) cc_final: 0.8110 (mmm160) REVERT: B 127 GLN cc_start: 0.9526 (tt0) cc_final: 0.9317 (tt0) REVERT: B 131 GLN cc_start: 0.9721 (mm-40) cc_final: 0.9202 (mm-40) REVERT: C 349 TRP cc_start: 0.9276 (p-90) cc_final: 0.8630 (p-90) REVERT: C 355 GLN cc_start: 0.9539 (tt0) cc_final: 0.9118 (tp40) REVERT: C 365 PHE cc_start: 0.8812 (t80) cc_final: 0.8343 (t80) REVERT: C 425 ARG cc_start: 0.9203 (mmm-85) cc_final: 0.8685 (mmm-85) REVERT: D 356 MET cc_start: 0.8399 (mmm) cc_final: 0.7989 (mmm) REVERT: D 364 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8053 (tm-30) REVERT: D 408 LEU cc_start: 0.9314 (tp) cc_final: 0.8993 (tp) REVERT: D 460 GLN cc_start: 0.9333 (mp10) cc_final: 0.9051 (mp10) REVERT: D 478 GLN cc_start: 0.9540 (tt0) cc_final: 0.9234 (mt0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0965 time to fit residues: 12.4514 Evaluate side-chains 81 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.4980 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 HIS ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.039860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.029912 restraints weight = 39956.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031055 restraints weight = 25525.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.031912 restraints weight = 18891.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032525 restraints weight = 15038.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.033035 restraints weight = 12642.956| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 5154 Z= 0.124 Angle : 0.689 12.266 7029 Z= 0.341 Chirality : 0.045 0.173 758 Planarity : 0.005 0.058 896 Dihedral : 7.423 84.283 679 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.25 (0.34), residues: 611 helix: 0.48 (0.32), residues: 273 sheet: -0.79 (0.48), residues: 121 loop : -0.40 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 92 TYR 0.008 0.001 TYR C 495 PHE 0.015 0.002 PHE B 45 TRP 0.027 0.002 TRP A 14 HIS 0.007 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5152) covalent geometry : angle 0.68862 ( 7029) hydrogen bonds : bond 0.02850 ( 261) hydrogen bonds : angle 4.88784 ( 735) Misc. bond : bond 0.07161 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9633 (tp) cc_final: 0.9289 (tp) REVERT: A 32 MET cc_start: 0.9202 (tpt) cc_final: 0.8952 (tpp) REVERT: A 54 GLN cc_start: 0.8728 (tt0) cc_final: 0.8376 (tt0) REVERT: A 64 ASP cc_start: 0.9580 (t0) cc_final: 0.9137 (m-30) REVERT: A 98 PHE cc_start: 0.9381 (m-80) cc_final: 0.9086 (m-80) REVERT: A 141 ARG cc_start: 0.8385 (mmp-170) cc_final: 0.8068 (mmm160) REVERT: B 15 TRP cc_start: 0.9478 (t-100) cc_final: 0.9146 (t60) REVERT: B 80 ASN cc_start: 0.9401 (t0) cc_final: 0.8900 (p0) REVERT: B 104 ARG cc_start: 0.9518 (ttp80) cc_final: 0.9097 (ptt-90) REVERT: B 127 GLN cc_start: 0.9544 (tt0) cc_final: 0.9223 (tt0) REVERT: B 131 GLN cc_start: 0.9617 (mm-40) cc_final: 0.9117 (mm-40) REVERT: B 132 LYS cc_start: 0.9570 (pttp) cc_final: 0.9327 (pptt) REVERT: C 349 TRP cc_start: 0.9292 (p-90) cc_final: 0.8655 (p-90) REVERT: C 356 MET cc_start: 0.8935 (mmp) cc_final: 0.8682 (mmm) REVERT: C 363 ARG cc_start: 0.9271 (ptp-110) cc_final: 0.8629 (ptm-80) REVERT: C 365 PHE cc_start: 0.8780 (t80) cc_final: 0.8576 (t80) REVERT: D 356 MET cc_start: 0.8316 (mmm) cc_final: 0.7826 (mmm) REVERT: D 364 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8078 (tm-30) REVERT: D 408 LEU cc_start: 0.9237 (tp) cc_final: 0.8901 (tp) REVERT: D 460 GLN cc_start: 0.9403 (mp10) cc_final: 0.9171 (mp10) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0876 time to fit residues: 11.8586 Evaluate side-chains 84 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 HIS ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.039717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029906 restraints weight = 39568.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.031061 restraints weight = 25358.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.031915 restraints weight = 18579.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.032550 restraints weight = 14745.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.033018 restraints weight = 12349.661| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 5154 Z= 0.120 Angle : 0.683 12.705 7029 Z= 0.334 Chirality : 0.045 0.173 758 Planarity : 0.005 0.070 896 Dihedral : 7.314 83.817 679 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.18 (0.34), residues: 611 helix: 0.49 (0.31), residues: 272 sheet: -0.60 (0.49), residues: 121 loop : -0.38 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 425 TYR 0.007 0.001 TYR C 415 PHE 0.012 0.002 PHE B 45 TRP 0.027 0.002 TRP A 14 HIS 0.006 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5152) covalent geometry : angle 0.68302 ( 7029) hydrogen bonds : bond 0.03004 ( 261) hydrogen bonds : angle 4.85801 ( 735) Misc. bond : bond 0.12462 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9617 (tp) cc_final: 0.9278 (tp) REVERT: A 54 GLN cc_start: 0.8744 (tt0) cc_final: 0.8381 (tt0) REVERT: A 64 ASP cc_start: 0.9585 (t0) cc_final: 0.9141 (m-30) REVERT: A 98 PHE cc_start: 0.9358 (m-80) cc_final: 0.8966 (m-80) REVERT: A 141 ARG cc_start: 0.8399 (mmp-170) cc_final: 0.8052 (mmm160) REVERT: B 79 ASP cc_start: 0.9034 (p0) cc_final: 0.8772 (p0) REVERT: B 80 ASN cc_start: 0.9468 (t0) cc_final: 0.8924 (p0) REVERT: B 85 PHE cc_start: 0.9616 (m-10) cc_final: 0.9395 (m-10) REVERT: B 104 ARG cc_start: 0.9519 (ttp80) cc_final: 0.9084 (ptt-90) REVERT: B 127 GLN cc_start: 0.9531 (tt0) cc_final: 0.9283 (tt0) REVERT: B 131 GLN cc_start: 0.9494 (mm-40) cc_final: 0.9183 (mm-40) REVERT: B 132 LYS cc_start: 0.9567 (pttp) cc_final: 0.9343 (pptt) REVERT: C 349 TRP cc_start: 0.9276 (p-90) cc_final: 0.8646 (p-90) REVERT: C 363 ARG cc_start: 0.9236 (ptp-110) cc_final: 0.8597 (ptm-80) REVERT: C 365 PHE cc_start: 0.8727 (t80) cc_final: 0.8357 (t80) REVERT: D 356 MET cc_start: 0.8319 (mmm) cc_final: 0.7852 (mmm) REVERT: D 364 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8041 (tm-30) REVERT: D 408 LEU cc_start: 0.9188 (tp) cc_final: 0.8864 (tp) REVERT: D 460 GLN cc_start: 0.9403 (mp10) cc_final: 0.9193 (mp10) REVERT: D 478 GLN cc_start: 0.9559 (tt0) cc_final: 0.9252 (mt0) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0732 time to fit residues: 9.4230 Evaluate side-chains 84 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.039710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.029851 restraints weight = 40255.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.031022 restraints weight = 25834.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.031870 restraints weight = 18884.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032467 restraints weight = 14993.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.032966 restraints weight = 12597.462| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 5154 Z= 0.124 Angle : 0.706 12.193 7029 Z= 0.345 Chirality : 0.045 0.174 758 Planarity : 0.005 0.067 896 Dihedral : 7.405 83.905 679 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.11 (0.34), residues: 611 helix: 0.58 (0.32), residues: 272 sheet: -0.65 (0.49), residues: 121 loop : -0.35 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 425 TYR 0.007 0.001 TYR C 415 PHE 0.010 0.001 PHE B 45 TRP 0.028 0.002 TRP A 14 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5152) covalent geometry : angle 0.70615 ( 7029) hydrogen bonds : bond 0.03128 ( 261) hydrogen bonds : angle 5.09400 ( 735) Misc. bond : bond 0.09022 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9599 (tp) cc_final: 0.9272 (tp) REVERT: A 32 MET cc_start: 0.9258 (tpt) cc_final: 0.9000 (tpt) REVERT: A 54 GLN cc_start: 0.8754 (tt0) cc_final: 0.8377 (tt0) REVERT: A 64 ASP cc_start: 0.9592 (t0) cc_final: 0.9138 (m-30) REVERT: A 74 ASP cc_start: 0.9259 (m-30) cc_final: 0.8684 (p0) REVERT: A 98 PHE cc_start: 0.9365 (m-80) cc_final: 0.8948 (m-80) REVERT: A 141 ARG cc_start: 0.8424 (mmp-170) cc_final: 0.8078 (mmm160) REVERT: B 79 ASP cc_start: 0.9022 (p0) cc_final: 0.8764 (p0) REVERT: B 80 ASN cc_start: 0.9469 (t0) cc_final: 0.8917 (p0) REVERT: B 85 PHE cc_start: 0.9638 (m-10) cc_final: 0.9435 (m-10) REVERT: B 104 ARG cc_start: 0.9512 (ttp80) cc_final: 0.9069 (ptt-90) REVERT: B 131 GLN cc_start: 0.9459 (mm-40) cc_final: 0.9225 (mm-40) REVERT: B 132 LYS cc_start: 0.9563 (pttp) cc_final: 0.9342 (pptt) REVERT: C 349 TRP cc_start: 0.9283 (p-90) cc_final: 0.8639 (p-90) REVERT: C 363 ARG cc_start: 0.9246 (ptp-110) cc_final: 0.8953 (tmm-80) REVERT: D 356 MET cc_start: 0.8376 (mmm) cc_final: 0.7954 (mmm) REVERT: D 364 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8015 (tm-30) REVERT: D 408 LEU cc_start: 0.9201 (tp) cc_final: 0.8890 (tp) REVERT: D 478 GLN cc_start: 0.9591 (tt0) cc_final: 0.9237 (mt0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0734 time to fit residues: 9.1289 Evaluate side-chains 83 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN ** D 355 GLN ** 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 = 0.2959 r_free = 0.2959 target = 0.039021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.029368 restraints weight = 39912.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.030481 restraints weight = 25782.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.031321 restraints weight = 18967.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.031945 restraints weight = 15017.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032402 restraints weight = 12581.493| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 5154 Z= 0.141 Angle : 0.699 11.340 7029 Z= 0.344 Chirality : 0.044 0.166 758 Planarity : 0.005 0.057 896 Dihedral : 7.408 85.719 679 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.11 (0.34), residues: 611 helix: 0.59 (0.32), residues: 272 sheet: -0.64 (0.49), residues: 122 loop : -0.37 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 425 TYR 0.006 0.001 TYR C 475 PHE 0.012 0.001 PHE B 71 TRP 0.028 0.002 TRP A 14 HIS 0.006 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5152) covalent geometry : angle 0.69905 ( 7029) hydrogen bonds : bond 0.02902 ( 261) hydrogen bonds : angle 4.97284 ( 735) Misc. bond : bond 0.11750 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9665 (tp) cc_final: 0.9335 (tp) REVERT: A 32 MET cc_start: 0.9272 (tpt) cc_final: 0.9019 (tpt) REVERT: A 54 GLN cc_start: 0.8761 (tt0) cc_final: 0.8496 (tt0) REVERT: A 64 ASP cc_start: 0.9597 (t0) cc_final: 0.9126 (m-30) REVERT: A 98 PHE cc_start: 0.9387 (m-80) cc_final: 0.8947 (m-80) REVERT: A 141 ARG cc_start: 0.8421 (mmp-170) cc_final: 0.8073 (mmm160) REVERT: B 79 ASP cc_start: 0.9076 (p0) cc_final: 0.8833 (p0) REVERT: B 80 ASN cc_start: 0.9473 (t0) cc_final: 0.8957 (p0) REVERT: B 104 ARG cc_start: 0.9526 (ttp80) cc_final: 0.9076 (ptt-90) REVERT: B 127 GLN cc_start: 0.9524 (tt0) cc_final: 0.9298 (tt0) REVERT: B 131 GLN cc_start: 0.9486 (mm-40) cc_final: 0.9240 (mm-40) REVERT: B 132 LYS cc_start: 0.9561 (pttp) cc_final: 0.9334 (pptt) REVERT: C 349 TRP cc_start: 0.9275 (p-90) cc_final: 0.8653 (p-90) REVERT: C 356 MET cc_start: 0.8733 (mmp) cc_final: 0.8393 (mmm) REVERT: C 363 ARG cc_start: 0.9240 (ptp-110) cc_final: 0.8948 (tmm-80) REVERT: D 356 MET cc_start: 0.8325 (mmm) cc_final: 0.7823 (mmm) REVERT: D 364 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8028 (tm-30) REVERT: D 408 LEU cc_start: 0.9208 (tp) cc_final: 0.8897 (tp) REVERT: D 443 TYR cc_start: 0.8908 (p90) cc_final: 0.8565 (p90) REVERT: D 478 GLN cc_start: 0.9588 (tt0) cc_final: 0.9210 (mt0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0780 time to fit residues: 9.4698 Evaluate side-chains 77 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** 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 = 0.2980 r_free = 0.2980 target = 0.039691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.029934 restraints weight = 40073.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.031109 restraints weight = 25593.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.031966 restraints weight = 18682.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.032608 restraints weight = 14759.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.033012 restraints weight = 12309.134| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 5154 Z= 0.119 Angle : 0.684 12.181 7029 Z= 0.334 Chirality : 0.044 0.173 758 Planarity : 0.005 0.056 896 Dihedral : 7.253 81.993 679 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.02 (0.35), residues: 611 helix: 0.72 (0.32), residues: 271 sheet: -0.63 (0.49), residues: 122 loop : -0.37 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 425 TYR 0.006 0.001 TYR C 415 PHE 0.011 0.001 PHE B 45 TRP 0.018 0.002 TRP A 14 HIS 0.006 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5152) covalent geometry : angle 0.68391 ( 7029) hydrogen bonds : bond 0.02835 ( 261) hydrogen bonds : angle 4.78520 ( 735) Misc. bond : bond 0.09286 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1020.43 seconds wall clock time: 18 minutes 22.10 seconds (1102.10 seconds total)