Starting phenix.real_space_refine on Fri Aug 22 19:28:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jy7_36722/08_2025/8jy7_36722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jy7_36722/08_2025/8jy7_36722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jy7_36722/08_2025/8jy7_36722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jy7_36722/08_2025/8jy7_36722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jy7_36722/08_2025/8jy7_36722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jy7_36722/08_2025/8jy7_36722.map" } resolution = 3.2 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= 0.185 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4912 2.51 5 N 1116 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7292 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1823 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Restraints were copied for chains: B, C, D Time building chain proxies: 1.51, per 1000 atoms: 0.21 Number of scatterers: 7292 At special positions: 0 Unit cell: (92.568, 92.568, 63.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1232 8.00 N 1116 7.00 C 4912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 448.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 71 through 98 Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.989A pdb=" N VAL A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.624A pdb=" N THR A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 136 through 139 removed outlier: 3.689A pdb=" N VAL A 139 " --> pdb=" O GLY A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 170 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.912A pdb=" N GLY A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.251A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 226 Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 261 through 276 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.811A pdb=" N VAL A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 281 " --> pdb=" O GLY A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 281' Processing helix chain 'A' and resid 288 through 310 Proline residue: A 295 - end of helix Processing helix chain 'B' and resid 72 through 98 Processing helix chain 'B' and resid 103 through 122 removed outlier: 3.989A pdb=" N VAL B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.624A pdb=" N THR B 134 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 130 through 135' Processing helix chain 'B' and resid 136 through 139 removed outlier: 3.690A pdb=" N VAL B 139 " --> pdb=" O GLY B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 170 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.913A pdb=" N GLY B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.251A pdb=" N PHE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 226 Processing helix chain 'B' and resid 236 through 253 Processing helix chain 'B' and resid 261 through 276 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.810A pdb=" N VAL B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 281 " --> pdb=" O GLY B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 281' Processing helix chain 'B' and resid 288 through 310 Proline residue: B 295 - end of helix Processing helix chain 'C' and resid 72 through 98 Processing helix chain 'C' and resid 103 through 122 removed outlier: 3.989A pdb=" N VAL C 120 " --> pdb=" O MET C 116 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.624A pdb=" N THR C 134 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 136 through 139 removed outlier: 3.689A pdb=" N VAL C 139 " --> pdb=" O GLY C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 170 Processing helix chain 'C' and resid 175 through 179 removed outlier: 3.913A pdb=" N GLY C 179 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.251A pdb=" N PHE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 226 Processing helix chain 'C' and resid 236 through 253 Processing helix chain 'C' and resid 261 through 276 Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.811A pdb=" N VAL C 280 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 281 " --> pdb=" O GLY C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 281' Processing helix chain 'C' and resid 288 through 310 Proline residue: C 295 - end of helix Processing helix chain 'D' and resid 72 through 98 Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.989A pdb=" N VAL D 120 " --> pdb=" O MET D 116 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 3.624A pdb=" N THR D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 130 through 135' Processing helix chain 'D' and resid 136 through 139 removed outlier: 3.689A pdb=" N VAL D 139 " --> pdb=" O GLY D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 147 through 170 Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.913A pdb=" N GLY D 179 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.250A pdb=" N PHE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 226 Processing helix chain 'D' and resid 236 through 253 Processing helix chain 'D' and resid 261 through 276 Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.810A pdb=" N VAL D 280 " --> pdb=" O GLY D 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 281 " --> pdb=" O GLY D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 277 through 281' Processing helix chain 'D' and resid 288 through 310 Proline residue: D 295 - end of helix 469 hydrogen bonds defined for protein. 1395 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: 1.10 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: 1.22 - 1.34: 2185 1.34 - 1.46: 1524 1.46 - 1.57: 3759 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 7520 Sorted by residual: bond pdb=" CA ASN B 137 " pdb=" CB ASN B 137 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.31e-02 5.83e+03 9.63e-01 bond pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.31e-02 5.83e+03 9.63e-01 bond pdb=" CA ASN D 137 " pdb=" CB ASN D 137 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.31e-02 5.83e+03 8.65e-01 bond pdb=" CA ASN C 137 " pdb=" CB ASN C 137 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.31e-02 5.83e+03 8.31e-01 bond pdb=" CB PRO C 232 " pdb=" CG PRO C 232 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 7.97e-01 ... (remaining 7515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 9740 1.14 - 2.28: 393 2.28 - 3.41: 82 3.41 - 4.55: 33 4.55 - 5.69: 16 Bond angle restraints: 10264 Sorted by residual: angle pdb=" C VAL D 290 " pdb=" CA VAL D 290 " pdb=" CB VAL D 290 " ideal model delta sigma weight residual 114.00 111.46 2.54 1.31e+00 5.83e-01 3.74e+00 angle pdb=" C VAL C 290 " pdb=" CA VAL C 290 " pdb=" CB VAL C 290 " ideal model delta sigma weight residual 114.00 111.48 2.52 1.31e+00 5.83e-01 3.71e+00 angle pdb=" C VAL A 290 " pdb=" CA VAL A 290 " pdb=" CB VAL A 290 " ideal model delta sigma weight residual 114.00 111.50 2.50 1.31e+00 5.83e-01 3.65e+00 angle pdb=" C VAL B 290 " pdb=" CA VAL B 290 " pdb=" CB VAL B 290 " ideal model delta sigma weight residual 114.00 111.53 2.47 1.31e+00 5.83e-01 3.57e+00 angle pdb=" CA TYR A 206 " pdb=" C TYR A 206 " pdb=" N PRO A 207 " ideal model delta sigma weight residual 118.44 121.43 -2.99 1.59e+00 3.96e-01 3.54e+00 ... (remaining 10259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.63: 3569 11.63 - 23.26: 379 23.26 - 34.89: 184 34.89 - 46.51: 24 46.51 - 58.14: 12 Dihedral angle restraints: 4168 sinusoidal: 1472 harmonic: 2696 Sorted by residual: dihedral pdb=" CB MET B 116 " pdb=" CG MET B 116 " pdb=" SD MET B 116 " pdb=" CE MET B 116 " ideal model delta sinusoidal sigma weight residual 60.00 118.14 -58.14 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET A 116 " pdb=" CG MET A 116 " pdb=" SD MET A 116 " pdb=" CE MET A 116 " ideal model delta sinusoidal sigma weight residual 60.00 118.12 -58.12 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET C 116 " pdb=" CG MET C 116 " pdb=" SD MET C 116 " pdb=" CE MET C 116 " ideal model delta sinusoidal sigma weight residual 60.00 118.12 -58.12 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 626 0.028 - 0.056: 356 0.056 - 0.084: 126 0.084 - 0.112: 32 0.112 - 0.140: 8 Chirality restraints: 1148 Sorted by residual: chirality pdb=" CA TYR A 206 " pdb=" N TYR A 206 " pdb=" C TYR A 206 " pdb=" CB TYR A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA TYR D 206 " pdb=" N TYR D 206 " pdb=" C TYR D 206 " pdb=" CB TYR D 206 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA TYR C 206 " pdb=" N TYR C 206 " pdb=" C TYR C 206 " pdb=" CB TYR C 206 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1145 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 148 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 149 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 148 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO D 149 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 148 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO C 149 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.018 5.00e-02 4.00e+02 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2543 2.85 - 3.36: 7318 3.36 - 3.88: 12558 3.88 - 4.39: 13826 4.39 - 4.90: 24561 Nonbonded interactions: 60806 Sorted by model distance: nonbonded pdb=" O SER B 121 " pdb=" OG SER B 125 " model vdw 2.340 3.040 nonbonded pdb=" O SER A 121 " pdb=" OG SER A 125 " model vdw 2.340 3.040 nonbonded pdb=" O SER C 121 " pdb=" OG SER C 125 " model vdw 2.341 3.040 nonbonded pdb=" O SER D 121 " pdb=" OG SER D 125 " model vdw 2.341 3.040 nonbonded pdb=" O ASN B 251 " pdb=" OG1 THR C 94 " model vdw 2.366 3.040 ... (remaining 60801 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.390 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.003 0.045 7520 Z= 0.126 Angle : 0.596 5.688 10264 Z= 0.309 Chirality : 0.039 0.140 1148 Planarity : 0.005 0.032 1292 Dihedral : 12.176 58.142 2488 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.27), residues: 960 helix: 1.98 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.96 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 146 TYR 0.019 0.001 TYR B 206 PHE 0.014 0.001 PHE D 185 TRP 0.007 0.001 TRP A 289 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7520) covalent geometry : angle 0.59588 (10264) hydrogen bonds : bond 0.13793 ( 469) hydrogen bonds : angle 5.91707 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.6788 (t80) cc_final: 0.6427 (t80) REVERT: B 236 TYR cc_start: 0.8098 (p90) cc_final: 0.7878 (p90) REVERT: B 286 TYR cc_start: 0.7484 (m-80) cc_final: 0.7279 (m-10) REVERT: B 304 PHE cc_start: 0.8251 (t80) cc_final: 0.8006 (t80) REVERT: C 205 PHE cc_start: 0.7090 (t80) cc_final: 0.6854 (t80) REVERT: C 236 TYR cc_start: 0.8172 (p90) cc_final: 0.7919 (p90) REVERT: C 308 TYR cc_start: 0.6762 (t80) cc_final: 0.6413 (t80) REVERT: D 100 ASP cc_start: 0.7110 (m-30) cc_final: 0.6887 (m-30) REVERT: D 205 PHE cc_start: 0.7131 (t80) cc_final: 0.6885 (t80) REVERT: D 308 TYR cc_start: 0.6787 (t80) cc_final: 0.6483 (t80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0601 time to fit residues: 17.9997 Evaluate side-chains 158 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.151269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.126694 restraints weight = 8996.693| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.66 r_work: 0.3108 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7520 Z= 0.145 Angle : 0.578 6.436 10264 Z= 0.292 Chirality : 0.039 0.114 1148 Planarity : 0.005 0.047 1292 Dihedral : 3.960 15.656 1028 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.61 % Allowed : 9.89 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.27), residues: 960 helix: 1.68 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.75 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 269 TYR 0.022 0.002 TYR B 206 PHE 0.018 0.002 PHE A 304 TRP 0.003 0.001 TRP A 192 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7520) covalent geometry : angle 0.57823 (10264) hydrogen bonds : bond 0.04279 ( 469) hydrogen bonds : angle 4.56018 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7401 (m-10) cc_final: 0.6918 (m-80) REVERT: B 236 TYR cc_start: 0.8417 (p90) cc_final: 0.8076 (p90) REVERT: C 236 TYR cc_start: 0.8386 (p90) cc_final: 0.8063 (p90) REVERT: D 100 ASP cc_start: 0.8016 (m-30) cc_final: 0.7783 (m-30) outliers start: 19 outliers final: 15 residues processed: 173 average time/residue: 0.0573 time to fit residues: 14.8095 Evaluate side-chains 174 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 172 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 chunk 83 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** 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 = 0.3562 r_free = 0.3562 target = 0.149288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.125057 restraints weight = 9037.638| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.67 r_work: 0.3126 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7520 Z= 0.117 Angle : 0.523 5.851 10264 Z= 0.267 Chirality : 0.037 0.112 1148 Planarity : 0.005 0.049 1292 Dihedral : 3.951 15.186 1028 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.79 % Allowed : 14.01 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.27), residues: 960 helix: 1.40 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.24 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.016 0.002 TYR C 206 PHE 0.021 0.001 PHE B 304 TRP 0.003 0.001 TRP D 289 HIS 0.002 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7520) covalent geometry : angle 0.52294 (10264) hydrogen bonds : bond 0.03707 ( 469) hydrogen bonds : angle 4.32558 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7414 (m-10) cc_final: 0.6919 (m-80) REVERT: B 236 TYR cc_start: 0.8437 (p90) cc_final: 0.8062 (p90) REVERT: C 236 TYR cc_start: 0.8425 (p90) cc_final: 0.8042 (p90) REVERT: D 106 LEU cc_start: 0.8638 (tt) cc_final: 0.8323 (tp) outliers start: 13 outliers final: 9 residues processed: 158 average time/residue: 0.0553 time to fit residues: 12.9982 Evaluate side-chains 167 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 0.3980 chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** 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 = 0.3561 r_free = 0.3561 target = 0.150010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.125305 restraints weight = 9168.871| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.69 r_work: 0.3112 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7520 Z= 0.110 Angle : 0.513 5.849 10264 Z= 0.262 Chirality : 0.037 0.110 1148 Planarity : 0.005 0.049 1292 Dihedral : 3.932 16.167 1028 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.79 % Allowed : 16.35 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.27), residues: 960 helix: 1.55 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.012 0.001 TYR D 206 PHE 0.009 0.001 PHE B 304 TRP 0.003 0.001 TRP B 289 HIS 0.001 0.001 HIS D 283 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7520) covalent geometry : angle 0.51272 (10264) hydrogen bonds : bond 0.03437 ( 469) hydrogen bonds : angle 4.22359 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7406 (m-10) cc_final: 0.6924 (m-80) REVERT: B 236 TYR cc_start: 0.8449 (p90) cc_final: 0.8042 (p90) REVERT: C 236 TYR cc_start: 0.8411 (p90) cc_final: 0.8011 (p90) REVERT: D 106 LEU cc_start: 0.8654 (tt) cc_final: 0.8287 (tp) outliers start: 13 outliers final: 10 residues processed: 164 average time/residue: 0.0516 time to fit residues: 12.6058 Evaluate side-chains 171 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 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 = 0.3561 r_free = 0.3561 target = 0.149912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.124838 restraints weight = 9049.856| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.71 r_work: 0.3126 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7520 Z= 0.110 Angle : 0.510 6.114 10264 Z= 0.260 Chirality : 0.037 0.118 1148 Planarity : 0.005 0.049 1292 Dihedral : 3.914 17.101 1028 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.79 % Allowed : 17.17 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.27), residues: 960 helix: 1.51 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.16 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.015 0.001 TYR D 206 PHE 0.025 0.001 PHE A 304 TRP 0.003 0.000 TRP D 289 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7520) covalent geometry : angle 0.50958 (10264) hydrogen bonds : bond 0.03408 ( 469) hydrogen bonds : angle 4.20552 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7358 (m-10) cc_final: 0.6857 (m-80) REVERT: B 236 TYR cc_start: 0.8446 (p90) cc_final: 0.8037 (p90) REVERT: C 236 TYR cc_start: 0.8436 (p90) cc_final: 0.8103 (p90) REVERT: D 106 LEU cc_start: 0.8638 (tt) cc_final: 0.8225 (tp) REVERT: D 206 TYR cc_start: 0.6999 (m-80) cc_final: 0.6539 (m-80) outliers start: 13 outliers final: 12 residues processed: 158 average time/residue: 0.0602 time to fit residues: 14.1427 Evaluate side-chains 170 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.2980 chunk 2 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.147811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.123004 restraints weight = 9135.172| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.68 r_work: 0.3077 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7520 Z= 0.124 Angle : 0.528 6.197 10264 Z= 0.271 Chirality : 0.037 0.116 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.031 18.367 1028 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.20 % Allowed : 16.48 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.27), residues: 960 helix: 1.55 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.29 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.013 0.001 TYR D 206 PHE 0.008 0.001 PHE C 246 TRP 0.002 0.001 TRP A 289 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7520) covalent geometry : angle 0.52752 (10264) hydrogen bonds : bond 0.03622 ( 469) hydrogen bonds : angle 4.28487 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7367 (m-10) cc_final: 0.6870 (m-80) REVERT: B 236 TYR cc_start: 0.8504 (p90) cc_final: 0.8165 (p90) REVERT: C 236 TYR cc_start: 0.8448 (p90) cc_final: 0.8118 (p90) REVERT: C 308 TYR cc_start: 0.6911 (t80) cc_final: 0.6701 (t80) outliers start: 16 outliers final: 15 residues processed: 163 average time/residue: 0.0609 time to fit residues: 14.7835 Evaluate side-chains 175 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.147768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.122667 restraints weight = 9153.077| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.69 r_work: 0.3072 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7520 Z= 0.120 Angle : 0.527 6.453 10264 Z= 0.271 Chirality : 0.037 0.114 1148 Planarity : 0.005 0.050 1292 Dihedral : 4.082 19.154 1028 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.47 % Allowed : 16.76 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.27), residues: 960 helix: 1.60 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.22 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.013 0.001 TYR D 206 PHE 0.008 0.001 PHE B 160 TRP 0.002 0.001 TRP C 289 HIS 0.005 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7520) covalent geometry : angle 0.52746 (10264) hydrogen bonds : bond 0.03513 ( 469) hydrogen bonds : angle 4.27645 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7376 (m-10) cc_final: 0.6683 (m-80) REVERT: B 236 TYR cc_start: 0.8500 (p90) cc_final: 0.8162 (p90) REVERT: C 236 TYR cc_start: 0.8468 (p90) cc_final: 0.8149 (p90) REVERT: C 237 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: C 308 TYR cc_start: 0.6943 (t80) cc_final: 0.6721 (t80) REVERT: D 206 TYR cc_start: 0.7041 (m-80) cc_final: 0.6622 (m-80) REVERT: D 237 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6405 (mp0) outliers start: 18 outliers final: 16 residues processed: 159 average time/residue: 0.0573 time to fit residues: 13.6075 Evaluate side-chains 171 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 88 optimal weight: 0.0670 chunk 80 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 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 = 0.3522 r_free = 0.3522 target = 0.146349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.120943 restraints weight = 9143.261| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.70 r_work: 0.3045 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7520 Z= 0.132 Angle : 0.535 6.247 10264 Z= 0.277 Chirality : 0.037 0.114 1148 Planarity : 0.005 0.050 1292 Dihedral : 4.164 19.815 1028 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.02 % Allowed : 15.38 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.27), residues: 960 helix: 1.56 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.17 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.013 0.001 TYR D 206 PHE 0.009 0.001 PHE D 246 TRP 0.003 0.001 TRP C 289 HIS 0.008 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7520) covalent geometry : angle 0.53472 (10264) hydrogen bonds : bond 0.03700 ( 469) hydrogen bonds : angle 4.33111 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: A 286 TYR cc_start: 0.7376 (m-10) cc_final: 0.6876 (m-80) REVERT: B 236 TYR cc_start: 0.8496 (p90) cc_final: 0.8148 (p90) REVERT: C 206 TYR cc_start: 0.7058 (m-80) cc_final: 0.6607 (m-80) REVERT: C 236 TYR cc_start: 0.8472 (p90) cc_final: 0.8147 (p90) REVERT: C 237 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: D 237 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: D 304 PHE cc_start: 0.8273 (t80) cc_final: 0.7987 (t80) outliers start: 22 outliers final: 16 residues processed: 164 average time/residue: 0.0548 time to fit residues: 13.4684 Evaluate side-chains 175 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.147068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.121676 restraints weight = 9062.444| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.70 r_work: 0.3070 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7520 Z= 0.118 Angle : 0.520 5.895 10264 Z= 0.269 Chirality : 0.037 0.114 1148 Planarity : 0.005 0.051 1292 Dihedral : 4.112 17.396 1028 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.20 % Allowed : 16.76 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.28), residues: 960 helix: 1.63 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.12 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.013 0.001 TYR D 206 PHE 0.028 0.001 PHE B 304 TRP 0.003 0.000 TRP D 289 HIS 0.013 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7520) covalent geometry : angle 0.51963 (10264) hydrogen bonds : bond 0.03487 ( 469) hydrogen bonds : angle 4.30016 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: A 286 TYR cc_start: 0.7374 (m-10) cc_final: 0.6684 (m-80) REVERT: B 236 TYR cc_start: 0.8480 (p90) cc_final: 0.8141 (p90) REVERT: C 236 TYR cc_start: 0.8457 (p90) cc_final: 0.8140 (p90) REVERT: C 237 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: C 307 LYS cc_start: 0.6342 (mmtt) cc_final: 0.5987 (mttp) REVERT: D 237 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6427 (mp0) outliers start: 16 outliers final: 12 residues processed: 157 average time/residue: 0.0559 time to fit residues: 13.0130 Evaluate side-chains 169 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 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 = 0.3507 r_free = 0.3507 target = 0.145199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.120005 restraints weight = 9116.492| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.67 r_work: 0.3040 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7520 Z= 0.135 Angle : 0.540 6.644 10264 Z= 0.280 Chirality : 0.038 0.114 1148 Planarity : 0.005 0.050 1292 Dihedral : 4.245 20.585 1028 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.06 % Allowed : 16.90 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.28), residues: 960 helix: 1.55 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.10 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.011 0.001 TYR D 206 PHE 0.036 0.001 PHE B 304 TRP 0.003 0.001 TRP C 289 HIS 0.008 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7520) covalent geometry : angle 0.53972 (10264) hydrogen bonds : bond 0.03742 ( 469) hydrogen bonds : angle 4.36642 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: A 286 TYR cc_start: 0.7393 (m-10) cc_final: 0.6768 (m-80) REVERT: B 236 TYR cc_start: 0.8493 (p90) cc_final: 0.8152 (p90) REVERT: C 236 TYR cc_start: 0.8448 (p90) cc_final: 0.8124 (p90) REVERT: C 237 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: C 304 PHE cc_start: 0.8333 (t80) cc_final: 0.8056 (t80) REVERT: C 307 LYS cc_start: 0.6392 (mmtt) cc_final: 0.6040 (mttp) REVERT: D 206 TYR cc_start: 0.7066 (m-80) cc_final: 0.6660 (m-80) REVERT: D 237 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: D 304 PHE cc_start: 0.8287 (t80) cc_final: 0.7987 (t80) outliers start: 15 outliers final: 12 residues processed: 166 average time/residue: 0.0547 time to fit residues: 13.4478 Evaluate side-chains 179 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 92 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.143868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.119783 restraints weight = 9036.632| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.56 r_work: 0.3065 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7520 Z= 0.117 Angle : 0.519 5.648 10264 Z= 0.270 Chirality : 0.037 0.113 1148 Planarity : 0.005 0.050 1292 Dihedral : 4.146 17.944 1028 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.92 % Allowed : 17.58 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.28), residues: 960 helix: 1.65 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.06 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.013 0.001 TYR D 206 PHE 0.034 0.001 PHE B 304 TRP 0.003 0.000 TRP B 289 HIS 0.008 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7520) covalent geometry : angle 0.51873 (10264) hydrogen bonds : bond 0.03461 ( 469) hydrogen bonds : angle 4.30502 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.47 seconds wall clock time: 27 minutes 49.45 seconds (1669.45 seconds total)