Starting phenix.real_space_refine on Fri Aug 22 16:24:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uet_64091/08_2025/9uet_64091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uet_64091/08_2025/9uet_64091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uet_64091/08_2025/9uet_64091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uet_64091/08_2025/9uet_64091.map" model { file = "/net/cci-nas-00/data/ceres_data/9uet_64091/08_2025/9uet_64091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uet_64091/08_2025/9uet_64091.cif" } resolution = 3.68 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= 0.005 sd= 0.060 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 4 5.21 5 S 42 5.16 5 C 3940 2.51 5 N 906 2.21 5 O 1012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5906 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2899 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 1.92, per 1000 atoms: 0.33 Number of scatterers: 5906 At special positions: 0 Unit cell: (90.95, 112.35, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 2 15.00 Mg 4 11.99 O 1012 8.00 N 906 7.00 C 3940 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: 0.54 Conformation dependent library (CDL) restraints added in 247.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 73.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 43 through 55 removed outlier: 4.416A pdb=" N LEU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 85 Processing helix chain 'A' and resid 93 through 118 removed outlier: 3.747A pdb=" N TYR A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 151 removed outlier: 4.092A pdb=" N SER A 137 " --> pdb=" O HIS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 removed outlier: 3.847A pdb=" N THR A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 156 through 180 removed outlier: 4.070A pdb=" N SER A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 208 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 226 through 248 removed outlier: 4.060A pdb=" N VAL A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 285 removed outlier: 4.144A pdb=" N ILE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.946A pdb=" N LYS A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.758A pdb=" N LEU A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 377 Processing helix chain 'B' and resid 22 through 32 Processing helix chain 'B' and resid 43 through 55 removed outlier: 4.417A pdb=" N LEU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 85 Processing helix chain 'B' and resid 93 through 118 removed outlier: 3.746A pdb=" N TYR B 97 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 151 removed outlier: 4.092A pdb=" N SER B 137 " --> pdb=" O HIS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 removed outlier: 3.847A pdb=" N THR B 155 " --> pdb=" O ARG B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 156 through 180 removed outlier: 4.070A pdb=" N SER B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 226 through 248 removed outlier: 4.060A pdb=" N VAL B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 285 removed outlier: 4.144A pdb=" N ILE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.945A pdb=" N LYS B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 318 Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.759A pdb=" N LEU B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 377 392 hydrogen bonds defined for protein. 1152 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: 0.94 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 878 1.31 - 1.43: 1748 1.43 - 1.56: 3370 1.56 - 1.68: 6 1.68 - 1.81: 64 Bond restraints: 6066 Sorted by residual: bond pdb=" N PRO A 126 " pdb=" CD PRO A 126 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.73e+01 bond pdb=" N PRO B 126 " pdb=" CD PRO B 126 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.73e+01 bond pdb=" CA PRO B 126 " pdb=" C PRO B 126 " ideal model delta sigma weight residual 1.520 1.474 0.046 9.50e-03 1.11e+04 2.34e+01 bond pdb=" CA PRO A 126 " pdb=" C PRO A 126 " ideal model delta sigma weight residual 1.520 1.474 0.046 9.50e-03 1.11e+04 2.34e+01 bond pdb=" C31 POV B 501 " pdb=" O31 POV B 501 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 6061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 8120 4.74 - 9.48: 88 9.48 - 14.22: 29 14.22 - 18.95: 3 18.95 - 23.69: 6 Bond angle restraints: 8246 Sorted by residual: angle pdb=" N ASN A 343 " pdb=" CA ASN A 343 " pdb=" C ASN A 343 " ideal model delta sigma weight residual 109.96 89.88 20.08 1.50e+00 4.44e-01 1.79e+02 angle pdb=" N ASN B 343 " pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 109.96 89.91 20.05 1.50e+00 4.44e-01 1.79e+02 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" C THR A 121 " ideal model delta sigma weight residual 109.81 90.30 19.51 1.53e+00 4.27e-01 1.63e+02 angle pdb=" N THR B 121 " pdb=" CA THR B 121 " pdb=" C THR B 121 " ideal model delta sigma weight residual 109.81 90.30 19.51 1.53e+00 4.27e-01 1.63e+02 angle pdb=" C GLN A 117 " pdb=" CA GLN A 117 " pdb=" CB GLN A 117 " ideal model delta sigma weight residual 109.95 86.26 23.69 1.99e+00 2.53e-01 1.42e+02 ... (remaining 8241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.07: 3123 20.07 - 40.13: 323 40.13 - 60.20: 52 60.20 - 80.27: 4 80.27 - 100.33: 2 Dihedral angle restraints: 3504 sinusoidal: 1368 harmonic: 2136 Sorted by residual: dihedral pdb=" C GLN A 117 " pdb=" N GLN A 117 " pdb=" CA GLN A 117 " pdb=" CB GLN A 117 " ideal model delta harmonic sigma weight residual -122.60 -97.65 -24.95 0 2.50e+00 1.60e-01 9.96e+01 dihedral pdb=" C GLN B 117 " pdb=" N GLN B 117 " pdb=" CA GLN B 117 " pdb=" CB GLN B 117 " ideal model delta harmonic sigma weight residual -122.60 -97.68 -24.92 0 2.50e+00 1.60e-01 9.94e+01 dihedral pdb=" C ASN A 122 " pdb=" N ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta harmonic sigma weight residual -122.60 -104.14 -18.46 0 2.50e+00 1.60e-01 5.45e+01 ... (remaining 3501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 841 0.088 - 0.175: 91 0.175 - 0.263: 4 0.263 - 0.351: 2 0.351 - 0.438: 6 Chirality restraints: 944 Sorted by residual: chirality pdb=" CA ASN A 122 " pdb=" N ASN A 122 " pdb=" C ASN A 122 " pdb=" CB ASN A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA ASN B 122 " pdb=" N ASN B 122 " pdb=" C ASN B 122 " pdb=" CB ASN B 122 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA SER A 125 " pdb=" N SER A 125 " pdb=" C SER A 125 " pdb=" CB SER A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 941 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 125 " -0.095 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO A 126 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 125 " 0.095 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO B 126 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 290 " -0.016 2.00e-02 2.50e+03 1.67e-02 4.88e+00 pdb=" CG PHE A 290 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 290 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 290 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 290 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 290 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 290 " -0.002 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 18 2.18 - 2.86: 2182 2.86 - 3.54: 8850 3.54 - 4.22: 13280 4.22 - 4.90: 22573 Nonbonded interactions: 46903 Sorted by model distance: nonbonded pdb=" OD1 ASP A 111 " pdb="MG MG A 503 " model vdw 1.497 2.170 nonbonded pdb=" OD1 ASP B 111 " pdb="MG MG B 503 " model vdw 1.498 2.170 nonbonded pdb=" OG1 THR B 67 " pdb=" CE2 PHE B 131 " model vdw 1.543 3.340 nonbonded pdb=" OG1 THR A 67 " pdb=" CE2 PHE A 131 " model vdw 1.543 3.340 nonbonded pdb=" OD2 ASP A 132 " pdb="MG MG A 502 " model vdw 1.673 2.170 ... (remaining 46898 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 6066 Z= 0.481 Angle : 1.420 23.694 8246 Z= 0.854 Chirality : 0.062 0.438 944 Planarity : 0.008 0.138 992 Dihedral : 15.614 100.334 2136 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.32 % Allowed : 1.27 % Favored : 98.41 % Cbeta Deviations : 1.46 % 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 aren not related in a simple way. whole: -0.36 (0.29), residues: 732 helix: 0.29 (0.22), residues: 488 sheet: None (None), residues: 0 loop : -1.17 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 120 TYR 0.023 0.002 TYR B 340 PHE 0.039 0.003 PHE A 290 TRP 0.006 0.001 TRP B 213 HIS 0.016 0.002 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00887 ( 6066) covalent geometry : angle 1.41984 ( 8246) hydrogen bonds : bond 0.14006 ( 392) hydrogen bonds : angle 6.41691 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 112 average time/residue: 0.0583 time to fit residues: 9.2051 Evaluate side-chains 94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 133 HIS A 175 HIS ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 133 HIS B 175 HIS ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.193307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151597 restraints weight = 7155.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157004 restraints weight = 3905.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160625 restraints weight = 2728.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162739 restraints weight = 2195.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163877 restraints weight = 1938.189| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6066 Z= 0.145 Angle : 0.611 6.587 8246 Z= 0.326 Chirality : 0.040 0.123 944 Planarity : 0.004 0.033 992 Dihedral : 10.630 85.257 872 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.90 % Allowed : 10.63 % Favored : 87.46 % 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 aren not related in a simple way. whole: 0.84 (0.31), residues: 732 helix: 1.43 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 120 TYR 0.012 0.001 TYR B 340 PHE 0.014 0.001 PHE B 165 TRP 0.005 0.001 TRP B 176 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6066) covalent geometry : angle 0.61101 ( 8246) hydrogen bonds : bond 0.05206 ( 392) hydrogen bonds : angle 4.39236 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.200 Fit side-chains REVERT: A 130 LEU cc_start: 0.8701 (tp) cc_final: 0.8474 (tp) REVERT: A 183 MET cc_start: 0.7199 (ptm) cc_final: 0.6946 (ptp) REVERT: A 345 ILE cc_start: 0.8310 (mt) cc_final: 0.7978 (mt) REVERT: B 130 LEU cc_start: 0.8693 (tp) cc_final: 0.8472 (tp) REVERT: B 183 MET cc_start: 0.7202 (ptm) cc_final: 0.6944 (ptp) REVERT: B 345 ILE cc_start: 0.8307 (mt) cc_final: 0.7969 (mt) outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.0500 time to fit residues: 7.1388 Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.181110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137751 restraints weight = 7156.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142490 restraints weight = 4110.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145626 restraints weight = 2980.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147487 restraints weight = 2463.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148776 restraints weight = 2200.727| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6066 Z= 0.186 Angle : 0.602 5.538 8246 Z= 0.322 Chirality : 0.041 0.117 944 Planarity : 0.004 0.029 992 Dihedral : 9.619 66.520 870 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.54 % Allowed : 13.33 % Favored : 84.13 % 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 aren not related in a simple way. whole: 0.76 (0.30), residues: 732 helix: 1.31 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 28 TYR 0.012 0.001 TYR A 340 PHE 0.021 0.002 PHE B 290 TRP 0.003 0.001 TRP B 52 HIS 0.006 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6066) covalent geometry : angle 0.60224 ( 8246) hydrogen bonds : bond 0.05255 ( 392) hydrogen bonds : angle 4.35721 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.231 Fit side-chains REVERT: A 183 MET cc_start: 0.7309 (ptm) cc_final: 0.7105 (ptp) REVERT: A 345 ILE cc_start: 0.8404 (mt) cc_final: 0.8034 (mt) REVERT: B 345 ILE cc_start: 0.8408 (mt) cc_final: 0.8034 (mt) outliers start: 16 outliers final: 8 residues processed: 123 average time/residue: 0.0609 time to fit residues: 10.8052 Evaluate side-chains 122 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.173895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128708 restraints weight = 7127.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133263 restraints weight = 4156.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136277 restraints weight = 3026.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137961 restraints weight = 2508.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139173 restraints weight = 2250.216| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6066 Z= 0.175 Angle : 0.582 7.616 8246 Z= 0.309 Chirality : 0.041 0.136 944 Planarity : 0.004 0.029 992 Dihedral : 9.424 66.815 870 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.13 % Allowed : 15.40 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.30), residues: 732 helix: 1.49 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -1.49 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 28 TYR 0.022 0.001 TYR B 340 PHE 0.016 0.002 PHE B 290 TRP 0.003 0.001 TRP B 213 HIS 0.006 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6066) covalent geometry : angle 0.58223 ( 8246) hydrogen bonds : bond 0.05001 ( 392) hydrogen bonds : angle 4.25692 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.214 Fit side-chains REVERT: A 183 MET cc_start: 0.7381 (ptm) cc_final: 0.7094 (ptp) REVERT: A 188 LYS cc_start: 0.7807 (mttt) cc_final: 0.6717 (tttm) REVERT: A 345 ILE cc_start: 0.8473 (mt) cc_final: 0.8100 (mt) REVERT: B 188 LYS cc_start: 0.7814 (mttt) cc_final: 0.6723 (tttm) REVERT: B 345 ILE cc_start: 0.8474 (mt) cc_final: 0.8100 (mt) outliers start: 26 outliers final: 14 residues processed: 128 average time/residue: 0.0648 time to fit residues: 11.7423 Evaluate side-chains 130 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129132 restraints weight = 7036.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133807 restraints weight = 4062.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136887 restraints weight = 2940.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138659 restraints weight = 2423.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139241 restraints weight = 2170.066| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6066 Z= 0.142 Angle : 0.572 8.349 8246 Z= 0.295 Chirality : 0.040 0.126 944 Planarity : 0.004 0.028 992 Dihedral : 9.342 68.077 870 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.49 % Allowed : 19.84 % Favored : 76.67 % 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 aren not related in a simple way. whole: 1.01 (0.31), residues: 732 helix: 1.65 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -1.57 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.016 0.001 TYR A 340 PHE 0.017 0.001 PHE A 344 TRP 0.004 0.001 TRP A 213 HIS 0.006 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6066) covalent geometry : angle 0.57215 ( 8246) hydrogen bonds : bond 0.04720 ( 392) hydrogen bonds : angle 4.09062 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.203 Fit side-chains REVERT: A 129 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 188 LYS cc_start: 0.7766 (mttt) cc_final: 0.6781 (tttt) REVERT: A 345 ILE cc_start: 0.8395 (mt) cc_final: 0.8053 (mt) REVERT: A 347 GLU cc_start: 0.8626 (tp30) cc_final: 0.8141 (mm-30) REVERT: B 188 LYS cc_start: 0.7780 (mttt) cc_final: 0.6794 (tttt) REVERT: B 345 ILE cc_start: 0.8376 (mt) cc_final: 0.8024 (mt) REVERT: B 347 GLU cc_start: 0.8627 (tp30) cc_final: 0.8140 (mm-30) outliers start: 22 outliers final: 16 residues processed: 126 average time/residue: 0.0642 time to fit residues: 11.4259 Evaluate side-chains 119 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 334 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.0020 chunk 49 optimal weight: 0.0670 chunk 41 optimal weight: 0.9980 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130571 restraints weight = 7006.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135548 restraints weight = 4023.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138800 restraints weight = 2886.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140308 restraints weight = 2366.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141721 restraints weight = 2131.016| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6066 Z= 0.124 Angle : 0.570 8.755 8246 Z= 0.289 Chirality : 0.039 0.133 944 Planarity : 0.004 0.029 992 Dihedral : 9.218 69.444 870 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.86 % Allowed : 21.43 % Favored : 75.71 % 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 aren not related in a simple way. whole: 1.21 (0.31), residues: 732 helix: 1.85 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.55 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 28 TYR 0.011 0.001 TYR A 340 PHE 0.013 0.001 PHE B 344 TRP 0.005 0.001 TRP A 213 HIS 0.005 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6066) covalent geometry : angle 0.57019 ( 8246) hydrogen bonds : bond 0.04476 ( 392) hydrogen bonds : angle 3.92044 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.230 Fit side-chains REVERT: A 183 MET cc_start: 0.7168 (ptm) cc_final: 0.6808 (ptp) REVERT: A 188 LYS cc_start: 0.7689 (mttt) cc_final: 0.6760 (tttt) REVERT: A 345 ILE cc_start: 0.8271 (mt) cc_final: 0.7911 (mt) REVERT: B 188 LYS cc_start: 0.7717 (mttt) cc_final: 0.6777 (tttt) REVERT: B 345 ILE cc_start: 0.8272 (mt) cc_final: 0.7911 (mt) outliers start: 18 outliers final: 15 residues processed: 107 average time/residue: 0.0645 time to fit residues: 9.8095 Evaluate side-chains 112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 31 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** B 316 HIS ** 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 = 0.4154 r_free = 0.4154 target = 0.188034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142869 restraints weight = 7244.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147699 restraints weight = 4179.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150869 restraints weight = 3002.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.152887 restraints weight = 2475.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153871 restraints weight = 2205.941| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6066 Z= 0.122 Angle : 0.571 8.383 8246 Z= 0.292 Chirality : 0.039 0.132 944 Planarity : 0.004 0.029 992 Dihedral : 9.151 68.916 870 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.65 % Allowed : 20.48 % Favored : 75.87 % 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 aren not related in a simple way. whole: 1.29 (0.31), residues: 732 helix: 1.94 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.58 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.011 0.001 TYR A 340 PHE 0.010 0.001 PHE A 344 TRP 0.004 0.001 TRP A 213 HIS 0.005 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6066) covalent geometry : angle 0.57147 ( 8246) hydrogen bonds : bond 0.04393 ( 392) hydrogen bonds : angle 3.89455 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.213 Fit side-chains REVERT: A 183 MET cc_start: 0.7123 (ptm) cc_final: 0.6771 (ptp) REVERT: A 188 LYS cc_start: 0.7648 (mttt) cc_final: 0.6780 (tttt) REVERT: A 345 ILE cc_start: 0.8251 (mt) cc_final: 0.7893 (mt) REVERT: B 188 LYS cc_start: 0.7667 (mttt) cc_final: 0.6767 (tttt) REVERT: B 345 ILE cc_start: 0.8261 (mt) cc_final: 0.7907 (mt) outliers start: 23 outliers final: 14 residues processed: 104 average time/residue: 0.0652 time to fit residues: 9.5775 Evaluate side-chains 103 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141436 restraints weight = 7241.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146345 restraints weight = 4182.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149490 restraints weight = 3008.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151450 restraints weight = 2477.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152823 restraints weight = 2205.911| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6066 Z= 0.123 Angle : 0.572 9.129 8246 Z= 0.289 Chirality : 0.039 0.136 944 Planarity : 0.004 0.030 992 Dihedral : 9.107 67.993 870 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.70 % Allowed : 21.75 % Favored : 75.56 % 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 aren not related in a simple way. whole: 1.32 (0.31), residues: 732 helix: 1.96 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.59 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.012 0.001 TYR B 340 PHE 0.009 0.001 PHE A 165 TRP 0.003 0.001 TRP A 56 HIS 0.005 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6066) covalent geometry : angle 0.57228 ( 8246) hydrogen bonds : bond 0.04416 ( 392) hydrogen bonds : angle 3.87198 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.214 Fit side-chains REVERT: A 183 MET cc_start: 0.7177 (ptm) cc_final: 0.6804 (ptp) REVERT: A 188 LYS cc_start: 0.7591 (mttt) cc_final: 0.6773 (tttt) REVERT: A 345 ILE cc_start: 0.8243 (mt) cc_final: 0.7885 (mt) REVERT: B 188 LYS cc_start: 0.7611 (mttt) cc_final: 0.6747 (tttt) REVERT: B 223 LYS cc_start: 0.8397 (tptp) cc_final: 0.7986 (mmmt) REVERT: B 345 ILE cc_start: 0.8244 (mt) cc_final: 0.7885 (mt) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.0660 time to fit residues: 9.1342 Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 2 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.190877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146441 restraints weight = 7125.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151305 restraints weight = 4089.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.154566 restraints weight = 2934.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156373 restraints weight = 2404.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157873 restraints weight = 2139.091| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6066 Z= 0.118 Angle : 0.569 8.911 8246 Z= 0.287 Chirality : 0.039 0.130 944 Planarity : 0.004 0.030 992 Dihedral : 9.006 68.920 870 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.54 % Allowed : 21.90 % Favored : 75.56 % 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 aren not related in a simple way. whole: 1.41 (0.31), residues: 732 helix: 1.98 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -1.47 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.012 0.001 TYR A 172 PHE 0.009 0.001 PHE A 161 TRP 0.004 0.001 TRP A 56 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6066) covalent geometry : angle 0.56851 ( 8246) hydrogen bonds : bond 0.04329 ( 392) hydrogen bonds : angle 3.80524 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.7522 (mttt) cc_final: 0.6866 (tttt) REVERT: A 223 LYS cc_start: 0.8268 (tptp) cc_final: 0.7883 (mmmt) REVERT: A 326 ASP cc_start: 0.8598 (m-30) cc_final: 0.8259 (m-30) REVERT: A 345 ILE cc_start: 0.8189 (mt) cc_final: 0.7836 (mt) REVERT: B 223 LYS cc_start: 0.8296 (tptp) cc_final: 0.7909 (mmmt) REVERT: B 326 ASP cc_start: 0.8599 (m-30) cc_final: 0.8258 (m-30) outliers start: 16 outliers final: 13 residues processed: 104 average time/residue: 0.0655 time to fit residues: 9.5857 Evaluate side-chains 109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** B 316 HIS ** 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 = 0.4157 r_free = 0.4157 target = 0.188419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142960 restraints weight = 7162.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147790 restraints weight = 4173.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151017 restraints weight = 3008.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152577 restraints weight = 2477.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152577 restraints weight = 2228.905| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6066 Z= 0.127 Angle : 0.620 10.711 8246 Z= 0.305 Chirality : 0.039 0.134 944 Planarity : 0.004 0.030 992 Dihedral : 8.969 67.785 870 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.22 % Allowed : 23.02 % Favored : 74.76 % 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 aren not related in a simple way. whole: 1.43 (0.31), residues: 732 helix: 2.02 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.011 0.001 TYR A 172 PHE 0.009 0.001 PHE A 161 TRP 0.004 0.000 TRP B 56 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6066) covalent geometry : angle 0.61998 ( 8246) hydrogen bonds : bond 0.04375 ( 392) hydrogen bonds : angle 3.82419 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TRP cc_start: 0.9055 (p-90) cc_final: 0.8842 (p90) REVERT: A 188 LYS cc_start: 0.7524 (mttt) cc_final: 0.6847 (tttt) REVERT: A 223 LYS cc_start: 0.8285 (tptp) cc_final: 0.7898 (mmmt) REVERT: A 345 ILE cc_start: 0.8215 (mt) cc_final: 0.7859 (mt) REVERT: B 60 TRP cc_start: 0.9057 (p-90) cc_final: 0.8844 (p90) REVERT: B 188 LYS cc_start: 0.7449 (mttt) cc_final: 0.6784 (tttt) REVERT: B 223 LYS cc_start: 0.8360 (tptp) cc_final: 0.7935 (mmmt) outliers start: 14 outliers final: 12 residues processed: 105 average time/residue: 0.0696 time to fit residues: 10.1505 Evaluate side-chains 109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** B 316 HIS ** 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 = 0.4096 r_free = 0.4096 target = 0.182572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136374 restraints weight = 7201.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141059 restraints weight = 4280.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144121 restraints weight = 3128.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146068 restraints weight = 2597.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146678 restraints weight = 2323.072| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6066 Z= 0.149 Angle : 0.633 11.528 8246 Z= 0.311 Chirality : 0.040 0.129 944 Planarity : 0.004 0.029 992 Dihedral : 9.006 66.751 870 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.90 % Allowed : 23.33 % Favored : 74.76 % 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 aren not related in a simple way. whole: 1.33 (0.31), residues: 732 helix: 1.96 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.54 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.014 0.001 TYR A 340 PHE 0.012 0.001 PHE B 290 TRP 0.004 0.001 TRP A 56 HIS 0.005 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6066) covalent geometry : angle 0.63340 ( 8246) hydrogen bonds : bond 0.04648 ( 392) hydrogen bonds : angle 3.94441 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1107.11 seconds wall clock time: 19 minutes 55.38 seconds (1195.38 seconds total)