Starting phenix.real_space_refine on Tue Mar 3 11:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qk3_14030/03_2026/7qk3_14030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qk3_14030/03_2026/7qk3_14030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qk3_14030/03_2026/7qk3_14030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qk3_14030/03_2026/7qk3_14030.map" model { file = "/net/cci-nas-00/data/ceres_data/7qk3_14030/03_2026/7qk3_14030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qk3_14030/03_2026/7qk3_14030.cif" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 831 2.51 5 N 249 2.21 5 O 249 1.98 5 H 1407 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2742 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 914 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "A" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 914 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 914 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Time building chain proxies: 0.53, per 1000 atoms: 0.19 Number of scatterers: 2742 At special positions: 0 Unit cell: (75.2445, 66.5205, 33.8055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 249 8.00 N 249 7.00 C 831 6.00 H 1407 1.00 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: 0.12 Conformation dependent library (CDL) restraints added in 41.4 milliseconds 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 312 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 277 removed outlier: 6.168A pdb=" N LYS B 274 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE C 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 280 through 283 removed outlier: 6.657A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 291 removed outlier: 7.007A pdb=" N SER B 289 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS A 290 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS B 291 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL B 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LYS C 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER B 289 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.542A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.482A pdb=" N VAL B 306 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 7.082A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 317 through 324 removed outlier: 6.807A pdb=" N SER A 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLY C 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N CYS B 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) 20 hydrogen bonds defined for protein. 60 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: 0.45 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: 0.95 - 1.12: 1401 1.12 - 1.30: 224 1.30 - 1.47: 464 1.47 - 1.64: 665 1.64 - 1.82: 6 Bond restraints: 2760 Sorted by residual: bond pdb=" CE1 TYR A 310 " pdb=" HE1 TYR A 310 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLY B 302 " pdb=" H GLY B 302 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N SER C 320 " pdb=" H SER C 320 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N GLN B 307 " pdb=" H GLN B 307 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" ND2 ASN B 327 " pdb="HD22 ASN B 327 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 2755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 4058 2.43 - 4.87: 735 4.87 - 7.30: 236 7.30 - 9.74: 10 9.74 - 12.17: 4 Bond angle restraints: 5043 Sorted by residual: angle pdb=" N LYS C 298 " pdb=" CA LYS C 298 " pdb=" CB LYS C 298 " ideal model delta sigma weight residual 110.71 100.98 9.73 1.66e+00 3.63e-01 3.44e+01 angle pdb=" N LYS A 298 " pdb=" CA LYS A 298 " pdb=" CB LYS A 298 " ideal model delta sigma weight residual 110.57 101.38 9.19 1.69e+00 3.50e-01 2.96e+01 angle pdb=" N SER C 285 " pdb=" CA SER C 285 " pdb=" C SER C 285 " ideal model delta sigma weight residual 110.53 117.18 -6.65 1.32e+00 5.74e-01 2.54e+01 angle pdb=" OE1 GLN A 288 " pdb=" CD GLN A 288 " pdb=" NE2 GLN A 288 " ideal model delta sigma weight residual 122.60 117.77 4.83 1.00e+00 1.00e+00 2.33e+01 angle pdb=" CB HIS C 299 " pdb=" CG HIS C 299 " pdb=" CD2 HIS C 299 " ideal model delta sigma weight residual 131.20 125.21 5.99 1.30e+00 5.92e-01 2.12e+01 ... (remaining 5038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1137 17.57 - 35.15: 51 35.15 - 52.72: 28 52.72 - 70.29: 56 70.29 - 87.87: 3 Dihedral angle restraints: 1275 sinusoidal: 741 harmonic: 534 Sorted by residual: dihedral pdb=" CA ILE B 297 " pdb=" C ILE B 297 " pdb=" N LYS B 298 " pdb=" CA LYS B 298 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" C GLN B 276 " pdb=" N GLN B 276 " pdb=" CA GLN B 276 " pdb=" CB GLN B 276 " ideal model delta harmonic sigma weight residual -122.60 -131.74 9.14 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C GLN C 276 " pdb=" N GLN C 276 " pdb=" CA GLN C 276 " pdb=" CB GLN C 276 " ideal model delta harmonic sigma weight residual -122.60 -131.69 9.09 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 1272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 116 0.069 - 0.139: 43 0.139 - 0.208: 35 0.208 - 0.277: 7 0.277 - 0.346: 6 Chirality restraints: 207 Sorted by residual: chirality pdb=" CA GLN B 276 " pdb=" N GLN B 276 " pdb=" C GLN B 276 " pdb=" CB GLN B 276 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA GLN C 276 " pdb=" N GLN C 276 " pdb=" C GLN C 276 " pdb=" CB GLN C 276 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA LEU C 325 " pdb=" N LEU C 325 " pdb=" C LEU C 325 " pdb=" CB LEU C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 204 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 307 " -0.053 2.00e-02 2.50e+03 5.41e-02 4.40e+01 pdb=" CD GLN C 307 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN C 307 " 0.057 2.00e-02 2.50e+03 pdb=" NE2 GLN C 307 " -0.019 2.00e-02 2.50e+03 pdb="HE21 GLN C 307 " 0.080 2.00e-02 2.50e+03 pdb="HE22 GLN C 307 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 329 " -0.074 2.00e-02 2.50e+03 4.00e-02 3.61e+01 pdb=" CG HIS A 329 " 0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS A 329 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS A 329 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS A 329 " 0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS A 329 " 0.014 2.00e-02 2.50e+03 pdb=" HD2 HIS A 329 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 HIS A 329 " -0.030 2.00e-02 2.50e+03 pdb=" HE2 HIS A 329 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 297 " 0.033 2.00e-02 2.50e+03 5.99e-02 3.59e+01 pdb=" N LYS B 298 " -0.103 2.00e-02 2.50e+03 pdb=" CA LYS B 298 " 0.030 2.00e-02 2.50e+03 pdb=" H LYS B 298 " 0.041 2.00e-02 2.50e+03 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 216 2.17 - 2.78: 4843 2.78 - 3.39: 7400 3.39 - 3.99: 10200 3.99 - 4.60: 13923 Nonbonded interactions: 36582 Sorted by model distance: nonbonded pdb=" OD1 ASP A 283 " pdb=" HG SER A 285 " model vdw 1.563 2.450 nonbonded pdb=" OD1 ASP B 283 " pdb=" HG SER B 285 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASP C 283 " pdb=" HG SER C 285 " model vdw 1.592 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.600 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.608 2.450 ... (remaining 36577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.970 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.690 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.010 0.035 1353 Z= 0.657 Angle : 2.070 9.729 1809 Z= 1.378 Chirality : 0.114 0.346 207 Planarity : 0.008 0.046 228 Dihedral : 12.548 87.865 516 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.46), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.35), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.004 TYR C 310 HIS 0.009 0.003 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.01037 ( 1353) covalent geometry : angle 2.06960 ( 1809) hydrogen bonds : bond 0.14458 ( 20) hydrogen bonds : angle 8.39007 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.045 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.9763 time to fit residues: 42.5569 Evaluate side-chains 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN B 288 GLN B 330 HIS A 286 ASN A 288 GLN C 286 ASN C 288 GLN C 330 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.136019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124333 restraints weight = 4660.415| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.80 r_work: 0.3916 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1353 Z= 0.162 Angle : 0.788 5.692 1809 Z= 0.410 Chirality : 0.058 0.155 207 Planarity : 0.005 0.038 228 Dihedral : 6.539 22.259 183 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.13 % Allowed : 17.31 % Favored : 77.56 % 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 are not related in a simple way. whole: -3.02 (0.47), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 310 HIS 0.005 0.002 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 1353) covalent geometry : angle 0.78811 ( 1809) hydrogen bonds : bond 0.04316 ( 20) hydrogen bonds : angle 6.24116 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.085 Fit side-chains REVERT: B 317 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8389 (mtpm) REVERT: A 281 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8306 (mtpp) outliers start: 8 outliers final: 2 residues processed: 33 average time/residue: 1.0800 time to fit residues: 36.1022 Evaluate side-chains 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 281 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.136337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.123492 restraints weight = 4574.627| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.86 r_work: 0.3899 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1353 Z= 0.161 Angle : 0.684 5.164 1809 Z= 0.348 Chirality : 0.054 0.138 207 Planarity : 0.004 0.037 228 Dihedral : 6.192 23.016 183 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.85 % Allowed : 19.87 % Favored : 76.28 % 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: -2.91 (0.49), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 310 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 1353) covalent geometry : angle 0.68408 ( 1809) hydrogen bonds : bond 0.03109 ( 20) hydrogen bonds : angle 5.63379 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8344 (mtpm) REVERT: A 281 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8354 (mtpp) REVERT: A 317 LYS cc_start: 0.8638 (mttt) cc_final: 0.8425 (ttmm) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 1.4692 time to fit residues: 47.5188 Evaluate side-chains 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain C residue 281 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 12 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: C 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.140451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.127798 restraints weight = 4552.737| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.83 r_work: 0.3946 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1353 Z= 0.112 Angle : 0.621 5.130 1809 Z= 0.310 Chirality : 0.054 0.129 207 Planarity : 0.004 0.031 228 Dihedral : 5.882 22.112 183 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.21 % Allowed : 21.79 % Favored : 75.00 % 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: -2.87 (0.50), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.38), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 310 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 1353) covalent geometry : angle 0.62057 ( 1809) hydrogen bonds : bond 0.02483 ( 20) hydrogen bonds : angle 5.13322 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.077 Fit side-chains REVERT: B 317 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8392 (mtpp) REVERT: A 281 LYS cc_start: 0.8631 (tppp) cc_final: 0.8347 (mtpp) outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 1.5282 time to fit residues: 47.8374 Evaluate side-chains 31 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 276 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.140937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.128539 restraints weight = 4482.613| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.78 r_work: 0.3968 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1353 Z= 0.112 Angle : 0.587 4.419 1809 Z= 0.294 Chirality : 0.053 0.129 207 Planarity : 0.003 0.029 228 Dihedral : 5.672 21.206 183 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.21 % Allowed : 23.08 % Favored : 73.72 % 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: -2.77 (0.52), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.39), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR C 310 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 1353) covalent geometry : angle 0.58738 ( 1809) hydrogen bonds : bond 0.02155 ( 20) hydrogen bonds : angle 5.02464 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.090 Fit side-chains REVERT: B 281 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7852 (mtpp) REVERT: A 281 LYS cc_start: 0.8604 (tppp) cc_final: 0.8353 (mtpp) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 1.4596 time to fit residues: 48.6783 Evaluate side-chains 31 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 276 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.136581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.124998 restraints weight = 4818.644| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.77 r_work: 0.3945 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1353 Z= 0.145 Angle : 0.625 5.504 1809 Z= 0.309 Chirality : 0.053 0.127 207 Planarity : 0.003 0.031 228 Dihedral : 5.683 21.184 183 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.92 % Allowed : 23.08 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.52), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.40), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR C 310 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 1353) covalent geometry : angle 0.62519 ( 1809) hydrogen bonds : bond 0.01901 ( 20) hydrogen bonds : angle 5.04866 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.079 Fit side-chains REVERT: A 281 LYS cc_start: 0.8603 (tppp) cc_final: 0.8369 (mtpp) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 1.4204 time to fit residues: 43.0514 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.139682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.127553 restraints weight = 4597.433| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.79 r_work: 0.3958 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1353 Z= 0.116 Angle : 0.613 5.068 1809 Z= 0.299 Chirality : 0.053 0.123 207 Planarity : 0.003 0.030 228 Dihedral : 5.571 20.954 183 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.64 % Allowed : 25.00 % Favored : 74.36 % 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: -2.65 (0.54), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR C 310 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 1353) covalent geometry : angle 0.61322 ( 1809) hydrogen bonds : bond 0.01804 ( 20) hydrogen bonds : angle 4.84980 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.093 Fit side-chains REVERT: A 281 LYS cc_start: 0.8615 (tppp) cc_final: 0.8385 (mtpp) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 1.2180 time to fit residues: 35.7608 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.140164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.128074 restraints weight = 4668.914| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.80 r_work: 0.3964 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1353 Z= 0.109 Angle : 0.612 5.058 1809 Z= 0.294 Chirality : 0.053 0.124 207 Planarity : 0.003 0.029 228 Dihedral : 5.499 20.962 183 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.64 % Allowed : 25.00 % Favored : 74.36 % 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: -2.62 (0.54), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR C 310 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 1353) covalent geometry : angle 0.61218 ( 1809) hydrogen bonds : bond 0.01765 ( 20) hydrogen bonds : angle 4.70229 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.046 Fit side-chains REVERT: A 281 LYS cc_start: 0.8615 (tppp) cc_final: 0.8376 (mtpp) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 1.3319 time to fit residues: 40.3562 Evaluate side-chains 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.138843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.126483 restraints weight = 4707.914| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.80 r_work: 0.3955 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1353 Z= 0.123 Angle : 0.626 5.751 1809 Z= 0.300 Chirality : 0.053 0.125 207 Planarity : 0.003 0.029 228 Dihedral : 5.546 21.098 183 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 25.64 % Favored : 74.36 % 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: -2.61 (0.54), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 310 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 1353) covalent geometry : angle 0.62636 ( 1809) hydrogen bonds : bond 0.01738 ( 20) hydrogen bonds : angle 4.72125 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.085 Fit side-chains REVERT: A 281 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8364 (mtpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 1.4734 time to fit residues: 40.1924 Evaluate side-chains 26 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.138798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.126289 restraints weight = 4615.280| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.79 r_work: 0.3960 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1353 Z= 0.118 Angle : 0.629 5.953 1809 Z= 0.299 Chirality : 0.053 0.133 207 Planarity : 0.003 0.028 228 Dihedral : 5.502 21.604 183 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.64 % Allowed : 26.28 % Favored : 73.08 % 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: -2.63 (0.54), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 310 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 1353) covalent geometry : angle 0.62867 ( 1809) hydrogen bonds : bond 0.01754 ( 20) hydrogen bonds : angle 4.71275 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 354 Ramachandran restraints generated. 177 Oldfield, 0 Emsley, 177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.075 Fit side-chains REVERT: A 281 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8336 (mtpp) outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 1.4253 time to fit residues: 38.9240 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.138773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.126356 restraints weight = 4539.808| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.78 r_work: 0.3956 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1353 Z= 0.122 Angle : 0.632 6.116 1809 Z= 0.299 Chirality : 0.053 0.143 207 Planarity : 0.003 0.028 228 Dihedral : 5.481 21.898 183 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.64 % Allowed : 26.28 % Favored : 73.08 % 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: -2.64 (0.54), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.000 TYR C 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 1353) covalent geometry : angle 0.63209 ( 1809) hydrogen bonds : bond 0.01749 ( 20) hydrogen bonds : angle 4.70394 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.52 seconds wall clock time: 32 minutes 3.98 seconds (1923.98 seconds total)