Starting phenix.real_space_refine on Mon Feb 10 21:35:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qk3_14030/02_2025/7qk3_14030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qk3_14030/02_2025/7qk3_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_14030/02_2025/7qk3_14030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qk3_14030/02_2025/7qk3_14030.map" model { file = "/net/cci-nas-00/data/ceres_data/7qk3_14030/02_2025/7qk3_14030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qk3_14030/02_2025/7qk3_14030.cif" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 2.41, per 1000 atoms: 0.88 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: 0.75 Conformation dependent library (CDL) restraints added in 206.9 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: 0.30 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: 0.96 Time building geometry restraints manager: 0.87 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: 0.01 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: 0.780 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: 0.060 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.380 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:15.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- 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= 0.719 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.009 0.003 HIS B 299 TYR 0.013 0.004 TYR C 310 *********************** 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 : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 2.1008 time to fit residues: 91.7664 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.135871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.124315 restraints weight = 4577.074| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.77 r_work: 0.3918 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1353 Z= 0.266 Angle : 0.773 5.559 1809 Z= 0.403 Chirality : 0.057 0.153 207 Planarity : 0.005 0.037 228 Dihedral : 6.531 22.474 183 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.13 % Allowed : 17.95 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.47), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 329 TYR 0.010 0.002 TYR A 310 *********************** 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 38 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.220 Fit side-chains REVERT: B 317 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8392 (mtpm) REVERT: A 281 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8329 (mtpp) outliers start: 8 outliers final: 2 residues processed: 32 average time/residue: 2.3923 time to fit residues: 77.6855 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 : 0.243 ------------------------------------------------------------------------------- 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 3 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.139081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.126305 restraints weight = 4451.702| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.84 r_work: 0.3924 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1353 Z= 0.234 Angle : 0.661 5.078 1809 Z= 0.336 Chirality : 0.054 0.134 207 Planarity : 0.004 0.036 228 Dihedral : 6.084 22.774 183 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.21 % Allowed : 20.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.49), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.005 0.001 TYR A 310 *********************** 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: 5 poor density : 31 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8393 (mtpp) REVERT: A 281 LYS cc_start: 0.8632 (tppp) cc_final: 0.8350 (mtpp) outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 2.7632 time to fit residues: 89.5661 Evaluate side-chains 30 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER 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: 2.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.125039 restraints weight = 4546.245| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.82 r_work: 0.3927 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4893 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= 0.237 Angle : 0.635 5.290 1809 Z= 0.319 Chirality : 0.053 0.134 207 Planarity : 0.004 0.033 228 Dihedral : 5.926 22.269 183 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.50), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.38), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.003 0.001 TYR A 310 *********************** 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 33 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.179 Fit side-chains REVERT: B 317 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8420 (mtpp) REVERT: A 281 LYS cc_start: 0.8629 (tppp) cc_final: 0.8350 (mtpp) outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 3.0371 time to fit residues: 95.2768 Evaluate side-chains 30 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 276 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.140260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.127743 restraints weight = 4560.340| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.81 r_work: 0.3962 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5063 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= 0.196 Angle : 0.613 5.337 1809 Z= 0.300 Chirality : 0.053 0.126 207 Planarity : 0.003 0.030 228 Dihedral : 5.722 21.446 183 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.92 % Allowed : 24.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.51), residues: 177 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.39), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.003 0.000 TYR C 310 *********************** 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 31 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.246 Fit side-chains REVERT: A 281 LYS cc_start: 0.8613 (tppp) cc_final: 0.8336 (mtpp) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 2.8783 time to fit residues: 87.4597 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 : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.141633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.129198 restraints weight = 4510.573| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.78 r_work: 0.3977 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1353 Z= 0.196 Angle : 0.626 5.222 1809 Z= 0.302 Chirality : 0.053 0.124 207 Planarity : 0.003 0.028 228 Dihedral : 5.566 20.731 183 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.28 % Allowed : 23.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.53), 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 HIS 0.002 0.000 HIS A 299 TYR 0.003 0.000 TYR C 310 *********************** 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 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.185 Fit side-chains REVERT: B 281 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7767 (mtpp) REVERT: A 281 LYS cc_start: 0.8624 (tppp) cc_final: 0.8370 (mtpp) outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 2.9945 time to fit residues: 97.0042 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 : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.139309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.127702 restraints weight = 5027.490| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.78 r_work: 0.3978 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5379 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= 0.206 Angle : 0.601 5.348 1809 Z= 0.293 Chirality : 0.053 0.124 207 Planarity : 0.003 0.029 228 Dihedral : 5.515 20.579 183 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (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 HIS 0.002 0.000 HIS A 299 TYR 0.003 0.000 TYR C 310 *********************** 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 30 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.233 Fit side-chains REVERT: A 281 LYS cc_start: 0.8629 (tppp) cc_final: 0.8393 (mtpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 3.0852 time to fit residues: 93.6530 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.128440 restraints weight = 4616.324| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.78 r_work: 0.3975 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5474 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= 0.203 Angle : 0.624 5.656 1809 Z= 0.299 Chirality : 0.053 0.124 207 Planarity : 0.003 0.028 228 Dihedral : 5.510 20.310 183 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.64 % Allowed : 25.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (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 HIS 0.001 0.000 HIS A 299 TYR 0.003 0.000 TYR C 310 *********************** 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 29 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.237 Fit side-chains REVERT: A 281 LYS cc_start: 0.8657 (tppp) cc_final: 0.8393 (mtpp) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 3.1064 time to fit residues: 91.1705 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.0050 chunk 4 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.142249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.129878 restraints weight = 4556.269| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.75 r_work: 0.3989 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5578 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= 0.188 Angle : 0.620 5.989 1809 Z= 0.292 Chirality : 0.053 0.135 207 Planarity : 0.003 0.026 228 Dihedral : 5.402 19.616 183 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS B 299 TYR 0.003 0.000 TYR C 310 *********************** 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 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.238 Fit side-chains REVERT: A 281 LYS cc_start: 0.8631 (ttpp) cc_final: 0.8376 (mtpp) REVERT: C 281 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7872 (mtpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 3.0162 time to fit residues: 85.5245 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 : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 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 = 0.4207 r_free = 0.4207 target = 0.142433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.129907 restraints weight = 4555.926| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.77 r_work: 0.3992 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5646 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= 0.193 Angle : 0.635 6.308 1809 Z= 0.297 Chirality : 0.053 0.139 207 Planarity : 0.003 0.027 228 Dihedral : 5.296 19.287 183 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS B 299 TYR 0.003 0.000 TYR C 310 ********************** 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 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.209 Fit side-chains REVERT: A 281 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8367 (mtpp) REVERT: C 281 LYS cc_start: 0.8460 (ttpt) cc_final: 0.7917 (mtpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 3.2281 time to fit residues: 88.1902 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 : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.137532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.125072 restraints weight = 4532.315| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.77 r_work: 0.3939 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1353 Z= 0.267 Angle : 0.659 6.335 1809 Z= 0.315 Chirality : 0.053 0.146 207 Planarity : 0.003 0.028 228 Dihedral : 5.494 19.955 183 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS A 299 TYR 0.003 0.000 TYR C 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.46 seconds wall clock time: 64 minutes 49.79 seconds (3889.79 seconds total)