Starting phenix.real_space_refine on Tue Jan 13 09:56:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f1z_4172/01_2026/6f1z_4172_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f1z_4172/01_2026/6f1z_4172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6f1z_4172/01_2026/6f1z_4172_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f1z_4172/01_2026/6f1z_4172_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6f1z_4172/01_2026/6f1z_4172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f1z_4172/01_2026/6f1z_4172.map" } resolution = 3.4 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= 0.004 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 1350 2.51 5 N 365 2.21 5 O 417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2138 Number of models: 1 Model: "" Number of chains: 4 Chain: "o" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "p" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 350 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 42} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "s" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 742 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "t" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 742 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Time building chain proxies: 0.65, per 1000 atoms: 0.30 Number of scatterers: 2138 At special positions: 0 Unit cell: (57.62, 76.38, 64.32, 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 417 8.00 N 365 7.00 C 1350 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: 0.14 Conformation dependent library (CDL) restraints added in 80.1 milliseconds 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 1 sheets defined 46.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'o' and resid 183 through 192 Processing helix chain 'o' and resid 195 through 210 removed outlier: 4.273A pdb=" N PHE o 199 " --> pdb=" O GLU o 195 " (cutoff:3.500A) Processing helix chain 'p' and resid 187 through 193 removed outlier: 3.946A pdb=" N LEU p 191 " --> pdb=" O LYS p 187 " (cutoff:3.500A) Processing helix chain 'p' and resid 195 through 211 Processing helix chain 's' and resid 4 through 11 Processing helix chain 's' and resid 35 through 61 removed outlier: 4.395A pdb=" N TYR s 42 " --> pdb=" O THR s 38 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 13 Processing helix chain 't' and resid 35 through 61 removed outlier: 4.042A pdb=" N GLN t 41 " --> pdb=" O PRO t 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR t 42 " --> pdb=" O THR t 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 's' and resid 17 through 20 removed outlier: 5.997A pdb=" N THR s 67 " --> pdb=" O PRO s 82 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL t 90 " --> pdb=" O MET t 79 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE t 91 " --> pdb=" O GLN t 18 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 327 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: 0.29 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 696 1.34 - 1.46: 247 1.46 - 1.57: 1213 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 2168 Sorted by residual: bond pdb=" C ASN t 36 " pdb=" N PRO t 37 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.23e-02 6.61e+03 1.20e+00 bond pdb=" CA ASN s 36 " pdb=" C ASN s 36 " ideal model delta sigma weight residual 1.521 1.533 -0.012 1.14e-02 7.69e+03 1.10e+00 bond pdb=" C ASN s 36 " pdb=" N PRO s 37 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.53e-01 bond pdb=" C MET t 46 " pdb=" O MET t 46 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.29e-02 6.01e+03 9.53e-01 bond pdb=" CB PHE s 87 " pdb=" CG PHE s 87 " ideal model delta sigma weight residual 1.502 1.524 -0.022 2.30e-02 1.89e+03 9.25e-01 ... (remaining 2163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 2804 1.97 - 3.95: 100 3.95 - 5.92: 12 5.92 - 7.89: 4 7.89 - 9.87: 5 Bond angle restraints: 2925 Sorted by residual: angle pdb=" N GLN p 188 " pdb=" CA GLN p 188 " pdb=" C GLN p 188 " ideal model delta sigma weight residual 111.28 121.15 -9.87 1.09e+00 8.42e-01 8.19e+01 angle pdb=" N THR p 183 " pdb=" CA THR p 183 " pdb=" C THR p 183 " ideal model delta sigma weight residual 111.07 119.17 -8.10 1.07e+00 8.73e-01 5.73e+01 angle pdb=" N GLN p 189 " pdb=" CA GLN p 189 " pdb=" C GLN p 189 " ideal model delta sigma weight residual 111.28 115.58 -4.30 1.09e+00 8.42e-01 1.56e+01 angle pdb=" N LYS p 187 " pdb=" CA LYS p 187 " pdb=" C LYS p 187 " ideal model delta sigma weight residual 111.36 115.22 -3.86 1.09e+00 8.42e-01 1.25e+01 angle pdb=" N GLU p 195 " pdb=" CA GLU p 195 " pdb=" C GLU p 195 " ideal model delta sigma weight residual 114.04 110.39 3.65 1.24e+00 6.50e-01 8.68e+00 ... (remaining 2920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1260 14.74 - 29.49: 58 29.49 - 44.23: 23 44.23 - 58.97: 4 58.97 - 73.72: 2 Dihedral angle restraints: 1347 sinusoidal: 566 harmonic: 781 Sorted by residual: dihedral pdb=" CA PHE t 49 " pdb=" C PHE t 49 " pdb=" N ILE t 50 " pdb=" CA ILE t 50 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA THR s 39 " pdb=" C THR s 39 " pdb=" N THR s 40 " pdb=" CA THR s 40 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR t 86 " pdb=" C TYR t 86 " pdb=" N PHE t 87 " pdb=" CA PHE t 87 " ideal model delta harmonic sigma weight residual 180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 1344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 264 0.068 - 0.135: 70 0.135 - 0.202: 9 0.202 - 0.269: 1 0.269 - 0.336: 2 Chirality restraints: 346 Sorted by residual: chirality pdb=" CB ILE s 20 " pdb=" CA ILE s 20 " pdb=" CG1 ILE s 20 " pdb=" CG2 ILE s 20 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLN p 188 " pdb=" N GLN p 188 " pdb=" C GLN p 188 " pdb=" CB GLN p 188 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA THR p 183 " pdb=" N THR p 183 " pdb=" C THR p 183 " pdb=" CB THR p 183 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 343 not shown) Planarity restraints: 377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA t 81 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO t 82 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO t 82 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO t 82 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE o 200 " 0.011 2.00e-02 2.50e+03 1.59e-02 4.44e+00 pdb=" CG PHE o 200 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE o 200 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE o 200 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE o 200 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE o 200 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE o 200 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU t 45 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LEU t 45 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU t 45 " 0.013 2.00e-02 2.50e+03 pdb=" N MET t 46 " 0.012 2.00e-02 2.50e+03 ... (remaining 374 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 495 2.79 - 3.32: 2025 3.32 - 3.85: 3496 3.85 - 4.37: 3838 4.37 - 4.90: 6630 Nonbonded interactions: 16484 Sorted by model distance: nonbonded pdb=" O ASN t 36 " pdb=" OG1 THR t 40 " model vdw 2.264 3.040 nonbonded pdb=" NZ LYS s 75 " pdb=" OD1 ASP t 61 " model vdw 2.275 3.120 nonbonded pdb=" OG SER s 73 " pdb=" OD1 ASN s 76 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR t 25 " pdb=" O ASP t 85 " model vdw 2.281 3.040 nonbonded pdb=" O GLU p 195 " pdb=" OG SER p 198 " model vdw 2.289 3.040 ... (remaining 16479 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 's' selection = chain 't' } 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: 14.270 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 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 0.037 2168 Z= 0.215 Angle : 0.973 9.866 2925 Z= 0.571 Chirality : 0.063 0.336 346 Planarity : 0.007 0.053 377 Dihedral : 11.170 73.718 831 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.81 % Allowed : 4.07 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.40), residues: 257 helix: -2.50 (0.36), residues: 105 sheet: -1.50 (0.75), residues: 40 loop : -3.56 (0.45), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG t 70 TYR 0.011 0.003 TYR t 42 PHE 0.036 0.004 PHE o 200 HIS 0.005 0.002 HIS p 202 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 2168) covalent geometry : angle 0.97276 ( 2925) hydrogen bonds : bond 0.18496 ( 111) hydrogen bonds : angle 9.73927 ( 327) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.054 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: o 214 GLN cc_start: 0.6014 (pm20) cc_final: 0.5681 (tm-30) REVERT: p 201 ASP cc_start: 0.9191 (t0) cc_final: 0.8787 (m-30) REVERT: s 24 ASN cc_start: 0.6927 (t0) cc_final: 0.6477 (m110) REVERT: s 25 THR cc_start: 0.7195 (m) cc_final: 0.6941 (p) REVERT: s 69 LEU cc_start: 0.8813 (tp) cc_final: 0.8594 (mm) REVERT: s 79 MET cc_start: 0.8189 (ptp) cc_final: 0.7945 (ppp) REVERT: s 80 VAL cc_start: 0.8661 (t) cc_final: 0.8453 (t) REVERT: s 84 LYS cc_start: 0.8031 (mttp) cc_final: 0.7787 (mtmt) REVERT: s 85 ASP cc_start: 0.8219 (t0) cc_final: 0.8010 (p0) REVERT: t 23 VAL cc_start: 0.5995 (p) cc_final: 0.5793 (t) REVERT: t 71 ILE cc_start: 0.7800 (mt) cc_final: 0.7501 (mt) outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.1073 time to fit residues: 11.3727 Evaluate side-chains 48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.0050 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 6 optimal weight: 0.0030 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 192 HIS p 189 GLN p 192 HIS ** s 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 36 ASN s 63 GLN s 93 ASN t 36 ASN ** t 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.065382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.058458 restraints weight = 17712.491| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 6.92 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2168 Z= 0.148 Angle : 0.821 12.528 2925 Z= 0.406 Chirality : 0.049 0.144 346 Planarity : 0.005 0.035 377 Dihedral : 5.974 23.878 279 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.85 % Allowed : 13.82 % Favored : 83.33 % 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: -3.20 (0.43), residues: 257 helix: -1.18 (0.41), residues: 113 sheet: -0.82 (0.78), residues: 40 loop : -3.77 (0.44), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG s 70 TYR 0.010 0.001 TYR t 86 PHE 0.014 0.002 PHE o 200 HIS 0.010 0.002 HIS p 192 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2168) covalent geometry : angle 0.82134 ( 2925) hydrogen bonds : bond 0.04447 ( 111) hydrogen bonds : angle 7.04721 ( 327) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.097 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: o 214 GLN cc_start: 0.6388 (pm20) cc_final: 0.5911 (tm-30) REVERT: s 24 ASN cc_start: 0.6822 (t0) cc_final: 0.6573 (m110) REVERT: s 30 ILE cc_start: 0.5721 (mt) cc_final: 0.5486 (mt) REVERT: s 46 MET cc_start: 0.9002 (mmm) cc_final: 0.8536 (ptp) REVERT: s 79 MET cc_start: 0.8137 (ptp) cc_final: 0.7474 (ppp) REVERT: s 80 VAL cc_start: 0.7868 (t) cc_final: 0.7463 (t) REVERT: s 84 LYS cc_start: 0.8460 (mttp) cc_final: 0.7946 (mtmt) REVERT: s 85 ASP cc_start: 0.8712 (t0) cc_final: 0.8264 (p0) REVERT: t 15 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7905 (tptp) REVERT: t 26 GLU cc_start: 0.8795 (tt0) cc_final: 0.8246 (tm-30) REVERT: t 46 MET cc_start: 0.9061 (mmm) cc_final: 0.8378 (ptp) REVERT: t 74 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8050 (mmmt) outliers start: 7 outliers final: 2 residues processed: 68 average time/residue: 0.1027 time to fit residues: 7.6889 Evaluate side-chains 48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain t residue 68 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 12 GLN ** s 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 36 ASN ** t 92 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 = 0.4012 r_free = 0.4012 target = 0.062312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.055774 restraints weight = 17344.021| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 6.36 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2168 Z= 0.167 Angle : 0.781 11.089 2925 Z= 0.388 Chirality : 0.049 0.164 346 Planarity : 0.006 0.033 377 Dihedral : 5.713 20.246 279 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.07 % Allowed : 16.67 % Favored : 79.27 % 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: -2.55 (0.47), residues: 257 helix: -0.52 (0.47), residues: 109 sheet: -0.43 (0.84), residues: 38 loop : -3.46 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG t 58 TYR 0.008 0.001 TYR s 42 PHE 0.017 0.003 PHE p 196 HIS 0.006 0.001 HIS p 192 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 2168) covalent geometry : angle 0.78063 ( 2925) hydrogen bonds : bond 0.04207 ( 111) hydrogen bonds : angle 6.64852 ( 327) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 24 ASN cc_start: 0.6693 (t0) cc_final: 0.6471 (m110) REVERT: s 30 ILE cc_start: 0.5444 (mt) cc_final: 0.5213 (mt) REVERT: s 78 ILE cc_start: 0.9301 (mt) cc_final: 0.9083 (mp) REVERT: s 79 MET cc_start: 0.8045 (ptp) cc_final: 0.7506 (ppp) REVERT: s 80 VAL cc_start: 0.7556 (t) cc_final: 0.7224 (t) REVERT: s 84 LYS cc_start: 0.8503 (mttp) cc_final: 0.7944 (mtmt) REVERT: s 85 ASP cc_start: 0.8434 (t0) cc_final: 0.8213 (p0) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.0980 time to fit residues: 6.6432 Evaluate side-chains 46 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 197 LEU Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain t residue 36 ASN Chi-restraints excluded: chain t residue 68 PHE Chi-restraints excluded: chain t residue 71 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS s 24 ASN t 36 ASN ** t 92 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 = 0.3999 r_free = 0.3999 target = 0.061248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.054981 restraints weight = 16815.643| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 5.98 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2168 Z= 0.169 Angle : 0.771 10.529 2925 Z= 0.388 Chirality : 0.048 0.159 346 Planarity : 0.005 0.030 377 Dihedral : 5.735 18.553 279 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.88 % Allowed : 19.92 % Favored : 75.20 % 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: -2.33 (0.49), residues: 257 helix: -0.28 (0.47), residues: 109 sheet: -1.30 (0.79), residues: 48 loop : -3.12 (0.51), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 70 TYR 0.021 0.004 TYR t 86 PHE 0.014 0.003 PHE p 196 HIS 0.006 0.001 HIS p 192 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2168) covalent geometry : angle 0.77058 ( 2925) hydrogen bonds : bond 0.04329 ( 111) hydrogen bonds : angle 6.55075 ( 327) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 214 GLN cc_start: 0.7140 (pm20) cc_final: 0.5519 (tm-30) REVERT: s 66 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5894 (pt) REVERT: s 79 MET cc_start: 0.8144 (ptp) cc_final: 0.7587 (ppp) REVERT: s 80 VAL cc_start: 0.7810 (t) cc_final: 0.7475 (t) REVERT: s 84 LYS cc_start: 0.8479 (mttp) cc_final: 0.7921 (mtmt) REVERT: t 46 MET cc_start: 0.8937 (mmm) cc_final: 0.8342 (ptp) outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 0.0907 time to fit residues: 5.4945 Evaluate side-chains 45 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 197 LEU Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 66 LEU Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain t residue 41 GLN Chi-restraints excluded: chain t residue 68 PHE Chi-restraints excluded: chain t residue 71 ILE Chi-restraints excluded: chain t residue 90 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.060486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.053926 restraints weight = 17453.468| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 6.30 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2168 Z= 0.156 Angle : 0.748 9.942 2925 Z= 0.374 Chirality : 0.047 0.149 346 Planarity : 0.005 0.032 377 Dihedral : 5.596 17.075 279 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.88 % Allowed : 21.54 % Favored : 73.58 % 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: -1.97 (0.48), residues: 257 helix: -0.11 (0.47), residues: 109 sheet: 0.02 (0.82), residues: 41 loop : -3.23 (0.48), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG t 70 TYR 0.021 0.003 TYR t 86 PHE 0.012 0.002 PHE p 196 HIS 0.007 0.002 HIS p 192 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2168) covalent geometry : angle 0.74792 ( 2925) hydrogen bonds : bond 0.04054 ( 111) hydrogen bonds : angle 6.30804 ( 327) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 214 GLN cc_start: 0.7544 (pm20) cc_final: 0.5762 (tm-30) REVERT: s 46 MET cc_start: 0.8485 (mmp) cc_final: 0.8011 (ptp) REVERT: s 66 LEU cc_start: 0.6203 (pt) cc_final: 0.5979 (pt) REVERT: s 79 MET cc_start: 0.8285 (ptp) cc_final: 0.7529 (ppp) REVERT: s 80 VAL cc_start: 0.8043 (t) cc_final: 0.7592 (t) REVERT: s 84 LYS cc_start: 0.8453 (mttp) cc_final: 0.7961 (mtmt) REVERT: t 46 MET cc_start: 0.9109 (mmm) cc_final: 0.8374 (ptp) outliers start: 12 outliers final: 12 residues processed: 54 average time/residue: 0.1014 time to fit residues: 6.0575 Evaluate side-chains 51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 197 LEU Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 71 ILE Chi-restraints excluded: chain t residue 36 ASN Chi-restraints excluded: chain t residue 41 GLN Chi-restraints excluded: chain t residue 68 PHE Chi-restraints excluded: chain t residue 71 ILE Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 90 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.057751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.052059 restraints weight = 18508.538| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 5.92 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2168 Z= 0.199 Angle : 0.772 9.409 2925 Z= 0.396 Chirality : 0.048 0.147 346 Planarity : 0.006 0.036 377 Dihedral : 5.768 17.540 279 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 6.91 % Allowed : 22.76 % Favored : 70.33 % 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: -1.93 (0.49), residues: 257 helix: -0.10 (0.47), residues: 109 sheet: -0.16 (0.80), residues: 41 loop : -3.08 (0.51), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 70 TYR 0.020 0.003 TYR t 86 PHE 0.017 0.003 PHE t 87 HIS 0.007 0.002 HIS p 192 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 2168) covalent geometry : angle 0.77217 ( 2925) hydrogen bonds : bond 0.04545 ( 111) hydrogen bonds : angle 6.43720 ( 327) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 202 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7778 (m-70) REVERT: o 214 GLN cc_start: 0.7632 (pm20) cc_final: 0.5751 (tm-30) REVERT: s 79 MET cc_start: 0.8275 (ptp) cc_final: 0.7672 (ppp) REVERT: s 80 VAL cc_start: 0.8050 (t) cc_final: 0.7679 (t) REVERT: s 84 LYS cc_start: 0.8536 (mttp) cc_final: 0.8014 (mtmt) outliers start: 17 outliers final: 13 residues processed: 54 average time/residue: 0.0920 time to fit residues: 5.5932 Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 197 LEU Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain o residue 202 HIS Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 71 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 36 ASN Chi-restraints excluded: chain t residue 41 GLN Chi-restraints excluded: chain t residue 68 PHE Chi-restraints excluded: chain t residue 73 SER Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 90 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 93 ASN ** 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 = 0.3944 r_free = 0.3944 target = 0.059189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.053546 restraints weight = 17725.411| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 5.55 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2168 Z= 0.171 Angle : 0.805 13.513 2925 Z= 0.390 Chirality : 0.049 0.146 346 Planarity : 0.006 0.042 377 Dihedral : 5.648 17.468 279 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 5.69 % Allowed : 24.39 % Favored : 69.92 % 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: -1.96 (0.49), residues: 257 helix: 0.08 (0.48), residues: 107 sheet: -1.23 (0.74), residues: 49 loop : -2.88 (0.53), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 58 TYR 0.016 0.003 TYR t 86 PHE 0.013 0.003 PHE t 87 HIS 0.003 0.001 HIS p 202 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 2168) covalent geometry : angle 0.80467 ( 2925) hydrogen bonds : bond 0.04286 ( 111) hydrogen bonds : angle 6.32893 ( 327) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 202 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7649 (m-70) REVERT: o 214 GLN cc_start: 0.7477 (pm20) cc_final: 0.5715 (tm-30) REVERT: s 79 MET cc_start: 0.8084 (ptp) cc_final: 0.7592 (ppp) REVERT: s 84 LYS cc_start: 0.8546 (mttp) cc_final: 0.8010 (mtmt) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.1000 time to fit residues: 5.9988 Evaluate side-chains 50 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 197 LEU Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain o residue 202 HIS Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 71 ILE Chi-restraints excluded: chain t residue 41 GLN Chi-restraints excluded: chain t residue 68 PHE Chi-restraints excluded: chain t residue 73 SER Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.059871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.054752 restraints weight = 18118.424| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 5.24 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.7462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2168 Z= 0.156 Angle : 0.805 11.947 2925 Z= 0.389 Chirality : 0.049 0.147 346 Planarity : 0.007 0.083 377 Dihedral : 5.592 18.419 279 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 6.50 % Allowed : 24.80 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.03 (0.49), residues: 257 helix: 0.01 (0.49), residues: 107 sheet: -1.23 (0.73), residues: 49 loop : -2.92 (0.52), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG t 58 TYR 0.014 0.002 TYR t 86 PHE 0.015 0.003 PHE t 49 HIS 0.003 0.001 HIS p 202 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2168) covalent geometry : angle 0.80534 ( 2925) hydrogen bonds : bond 0.04258 ( 111) hydrogen bonds : angle 6.25288 ( 327) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 202 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7576 (m-70) REVERT: o 214 GLN cc_start: 0.7465 (pm20) cc_final: 0.5736 (tm-30) REVERT: s 79 MET cc_start: 0.8172 (ptp) cc_final: 0.7693 (ppp) REVERT: s 84 LYS cc_start: 0.8469 (mttp) cc_final: 0.7945 (mtmt) REVERT: t 46 MET cc_start: 0.8806 (mmm) cc_final: 0.8238 (ptp) outliers start: 16 outliers final: 12 residues processed: 50 average time/residue: 0.0907 time to fit residues: 5.1209 Evaluate side-chains 50 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 197 LEU Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain o residue 202 HIS Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 71 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 36 ASN Chi-restraints excluded: chain t residue 41 GLN Chi-restraints excluded: chain t residue 68 PHE Chi-restraints excluded: chain t residue 73 SER Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 93 ASN ** 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 = 0.3941 r_free = 0.3941 target = 0.059344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.053726 restraints weight = 18766.127| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 5.91 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2168 Z= 0.156 Angle : 0.876 18.205 2925 Z= 0.406 Chirality : 0.049 0.153 346 Planarity : 0.007 0.084 377 Dihedral : 5.531 16.414 279 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 6.10 % Allowed : 24.80 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.91 (0.50), residues: 257 helix: 0.05 (0.48), residues: 108 sheet: -1.16 (0.74), residues: 49 loop : -2.80 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG t 58 TYR 0.013 0.002 TYR t 86 PHE 0.017 0.003 PHE t 49 HIS 0.011 0.002 HIS p 192 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2168) covalent geometry : angle 0.87561 ( 2925) hydrogen bonds : bond 0.04227 ( 111) hydrogen bonds : angle 6.10313 ( 327) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 202 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7398 (m-70) REVERT: o 214 GLN cc_start: 0.7437 (pm20) cc_final: 0.5745 (tm-30) REVERT: s 46 MET cc_start: 0.9026 (tpp) cc_final: 0.8715 (tpp) REVERT: s 84 LYS cc_start: 0.8396 (mttp) cc_final: 0.7849 (mtmt) REVERT: t 46 MET cc_start: 0.8701 (mmm) cc_final: 0.8196 (ptp) REVERT: t 70 ARG cc_start: 0.7458 (mmm160) cc_final: 0.6971 (mmp-170) outliers start: 15 outliers final: 13 residues processed: 49 average time/residue: 0.0850 time to fit residues: 4.6964 Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 197 LEU Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain o residue 202 HIS Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 71 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 36 ASN Chi-restraints excluded: chain t residue 41 GLN Chi-restraints excluded: chain t residue 68 PHE Chi-restraints excluded: chain t residue 73 SER Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 13 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 12 GLN t 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.059966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.054800 restraints weight = 19683.953| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 5.24 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.7697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2168 Z= 0.148 Angle : 0.898 17.661 2925 Z= 0.424 Chirality : 0.051 0.226 346 Planarity : 0.007 0.074 377 Dihedral : 5.543 16.042 279 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.28 % Allowed : 26.83 % Favored : 67.89 % 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: -1.76 (0.51), residues: 257 helix: 0.23 (0.49), residues: 108 sheet: -1.20 (0.73), residues: 49 loop : -2.73 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG t 58 TYR 0.012 0.002 TYR t 86 PHE 0.016 0.002 PHE t 49 HIS 0.003 0.001 HIS p 202 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2168) covalent geometry : angle 0.89829 ( 2925) hydrogen bonds : bond 0.04381 ( 111) hydrogen bonds : angle 5.93324 ( 327) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 214 GLN cc_start: 0.7035 (pm20) cc_final: 0.5515 (tm-30) REVERT: s 84 LYS cc_start: 0.8303 (mttp) cc_final: 0.7775 (mtmt) REVERT: t 70 ARG cc_start: 0.6811 (mmm160) cc_final: 0.6373 (mmp-170) outliers start: 13 outliers final: 12 residues processed: 46 average time/residue: 0.0850 time to fit residues: 4.4196 Evaluate side-chains 48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 197 LEU Chi-restraints excluded: chain o residue 201 ASP Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain s residue 56 THR Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 36 ASN Chi-restraints excluded: chain t residue 41 GLN Chi-restraints excluded: chain t residue 68 PHE Chi-restraints excluded: chain t residue 71 ILE Chi-restraints excluded: chain t residue 73 SER Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.060335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.054721 restraints weight = 18487.819| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 5.90 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.7864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2168 Z= 0.159 Angle : 0.932 17.399 2925 Z= 0.445 Chirality : 0.052 0.196 346 Planarity : 0.007 0.074 377 Dihedral : 5.618 15.793 279 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 5.28 % Allowed : 26.02 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.69 (0.51), residues: 257 helix: 0.30 (0.50), residues: 108 sheet: -1.08 (0.74), residues: 49 loop : -2.75 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG t 58 TYR 0.013 0.002 TYR t 42 PHE 0.017 0.002 PHE t 49 HIS 0.003 0.001 HIS p 202 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 2168) covalent geometry : angle 0.93156 ( 2925) hydrogen bonds : bond 0.04569 ( 111) hydrogen bonds : angle 5.83513 ( 327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 996.96 seconds wall clock time: 17 minutes 48.41 seconds (1068.41 seconds total)