Starting phenix.real_space_refine on Mon Apr 28 08:32:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jy7_36722/04_2025/8jy7_36722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jy7_36722/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jy7_36722/04_2025/8jy7_36722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jy7_36722/04_2025/8jy7_36722.map" model { file = "/net/cci-nas-00/data/ceres_data/8jy7_36722/04_2025/8jy7_36722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jy7_36722/04_2025/8jy7_36722.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.185 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: C, B, D Time building chain proxies: 3.63, per 1000 atoms: 0.50 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: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.75 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: 2.02 Time building geometry restraints manager: 2.05 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.330 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.070 Find NCS groups from input model: 0.150 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP A 289 HIS 0.003 0.001 HIS B 283 PHE 0.014 0.001 PHE D 185 TYR 0.019 0.001 TYR B 206 ARG 0.003 0.001 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.13793 ( 469) hydrogen bonds : angle 5.91707 ( 1395) covalent geometry : bond 0.00272 ( 7520) covalent geometry : angle 0.59588 (10264) *********************** 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 : 0.716 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: 0.1364 time to fit residues: 39.7874 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 : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.150477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.125781 restraints weight = 8863.999| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.66 r_work: 0.3103 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7520 Z= 0.151 Angle : 0.580 6.541 10264 Z= 0.293 Chirality : 0.040 0.115 1148 Planarity : 0.005 0.048 1292 Dihedral : 3.988 15.688 1028 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 960 helix: 1.67 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.76 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 192 HIS 0.003 0.001 HIS C 128 PHE 0.016 0.002 PHE A 304 TYR 0.023 0.002 TYR A 206 ARG 0.004 0.001 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 469) hydrogen bonds : angle 4.56690 ( 1395) covalent geometry : bond 0.00363 ( 7520) covalent geometry : angle 0.57957 (10264) *********************** 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 : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7371 (m-10) cc_final: 0.6753 (m-80) REVERT: B 236 TYR cc_start: 0.8419 (p90) cc_final: 0.8083 (p90) REVERT: C 236 TYR cc_start: 0.8391 (p90) cc_final: 0.8068 (p90) outliers start: 19 outliers final: 14 residues processed: 173 average time/residue: 0.1418 time to fit residues: 35.6791 Evaluate side-chains 173 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.0270 chunk 81 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 overall best weight: 0.2816 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.150077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.125731 restraints weight = 9087.606| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.69 r_work: 0.3139 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 7520 Z= 0.105 Angle : 0.507 5.889 10264 Z= 0.257 Chirality : 0.036 0.112 1148 Planarity : 0.005 0.047 1292 Dihedral : 3.863 15.215 1028 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.51 % Allowed : 14.56 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 960 helix: 1.80 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.92 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 289 HIS 0.001 0.001 HIS A 283 PHE 0.020 0.001 PHE B 304 TYR 0.015 0.001 TYR C 206 ARG 0.002 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 469) hydrogen bonds : angle 4.25673 ( 1395) covalent geometry : bond 0.00246 ( 7520) covalent geometry : angle 0.50732 (10264) *********************** 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: 11 poor density : 160 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7410 (m-10) cc_final: 0.6907 (m-80) REVERT: B 236 TYR cc_start: 0.8419 (p90) cc_final: 0.8023 (p90) REVERT: C 236 TYR cc_start: 0.8416 (p90) cc_final: 0.8016 (p90) REVERT: D 106 LEU cc_start: 0.8621 (tt) cc_final: 0.8334 (tp) outliers start: 11 outliers final: 7 residues processed: 162 average time/residue: 0.2003 time to fit residues: 47.3984 Evaluate side-chains 166 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 2 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.148349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.123185 restraints weight = 9064.457| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.69 r_work: 0.3074 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: 0.7959 moved from start: 0.2569 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= 0.125 Angle : 0.530 5.899 10264 Z= 0.273 Chirality : 0.038 0.111 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.001 16.119 1028 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.06 % Allowed : 16.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 960 helix: 1.42 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.31 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 289 HIS 0.002 0.001 HIS A 128 PHE 0.010 0.001 PHE A 246 TYR 0.012 0.001 TYR C 151 ARG 0.002 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 469) hydrogen bonds : angle 4.29707 ( 1395) covalent geometry : bond 0.00297 ( 7520) covalent geometry : angle 0.53039 (10264) *********************** 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 176 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7434 (m-10) cc_final: 0.6945 (m-80) REVERT: A 308 TYR cc_start: 0.7075 (t80) cc_final: 0.6865 (t80) REVERT: B 236 TYR cc_start: 0.8466 (p90) cc_final: 0.8137 (p90) REVERT: C 236 TYR cc_start: 0.8445 (p90) cc_final: 0.8119 (p90) REVERT: D 106 LEU cc_start: 0.8658 (tt) cc_final: 0.8284 (tp) outliers start: 15 outliers final: 11 residues processed: 163 average time/residue: 0.1630 time to fit residues: 38.3708 Evaluate side-chains 172 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain B residue 157 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.0370 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 66 optimal weight: 0.0170 chunk 80 optimal weight: 0.9990 overall best weight: 0.1794 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.150784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.125870 restraints weight = 8875.967| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.68 r_work: 0.3135 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7520 Z= 0.099 Angle : 0.497 6.216 10264 Z= 0.252 Chirality : 0.036 0.111 1148 Planarity : 0.005 0.049 1292 Dihedral : 3.840 16.997 1028 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.55 % Allowed : 17.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 960 helix: 1.91 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -0.87 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 289 HIS 0.002 0.001 HIS B 177 PHE 0.007 0.001 PHE A 160 TYR 0.009 0.001 TYR D 236 ARG 0.002 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 469) hydrogen bonds : angle 4.11278 ( 1395) covalent geometry : bond 0.00225 ( 7520) covalent geometry : angle 0.49654 (10264) *********************** 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 164 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.6863 (m-80) cc_final: 0.6416 (m-80) REVERT: A 286 TYR cc_start: 0.7299 (m-10) cc_final: 0.6629 (m-80) REVERT: B 236 TYR cc_start: 0.8400 (p90) cc_final: 0.7969 (p90) REVERT: C 119 TYR cc_start: 0.8364 (m-80) cc_final: 0.8151 (m-80) REVERT: C 236 TYR cc_start: 0.8386 (p90) cc_final: 0.7979 (p90) REVERT: D 206 TYR cc_start: 0.6792 (m-80) cc_final: 0.6432 (m-80) outliers start: 4 outliers final: 4 residues processed: 163 average time/residue: 0.1650 time to fit residues: 39.2835 Evaluate side-chains 162 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain D residue 157 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 0.0040 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0030 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 overall best weight: 0.2600 ------------------------------------------------------------------------------- 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** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** 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 = 0.3586 r_free = 0.3586 target = 0.152133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.127248 restraints weight = 8981.539| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.68 r_work: 0.3161 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7520 Z= 0.100 Angle : 0.509 6.230 10264 Z= 0.255 Chirality : 0.036 0.120 1148 Planarity : 0.005 0.050 1292 Dihedral : 3.816 17.816 1028 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.10 % Allowed : 18.54 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.27), residues: 960 helix: 1.99 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -0.85 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 289 HIS 0.002 0.001 HIS A 177 PHE 0.016 0.001 PHE A 304 TYR 0.007 0.001 TYR A 151 ARG 0.001 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 469) hydrogen bonds : angle 4.10707 ( 1395) covalent geometry : bond 0.00235 ( 7520) covalent geometry : angle 0.50946 (10264) *********************** 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 161 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7345 (m-10) cc_final: 0.6702 (m-80) REVERT: B 236 TYR cc_start: 0.8442 (p90) cc_final: 0.8045 (p90) REVERT: C 119 TYR cc_start: 0.8373 (m-80) cc_final: 0.8160 (m-80) REVERT: C 236 TYR cc_start: 0.8440 (p90) cc_final: 0.8058 (p90) REVERT: C 308 TYR cc_start: 0.6920 (t80) cc_final: 0.6716 (t80) outliers start: 8 outliers final: 7 residues processed: 157 average time/residue: 0.1852 time to fit residues: 41.6061 Evaluate side-chains 160 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain D residue 157 LEU 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 36 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 78 optimal weight: 0.3980 chunk 79 optimal weight: 0.0000 overall best weight: 0.1068 ------------------------------------------------------------------------------- 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** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.155395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.130882 restraints weight = 8978.178| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.68 r_work: 0.3201 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 7520 Z= 0.093 Angle : 0.488 6.372 10264 Z= 0.247 Chirality : 0.036 0.114 1148 Planarity : 0.005 0.052 1292 Dihedral : 3.753 19.376 1028 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.65 % Allowed : 17.72 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.28), residues: 960 helix: 2.26 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.83 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 289 HIS 0.002 0.001 HIS B 177 PHE 0.005 0.001 PHE C 160 TYR 0.010 0.001 TYR D 236 ARG 0.001 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.02762 ( 469) hydrogen bonds : angle 4.01334 ( 1395) covalent geometry : bond 0.00213 ( 7520) covalent geometry : angle 0.48848 (10264) *********************** 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 171 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.6501 (m-80) cc_final: 0.6200 (m-80) REVERT: A 286 TYR cc_start: 0.7354 (m-10) cc_final: 0.6683 (m-80) REVERT: B 236 TYR cc_start: 0.8427 (p90) cc_final: 0.8035 (p90) REVERT: C 119 TYR cc_start: 0.8346 (m-80) cc_final: 0.8068 (m-80) REVERT: C 236 TYR cc_start: 0.8399 (p90) cc_final: 0.8000 (p90) outliers start: 12 outliers final: 10 residues processed: 162 average time/residue: 0.2197 time to fit residues: 52.0658 Evaluate side-chains 168 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 196 MET Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 135 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.147086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.121718 restraints weight = 9044.323| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.68 r_work: 0.3060 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7520 Z= 0.144 Angle : 0.567 8.141 10264 Z= 0.287 Chirality : 0.038 0.113 1148 Planarity : 0.005 0.052 1292 Dihedral : 4.085 20.713 1028 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.92 % Allowed : 18.27 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 960 helix: 1.58 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.15 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 289 HIS 0.002 0.001 HIS A 283 PHE 0.026 0.002 PHE B 304 TYR 0.007 0.001 TYR A 151 ARG 0.002 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 469) hydrogen bonds : angle 4.31362 ( 1395) covalent geometry : bond 0.00351 ( 7520) covalent geometry : angle 0.56663 (10264) *********************** 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 178 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.452 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: 0.6659 (m-80) REVERT: B 236 TYR cc_start: 0.8512 (p90) cc_final: 0.8168 (p90) REVERT: B 307 LYS cc_start: 0.6439 (mmtt) cc_final: 0.6106 (mttp) REVERT: C 236 TYR cc_start: 0.8469 (p90) cc_final: 0.8138 (p90) REVERT: C 304 PHE cc_start: 0.8346 (t80) cc_final: 0.8097 (t80) REVERT: C 307 LYS cc_start: 0.6353 (mmtt) cc_final: 0.5935 (mttp) REVERT: D 304 PHE cc_start: 0.8309 (t80) cc_final: 0.8046 (t80) outliers start: 14 outliers final: 13 residues processed: 166 average time/residue: 0.2275 time to fit residues: 54.5852 Evaluate side-chains 177 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 80 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.145475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.119743 restraints weight = 9196.894| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.72 r_work: 0.3051 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3063 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= 0.129 Angle : 0.543 7.461 10264 Z= 0.276 Chirality : 0.037 0.115 1148 Planarity : 0.005 0.052 1292 Dihedral : 4.072 18.133 1028 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.92 % Allowed : 17.99 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.28), residues: 960 helix: 1.57 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.13 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 289 HIS 0.005 0.001 HIS B 177 PHE 0.034 0.001 PHE B 304 TYR 0.008 0.001 TYR B 167 ARG 0.002 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 469) hydrogen bonds : angle 4.29675 ( 1395) covalent geometry : bond 0.00309 ( 7520) covalent geometry : angle 0.54347 (10264) *********************** 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 179 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.920 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: 0.6654 (m-80) REVERT: B 202 ASN cc_start: 0.7291 (t0) cc_final: 0.7075 (t0) REVERT: B 236 TYR cc_start: 0.8503 (p90) cc_final: 0.8173 (p90) REVERT: C 202 ASN cc_start: 0.7436 (t0) cc_final: 0.6844 (t0) REVERT: C 236 TYR cc_start: 0.8471 (p90) cc_final: 0.8144 (p90) REVERT: C 237 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: C 304 PHE cc_start: 0.8342 (t80) cc_final: 0.8085 (t80) REVERT: C 307 LYS cc_start: 0.6404 (mmtt) cc_final: 0.6053 (mttp) REVERT: D 202 ASN cc_start: 0.7348 (t0) cc_final: 0.7115 (t0) REVERT: D 304 PHE cc_start: 0.8283 (t80) cc_final: 0.8018 (t80) outliers start: 14 outliers final: 12 residues processed: 166 average time/residue: 0.1610 time to fit residues: 39.0113 Evaluate side-chains 175 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 C residue 237 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 79 optimal weight: 0.0170 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.145315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.120265 restraints weight = 9220.312| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.69 r_work: 0.3058 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7520 Z= 0.137 Angle : 0.553 7.546 10264 Z= 0.281 Chirality : 0.038 0.115 1148 Planarity : 0.005 0.051 1292 Dihedral : 4.196 18.451 1028 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.06 % Allowed : 18.13 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.28), residues: 960 helix: 1.52 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.12 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 289 HIS 0.006 0.001 HIS C 177 PHE 0.030 0.002 PHE B 304 TYR 0.009 0.001 TYR D 236 ARG 0.002 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 469) hydrogen bonds : angle 4.35413 ( 1395) covalent geometry : bond 0.00327 ( 7520) covalent geometry : angle 0.55323 (10264) ********************** 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 190 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.852 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: 0.6653 (m-80) REVERT: A 307 LYS cc_start: 0.6481 (mmtt) cc_final: 0.6054 (mttp) REVERT: B 236 TYR cc_start: 0.8492 (p90) cc_final: 0.8150 (p90) REVERT: B 304 PHE cc_start: 0.8227 (t80) cc_final: 0.8010 (t80) REVERT: C 236 TYR cc_start: 0.8481 (p90) cc_final: 0.8139 (p90) REVERT: C 237 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: C 304 PHE cc_start: 0.8362 (t80) cc_final: 0.8100 (t80) REVERT: C 307 LYS cc_start: 0.6425 (mmtt) cc_final: 0.6088 (mttp) REVERT: D 304 PHE cc_start: 0.8339 (t80) cc_final: 0.8072 (t80) REVERT: D 307 LYS cc_start: 0.6393 (mmtt) cc_final: 0.6017 (mttp) outliers start: 15 outliers final: 12 residues processed: 175 average time/residue: 0.1722 time to fit residues: 43.0914 Evaluate side-chains 188 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 C residue 237 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 8 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: ** 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 202 ASN ** 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 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 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 = 0.3487 r_free = 0.3487 target = 0.142830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.119150 restraints weight = 8986.019| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.54 r_work: 0.3048 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7520 Z= 0.137 Angle : 0.556 7.534 10264 Z= 0.283 Chirality : 0.038 0.115 1148 Planarity : 0.005 0.051 1292 Dihedral : 4.272 21.550 1028 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.06 % Allowed : 19.09 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 960 helix: 1.54 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.13 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 289 HIS 0.006 0.001 HIS C 177 PHE 0.026 0.002 PHE B 304 TYR 0.010 0.001 TYR C 151 ARG 0.002 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 469) hydrogen bonds : angle 4.37166 ( 1395) covalent geometry : bond 0.00328 ( 7520) covalent geometry : angle 0.55603 (10264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4276.52 seconds wall clock time: 78 minutes 19.07 seconds (4699.07 seconds total)