Starting phenix.real_space_refine on Tue Feb 3 12:35:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s2b_54485/02_2026/9s2b_54485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s2b_54485/02_2026/9s2b_54485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s2b_54485/02_2026/9s2b_54485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s2b_54485/02_2026/9s2b_54485.map" model { file = "/net/cci-nas-00/data/ceres_data/9s2b_54485/02_2026/9s2b_54485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s2b_54485/02_2026/9s2b_54485.cif" } resolution = 2.9 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: 4 Type Number sf(0) Gaussians C 642 2.51 5 N 168 2.21 5 O 168 1.98 5 H 1080 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2058 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Classifications: {'peptide': 22} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Classifications: {'peptide': 22} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Classifications: {'peptide': 22} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "B" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Classifications: {'peptide': 22} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "C" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Classifications: {'peptide': 22} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Classifications: {'peptide': 22} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Time building chain proxies: 0.32, per 1000 atoms: 0.16 Number of scatterers: 2058 At special positions: 0 Unit cell: (59.584, 81.472, 35.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 168 8.00 N 168 7.00 C 642 6.00 H 1080 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: 0.10 Conformation dependent library (CDL) restraints added in 29.2 milliseconds 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 228 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 298 through 299 removed outlier: 6.880A pdb=" N LYS F 298 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS A 298 " --> pdb=" O HIS C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 306 through 310 Processing sheet with id=AA3, first strand: chain 'F' and resid 313 through 314 removed outlier: 7.027A pdb=" N VAL F 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 298 through 299 removed outlier: 6.690A pdb=" N LYS E 298 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS B 298 " --> pdb=" O HIS D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.641A pdb=" N VAL E 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL B 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE E 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 313 through 314 removed outlier: 7.170A pdb=" N VAL E 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 12 hydrogen bonds defined for protein. 36 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: 0.28 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.07: 222 1.07 - 1.19: 858 1.19 - 1.31: 156 1.31 - 1.43: 210 1.43 - 1.55: 630 Bond restraints: 2076 Sorted by residual: bond pdb=" CE1 TYR F 310 " pdb=" HE1 TYR F 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 LYS D 317 " pdb=" H LYS D 317 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N SER D 305 " pdb=" H SER D 305 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLY A 302 " pdb=" H GLY A 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 VAL D 309 " pdb=" H VAL D 309 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 2071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 2489 1.53 - 3.07: 963 3.07 - 4.60: 223 4.60 - 6.14: 101 6.14 - 7.67: 52 Bond angle restraints: 3828 Sorted by residual: angle pdb=" CB HIS D 299 " pdb=" CG HIS D 299 " pdb=" CD2 HIS D 299 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.30e+01 angle pdb=" CB HIS A 299 " pdb=" CG HIS A 299 " pdb=" CD2 HIS A 299 " ideal model delta sigma weight residual 131.20 125.14 6.06 1.30e+00 5.92e-01 2.17e+01 angle pdb=" OE1 GLN C 307 " pdb=" CD GLN C 307 " pdb=" NE2 GLN C 307 " ideal model delta sigma weight residual 122.60 117.95 4.65 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CB HIS F 299 " pdb=" CG HIS F 299 " pdb=" CD2 HIS F 299 " ideal model delta sigma weight residual 131.20 125.19 6.01 1.30e+00 5.92e-01 2.14e+01 angle pdb=" OE1 GLN A 307 " pdb=" CD GLN A 307 " pdb=" NE2 GLN A 307 " ideal model delta sigma weight residual 122.60 117.99 4.61 1.00e+00 1.00e+00 2.12e+01 ... (remaining 3823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 836 16.92 - 33.85: 46 33.85 - 50.77: 15 50.77 - 67.69: 45 67.69 - 84.61: 6 Dihedral angle restraints: 948 sinusoidal: 546 harmonic: 402 Sorted by residual: dihedral pdb=" CA VAL E 306 " pdb=" C VAL E 306 " pdb=" N GLN E 307 " pdb=" CA GLN E 307 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA VAL C 306 " pdb=" C VAL C 306 " pdb=" N GLN C 307 " pdb=" CA GLN C 307 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA VAL B 306 " pdb=" C VAL B 306 " pdb=" N GLN B 307 " pdb=" CA GLN B 307 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 74 0.044 - 0.088: 52 0.088 - 0.131: 16 0.131 - 0.175: 11 0.175 - 0.219: 9 Chirality restraints: 162 Sorted by residual: chirality pdb=" CA LYS F 311 " pdb=" N LYS F 311 " pdb=" C LYS F 311 " pdb=" CB LYS F 311 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LYS A 311 " pdb=" N LYS A 311 " pdb=" C LYS A 311 " pdb=" CB LYS A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 159 not shown) Planarity restraints: 276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 307 " 0.057 2.00e-02 2.50e+03 5.28e-02 4.19e+01 pdb=" CD GLN B 307 " -0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN B 307 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 GLN B 307 " -0.028 2.00e-02 2.50e+03 pdb="HE21 GLN B 307 " -0.054 2.00e-02 2.50e+03 pdb="HE22 GLN B 307 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 299 " 0.071 2.00e-02 2.50e+03 4.01e-02 3.62e+01 pdb=" CG HIS D 299 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS D 299 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS D 299 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS D 299 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS D 299 " -0.028 2.00e-02 2.50e+03 pdb=" HD2 HIS D 299 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 HIS D 299 " 0.026 2.00e-02 2.50e+03 pdb=" HE2 HIS D 299 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 299 " -0.073 2.00e-02 2.50e+03 3.96e-02 3.52e+01 pdb=" CG HIS A 299 " 0.049 2.00e-02 2.50e+03 pdb=" ND1 HIS A 299 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS A 299 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 HIS A 299 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 299 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 HIS A 299 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS A 299 " -0.022 2.00e-02 2.50e+03 pdb=" HE2 HIS A 299 " -0.056 2.00e-02 2.50e+03 ... (remaining 273 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.16: 115 2.16 - 2.75: 3049 2.75 - 3.33: 5344 3.33 - 3.92: 6476 3.92 - 4.50: 8778 Nonbonded interactions: 23762 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.579 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.592 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.592 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.596 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.610 2.450 ... (remaining 23757 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.000 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 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 : 0.012 0.033 996 Z= 0.719 Angle : 1.841 6.417 1344 Z= 1.236 Chirality : 0.081 0.219 162 Planarity : 0.010 0.037 162 Dihedral : 13.621 84.611 372 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: 0.42 (0.71), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.33 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.009 TYR B 310 HIS 0.015 0.007 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.01151 ( 996) covalent geometry : angle 1.84095 ( 1344) hydrogen bonds : bond 0.17469 ( 12) hydrogen bonds : angle 6.79478 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 298 LYS cc_start: 0.7495 (mtmt) cc_final: 0.6251 (mptt) REVERT: F 317 LYS cc_start: 0.7962 (mttt) cc_final: 0.7741 (tmtt) REVERT: A 298 LYS cc_start: 0.7232 (mtmt) cc_final: 0.6043 (mptt) REVERT: A 311 LYS cc_start: 0.8575 (mttt) cc_final: 0.8353 (mttp) REVERT: A 317 LYS cc_start: 0.8052 (mttt) cc_final: 0.7791 (tmtt) REVERT: C 298 LYS cc_start: 0.8073 (mtmt) cc_final: 0.6823 (mptt) REVERT: C 311 LYS cc_start: 0.8747 (mttt) cc_final: 0.8453 (mttp) REVERT: C 317 LYS cc_start: 0.8416 (mttt) cc_final: 0.8091 (pmtt) REVERT: D 298 LYS cc_start: 0.7906 (mtmt) cc_final: 0.6982 (mptt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 1.0977 time to fit residues: 27.7051 Evaluate side-chains 23 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.120751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.091273 restraints weight = 3769.083| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.76 r_work: 0.3716 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 996 Z= 0.156 Angle : 0.640 3.736 1344 Z= 0.315 Chirality : 0.057 0.118 162 Planarity : 0.003 0.017 162 Dihedral : 6.946 15.677 132 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % 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: 0.52 (0.66), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.41 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 310 HIS 0.005 0.002 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 996) covalent geometry : angle 0.64016 ( 1344) hydrogen bonds : bond 0.04809 ( 12) hydrogen bonds : angle 5.00653 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 298 LYS cc_start: 0.7915 (mtmt) cc_final: 0.6815 (mptt) REVERT: A 298 LYS cc_start: 0.7720 (mtmt) cc_final: 0.6734 (mptt) REVERT: A 311 LYS cc_start: 0.8464 (mttt) cc_final: 0.8213 (mttp) REVERT: A 317 LYS cc_start: 0.8071 (mttt) cc_final: 0.7602 (tmtt) REVERT: C 298 LYS cc_start: 0.8423 (mtmt) cc_final: 0.7478 (mptt) REVERT: C 317 LYS cc_start: 0.8727 (mttt) cc_final: 0.7949 (pmtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.3921 time to fit residues: 30.8753 Evaluate side-chains 19 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.137498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109323 restraints weight = 3501.679| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.72 r_work: 0.3745 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 996 Z= 0.111 Angle : 0.601 5.617 1344 Z= 0.280 Chirality : 0.058 0.120 162 Planarity : 0.004 0.023 162 Dihedral : 5.949 14.320 132 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.67), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.39 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 310 HIS 0.003 0.001 HIS F 299 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 996) covalent geometry : angle 0.60103 ( 1344) hydrogen bonds : bond 0.03093 ( 12) hydrogen bonds : angle 4.37498 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: F 298 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7021 (mptt) REVERT: A 311 LYS cc_start: 0.8639 (mttt) cc_final: 0.8406 (mttp) REVERT: A 317 LYS cc_start: 0.8186 (mttt) cc_final: 0.7751 (tmtt) REVERT: C 298 LYS cc_start: 0.8435 (mtmt) cc_final: 0.7563 (mptt) REVERT: C 317 LYS cc_start: 0.8794 (mttt) cc_final: 0.8049 (pmtt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 1.5127 time to fit residues: 32.0617 Evaluate side-chains 18 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.122052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.092230 restraints weight = 3831.410| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.93 r_work: 0.3633 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 996 Z= 0.105 Angle : 0.601 3.932 1344 Z= 0.271 Chirality : 0.058 0.123 162 Planarity : 0.004 0.027 162 Dihedral : 5.457 12.858 132 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 18.42 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.72), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.51 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 310 HIS 0.003 0.001 HIS F 299 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 996) covalent geometry : angle 0.60080 ( 1344) hydrogen bonds : bond 0.02336 ( 12) hydrogen bonds : angle 4.05735 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.064 Fit side-chains REVERT: F 298 LYS cc_start: 0.7910 (mtmt) cc_final: 0.6802 (mptt) REVERT: F 317 LYS cc_start: 0.8132 (mttt) cc_final: 0.7658 (tmtt) REVERT: A 298 LYS cc_start: 0.7618 (mtmt) cc_final: 0.6710 (mptt) REVERT: A 311 LYS cc_start: 0.8613 (mttt) cc_final: 0.8381 (mttp) REVERT: A 317 LYS cc_start: 0.8076 (mttt) cc_final: 0.7607 (tmtt) REVERT: B 317 LYS cc_start: 0.8272 (pptt) cc_final: 0.8069 (pptt) REVERT: C 317 LYS cc_start: 0.8754 (mttt) cc_final: 0.7919 (pmtt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 1.0721 time to fit residues: 20.5944 Evaluate side-chains 18 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.131340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.101509 restraints weight = 3569.765| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.74 r_work: 0.3742 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 996 Z= 0.091 Angle : 0.583 4.516 1344 Z= 0.261 Chirality : 0.057 0.123 162 Planarity : 0.004 0.028 162 Dihedral : 5.148 11.807 132 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 21.05 % Favored : 78.95 % 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: 0.76 (0.75), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.59 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 310 HIS 0.002 0.001 HIS F 299 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 996) covalent geometry : angle 0.58256 ( 1344) hydrogen bonds : bond 0.02099 ( 12) hydrogen bonds : angle 3.82668 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: F 298 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7005 (mptt) REVERT: A 298 LYS cc_start: 0.7657 (mtmt) cc_final: 0.6801 (mptt) REVERT: A 311 LYS cc_start: 0.8732 (mttt) cc_final: 0.8516 (mttp) REVERT: A 317 LYS cc_start: 0.8208 (mttt) cc_final: 0.7751 (tmtt) REVERT: B 317 LYS cc_start: 0.8398 (pptt) cc_final: 0.8140 (pptt) REVERT: C 317 LYS cc_start: 0.8831 (mttt) cc_final: 0.7918 (pmtt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.3957 time to fit residues: 25.3745 Evaluate side-chains 18 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.130761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.100682 restraints weight = 3598.823| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.76 r_work: 0.3733 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 996 Z= 0.101 Angle : 0.600 4.881 1344 Z= 0.264 Chirality : 0.057 0.121 162 Planarity : 0.004 0.027 162 Dihedral : 5.050 11.479 132 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 24.56 % Favored : 75.44 % 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: 0.88 (0.78), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.68 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 310 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 996) covalent geometry : angle 0.59976 ( 1344) hydrogen bonds : bond 0.02236 ( 12) hydrogen bonds : angle 3.71076 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.040 Fit side-chains revert: symmetry clash REVERT: F 298 LYS cc_start: 0.8025 (mtmt) cc_final: 0.6987 (mptt) REVERT: A 298 LYS cc_start: 0.7711 (mtmt) cc_final: 0.6784 (mptt) REVERT: A 311 LYS cc_start: 0.8723 (mttt) cc_final: 0.8515 (mttp) REVERT: A 317 LYS cc_start: 0.8227 (mttt) cc_final: 0.7770 (tmtt) REVERT: C 317 LYS cc_start: 0.8864 (mttt) cc_final: 0.7896 (pmtt) REVERT: D 314 ASP cc_start: 0.8445 (t0) cc_final: 0.7864 (t0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 1.5547 time to fit residues: 32.9239 Evaluate side-chains 19 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.130569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.101028 restraints weight = 3707.197| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.74 r_work: 0.3747 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 996 Z= 0.103 Angle : 0.622 5.962 1344 Z= 0.275 Chirality : 0.057 0.122 162 Planarity : 0.004 0.027 162 Dihedral : 4.913 11.407 132 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 24.56 % Favored : 75.44 % 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: 0.94 (0.79), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.73 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR D 310 HIS 0.002 0.001 HIS F 299 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 996) covalent geometry : angle 0.62207 ( 1344) hydrogen bonds : bond 0.02030 ( 12) hydrogen bonds : angle 3.57964 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: F 298 LYS cc_start: 0.8013 (mtmt) cc_final: 0.6937 (mptt) REVERT: A 298 LYS cc_start: 0.7705 (mtmt) cc_final: 0.6757 (mptt) REVERT: A 311 LYS cc_start: 0.8705 (mttt) cc_final: 0.8494 (mttp) REVERT: A 317 LYS cc_start: 0.8215 (mttt) cc_final: 0.7747 (tmtt) REVERT: B 317 LYS cc_start: 0.8333 (pptt) cc_final: 0.8012 (pptt) REVERT: C 317 LYS cc_start: 0.8877 (mttt) cc_final: 0.7878 (pmtt) REVERT: D 314 ASP cc_start: 0.8412 (t0) cc_final: 0.7633 (t0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 1.3517 time to fit residues: 27.3306 Evaluate side-chains 19 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.131055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.100762 restraints weight = 3674.594| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.79 r_work: 0.3733 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 996 Z= 0.100 Angle : 0.627 5.632 1344 Z= 0.274 Chirality : 0.057 0.121 162 Planarity : 0.004 0.026 162 Dihedral : 4.842 11.396 132 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 25.44 % Favored : 74.56 % 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: 0.94 (0.80), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.73 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 310 HIS 0.002 0.001 HIS F 299 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 996) covalent geometry : angle 0.62745 ( 1344) hydrogen bonds : bond 0.02137 ( 12) hydrogen bonds : angle 3.53312 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 298 LYS cc_start: 0.8081 (mtmt) cc_final: 0.6978 (mptt) REVERT: A 298 LYS cc_start: 0.7715 (mtmt) cc_final: 0.6770 (mptt) REVERT: A 311 LYS cc_start: 0.8697 (mttt) cc_final: 0.8490 (mttp) REVERT: A 317 LYS cc_start: 0.8226 (mttt) cc_final: 0.7756 (tmtt) REVERT: C 317 LYS cc_start: 0.8881 (mttt) cc_final: 0.7868 (pmtt) REVERT: D 314 ASP cc_start: 0.8410 (t0) cc_final: 0.8022 (t0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 1.0063 time to fit residues: 20.3469 Evaluate side-chains 20 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.130851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.100456 restraints weight = 3639.567| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.79 r_work: 0.3724 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 996 Z= 0.103 Angle : 0.621 5.188 1344 Z= 0.269 Chirality : 0.057 0.122 162 Planarity : 0.004 0.026 162 Dihedral : 4.791 11.473 132 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 25.44 % Favored : 74.56 % 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: 0.87 (0.79), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.67 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 310 HIS 0.002 0.001 HIS F 299 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 996) covalent geometry : angle 0.62143 ( 1344) hydrogen bonds : bond 0.02159 ( 12) hydrogen bonds : angle 3.46402 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: F 298 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7139 (mptt) REVERT: F 317 LYS cc_start: 0.8259 (mttt) cc_final: 0.7872 (tmtt) REVERT: A 298 LYS cc_start: 0.7723 (mtmt) cc_final: 0.6782 (mptt) REVERT: A 311 LYS cc_start: 0.8733 (mttt) cc_final: 0.8531 (mttp) REVERT: A 317 LYS cc_start: 0.8238 (mttt) cc_final: 0.7755 (tmtt) REVERT: C 317 LYS cc_start: 0.8879 (mttt) cc_final: 0.7875 (pmtt) REVERT: D 314 ASP cc_start: 0.8457 (t0) cc_final: 0.8034 (t0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 1.2512 time to fit residues: 26.5690 Evaluate side-chains 19 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.131209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.100673 restraints weight = 3651.374| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.79 r_work: 0.3728 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 996 Z= 0.101 Angle : 0.623 5.310 1344 Z= 0.270 Chirality : 0.057 0.121 162 Planarity : 0.004 0.025 162 Dihedral : 4.740 11.287 132 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 25.44 % Favored : 74.56 % 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: 0.92 (0.79), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.71 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.001 TYR E 310 HIS 0.002 0.001 HIS F 299 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 996) covalent geometry : angle 0.62290 ( 1344) hydrogen bonds : bond 0.02045 ( 12) hydrogen bonds : angle 3.42797 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 298 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7113 (mptt) REVERT: A 298 LYS cc_start: 0.7742 (mtmt) cc_final: 0.6802 (mptt) REVERT: A 311 LYS cc_start: 0.8722 (mttt) cc_final: 0.8521 (mttp) REVERT: A 317 LYS cc_start: 0.8251 (mttt) cc_final: 0.7776 (tmtt) REVERT: C 298 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7330 (mptt) REVERT: C 317 LYS cc_start: 0.8845 (mttt) cc_final: 0.7887 (pmtt) REVERT: D 314 ASP cc_start: 0.8428 (t0) cc_final: 0.8011 (t0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 1.0924 time to fit residues: 23.1876 Evaluate side-chains 21 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.130547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.100578 restraints weight = 3687.403| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.76 r_work: 0.3734 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 996 Z= 0.101 Angle : 0.626 5.246 1344 Z= 0.269 Chirality : 0.057 0.121 162 Planarity : 0.004 0.025 162 Dihedral : 4.721 11.275 132 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 25.44 % Favored : 74.56 % 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: 0.90 (0.79), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.70 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 310 HIS 0.002 0.001 HIS F 299 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 996) covalent geometry : angle 0.62573 ( 1344) hydrogen bonds : bond 0.02100 ( 12) hydrogen bonds : angle 3.39938 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1506.51 seconds wall clock time: 26 minutes 13.94 seconds (1573.94 seconds total)