Starting phenix.real_space_refine on Sat Dec 28 01:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jy7_36722/12_2024/8jy7_36722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jy7_36722/12_2024/8jy7_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_36722/12_2024/8jy7_36722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jy7_36722/12_2024/8jy7_36722.map" model { file = "/net/cci-nas-00/data/ceres_data/8jy7_36722/12_2024/8jy7_36722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jy7_36722/12_2024/8jy7_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.84, per 1000 atoms: 0.53 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 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: 0.73 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: 1.93 Time building geometry restraints manager: 2.28 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: 0.00 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: 1.020 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.520 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.290 ------------------------------------------------------------------------------- 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= 0.174 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 *********************** 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 : 0.674 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: 0.1459 time to fit residues: 42.3285 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 : 0.806 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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= 0.231 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 *********************** 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 : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7342 (m-10) cc_final: 0.6735 (m-80) REVERT: B 236 TYR cc_start: 0.8245 (p90) cc_final: 0.7844 (p90) REVERT: B 304 PHE cc_start: 0.8177 (t80) cc_final: 0.7944 (t80) REVERT: C 236 TYR cc_start: 0.8227 (p90) cc_final: 0.7833 (p90) outliers start: 19 outliers final: 14 residues processed: 173 average time/residue: 0.1453 time to fit residues: 36.7058 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 : 0.673 ------------------------------------------------------------------------------- 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 48 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7520 Z= 0.295 Angle : 0.610 7.112 10264 Z= 0.315 Chirality : 0.040 0.117 1148 Planarity : 0.005 0.045 1292 Dihedral : 4.402 15.201 1028 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.06 % Allowed : 13.87 % Favored : 84.07 % 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: 0.56 (0.27), residues: 960 helix: 1.22 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.36 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 289 HIS 0.004 0.001 HIS D 128 PHE 0.013 0.002 PHE C 226 TYR 0.022 0.002 TYR C 151 ARG 0.003 0.001 ARG A 269 *********************** 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 187 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7510 (m-10) cc_final: 0.6927 (m-80) REVERT: B 236 TYR cc_start: 0.8291 (p90) cc_final: 0.7886 (p90) REVERT: B 286 TYR cc_start: 0.7680 (m-80) cc_final: 0.7417 (m-80) REVERT: B 304 PHE cc_start: 0.8189 (t80) cc_final: 0.7966 (t80) REVERT: C 236 TYR cc_start: 0.8276 (p90) cc_final: 0.7889 (p90) REVERT: C 286 TYR cc_start: 0.7691 (m-80) cc_final: 0.7474 (m-80) REVERT: C 304 PHE cc_start: 0.8187 (t80) cc_final: 0.7976 (t80) REVERT: D 304 PHE cc_start: 0.8170 (t80) cc_final: 0.7948 (t80) outliers start: 15 outliers final: 11 residues processed: 175 average time/residue: 0.1417 time to fit residues: 36.0357 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 : 0.772 ------------------------------------------------------------------------------- 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 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 139 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 86 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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** A 177 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2881 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= 0.207 Angle : 0.548 6.601 10264 Z= 0.283 Chirality : 0.038 0.122 1148 Planarity : 0.005 0.048 1292 Dihedral : 4.262 15.429 1028 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.57 % Allowed : 15.80 % 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: 0.62 (0.27), residues: 960 helix: 1.20 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.44 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 289 HIS 0.009 0.002 HIS A 177 PHE 0.011 0.001 PHE D 160 TYR 0.015 0.001 TYR B 206 ARG 0.002 0.000 ARG A 269 *********************** 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 193 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7464 (m-10) cc_final: 0.6846 (m-80) REVERT: B 236 TYR cc_start: 0.8297 (p90) cc_final: 0.7862 (p90) REVERT: B 286 TYR cc_start: 0.7680 (m-80) cc_final: 0.7435 (m-80) REVERT: B 304 PHE cc_start: 0.8224 (t80) cc_final: 0.7969 (t80) REVERT: C 236 TYR cc_start: 0.8282 (p90) cc_final: 0.7866 (p90) REVERT: C 286 TYR cc_start: 0.7681 (m-80) cc_final: 0.7425 (m-80) REVERT: C 304 PHE cc_start: 0.8212 (t80) cc_final: 0.7963 (t80) REVERT: D 304 PHE cc_start: 0.8196 (t80) cc_final: 0.7930 (t80) outliers start: 26 outliers final: 18 residues processed: 179 average time/residue: 0.1463 time to fit residues: 38.4885 Evaluate side-chains 179 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 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 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 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 251 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7520 Z= 0.206 Angle : 0.548 6.596 10264 Z= 0.281 Chirality : 0.038 0.124 1148 Planarity : 0.005 0.048 1292 Dihedral : 4.231 15.616 1028 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.30 % Allowed : 16.07 % 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: 0.70 (0.27), residues: 960 helix: 1.26 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.42 (0.34), 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 0.010 0.001 PHE A 304 TYR 0.018 0.001 TYR D 206 ARG 0.002 0.000 ARG A 269 *********************** 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 191 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5964 (mp0) REVERT: A 286 TYR cc_start: 0.7446 (m-10) cc_final: 0.6900 (m-80) REVERT: B 236 TYR cc_start: 0.8304 (p90) cc_final: 0.7879 (p90) REVERT: B 286 TYR cc_start: 0.7701 (m-80) cc_final: 0.7395 (m-80) REVERT: B 304 PHE cc_start: 0.8218 (t80) cc_final: 0.7935 (t80) REVERT: C 236 TYR cc_start: 0.8284 (p90) cc_final: 0.7891 (p90) REVERT: C 237 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5996 (mp0) REVERT: C 286 TYR cc_start: 0.7689 (m-80) cc_final: 0.7367 (m-80) REVERT: C 304 PHE cc_start: 0.8219 (t80) cc_final: 0.7956 (t80) REVERT: D 237 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5961 (mp0) REVERT: D 304 PHE cc_start: 0.8202 (t80) cc_final: 0.7922 (t80) outliers start: 24 outliers final: 17 residues processed: 176 average time/residue: 0.1388 time to fit residues: 35.6762 Evaluate side-chains 182 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 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 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** 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 ** C 261 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3120 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= 0.216 Angle : 0.554 6.495 10264 Z= 0.286 Chirality : 0.038 0.120 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.283 16.296 1028 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.98 % Allowed : 14.29 % Favored : 81.73 % 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: 0.78 (0.27), residues: 960 helix: 1.31 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.36 (0.34), 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 128 PHE 0.012 0.001 PHE A 304 TYR 0.017 0.001 TYR C 206 ARG 0.002 0.000 ARG A 269 *********************** 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 192 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: A 286 TYR cc_start: 0.7468 (m-10) cc_final: 0.6906 (m-80) REVERT: B 236 TYR cc_start: 0.8334 (p90) cc_final: 0.7917 (p90) REVERT: B 286 TYR cc_start: 0.7717 (m-80) cc_final: 0.7405 (m-80) REVERT: C 236 TYR cc_start: 0.8280 (p90) cc_final: 0.7882 (p90) REVERT: C 237 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: C 286 TYR cc_start: 0.7677 (m-80) cc_final: 0.7297 (m-80) REVERT: C 304 PHE cc_start: 0.8248 (t80) cc_final: 0.7967 (t80) REVERT: D 237 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.5937 (mp0) REVERT: D 304 PHE cc_start: 0.8219 (t80) cc_final: 0.7914 (t80) outliers start: 29 outliers final: 19 residues processed: 175 average time/residue: 0.1409 time to fit residues: 35.8356 Evaluate side-chains 178 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 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 139 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 161 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 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 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** A 251 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** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7520 Z= 0.211 Angle : 0.551 6.172 10264 Z= 0.284 Chirality : 0.038 0.116 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.301 16.861 1028 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.57 % Allowed : 13.87 % Favored : 82.55 % 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: 0.87 (0.28), residues: 960 helix: 1.36 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.27 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 289 HIS 0.001 0.001 HIS A 283 PHE 0.010 0.001 PHE A 246 TYR 0.015 0.001 TYR B 206 ARG 0.002 0.000 ARG A 269 *********************** 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 192 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 PHE cc_start: 0.6714 (t80) cc_final: 0.6508 (t80) REVERT: A 206 TYR cc_start: 0.6982 (m-80) cc_final: 0.6601 (m-80) REVERT: A 237 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5931 (mp0) REVERT: A 286 TYR cc_start: 0.7456 (m-10) cc_final: 0.6947 (m-80) REVERT: B 236 TYR cc_start: 0.8317 (p90) cc_final: 0.7900 (p90) REVERT: B 237 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5977 (mp0) REVERT: B 286 TYR cc_start: 0.7713 (m-80) cc_final: 0.7393 (m-80) REVERT: C 206 TYR cc_start: 0.7078 (m-80) cc_final: 0.6580 (m-80) REVERT: C 236 TYR cc_start: 0.8272 (p90) cc_final: 0.7880 (p90) REVERT: C 237 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: C 286 TYR cc_start: 0.7662 (m-80) cc_final: 0.7222 (m-80) REVERT: D 206 TYR cc_start: 0.7123 (m-80) cc_final: 0.6622 (m-80) REVERT: D 237 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.5920 (mp0) REVERT: D 304 PHE cc_start: 0.8236 (t80) cc_final: 0.7925 (t80) outliers start: 26 outliers final: 22 residues processed: 178 average time/residue: 0.1401 time to fit residues: 36.3344 Evaluate side-chains 192 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 161 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 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 80 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3153 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= 0.160 Angle : 0.516 6.145 10264 Z= 0.267 Chirality : 0.037 0.113 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.191 18.070 1028 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.92 % Allowed : 15.93 % Favored : 82.14 % 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 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.16 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 289 HIS 0.001 0.000 HIS D 283 PHE 0.009 0.001 PHE D 160 TYR 0.014 0.001 TYR C 206 ARG 0.001 0.000 ARG A 269 *********************** 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 176 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.6805 (m-80) cc_final: 0.6460 (m-80) REVERT: A 237 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: A 286 TYR cc_start: 0.7285 (m-10) cc_final: 0.6754 (m-80) REVERT: B 206 TYR cc_start: 0.6923 (m-80) cc_final: 0.6520 (m-80) REVERT: B 236 TYR cc_start: 0.8289 (p90) cc_final: 0.7870 (p90) REVERT: B 237 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5964 (mp0) REVERT: B 286 TYR cc_start: 0.7623 (m-80) cc_final: 0.7335 (m-80) REVERT: C 206 TYR cc_start: 0.6894 (m-80) cc_final: 0.6482 (m-80) REVERT: C 236 TYR cc_start: 0.8250 (p90) cc_final: 0.7852 (p90) REVERT: C 237 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: C 286 TYR cc_start: 0.7583 (m-80) cc_final: 0.7223 (m-80) REVERT: C 304 PHE cc_start: 0.8229 (t80) cc_final: 0.7960 (t80) REVERT: D 206 TYR cc_start: 0.6921 (m-80) cc_final: 0.6547 (m-80) REVERT: D 237 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5925 (mp0) REVERT: D 304 PHE cc_start: 0.8211 (t80) cc_final: 0.7910 (t80) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.1481 time to fit residues: 35.2980 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 : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 237 GLU 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 237 GLU Chi-restraints excluded: chain D residue 161 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 86 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 91 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** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3214 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= 0.201 Angle : 0.540 6.142 10264 Z= 0.280 Chirality : 0.037 0.114 1148 Planarity : 0.005 0.049 1292 Dihedral : 4.290 19.049 1028 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.34 % Allowed : 16.07 % 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: 1.09 (0.28), residues: 960 helix: 1.51 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.16 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 289 HIS 0.002 0.001 HIS A 283 PHE 0.011 0.001 PHE C 205 TYR 0.014 0.001 TYR C 287 ARG 0.002 0.000 ARG A 269 *********************** 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 186 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.6936 (m-80) cc_final: 0.6552 (m-80) REVERT: A 237 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: A 286 TYR cc_start: 0.7306 (m-10) cc_final: 0.6773 (m-80) REVERT: B 206 TYR cc_start: 0.7022 (m-80) cc_final: 0.6574 (m-80) REVERT: B 236 TYR cc_start: 0.8307 (p90) cc_final: 0.7887 (p90) REVERT: B 237 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: B 286 TYR cc_start: 0.7587 (m-80) cc_final: 0.7289 (m-80) REVERT: C 206 TYR cc_start: 0.7048 (m-80) cc_final: 0.6579 (m-80) REVERT: C 236 TYR cc_start: 0.8267 (p90) cc_final: 0.7869 (p90) REVERT: C 237 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5980 (mp0) REVERT: C 286 TYR cc_start: 0.7578 (m-80) cc_final: 0.7131 (m-80) REVERT: C 304 PHE cc_start: 0.8249 (t80) cc_final: 0.7965 (t80) REVERT: D 206 TYR cc_start: 0.7022 (m-80) cc_final: 0.6576 (m-80) REVERT: D 237 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5913 (mp0) REVERT: D 304 PHE cc_start: 0.8204 (t80) cc_final: 0.7894 (t80) outliers start: 17 outliers final: 12 residues processed: 175 average time/residue: 0.1419 time to fit residues: 35.9241 Evaluate side-chains 183 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 95 SER 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 237 GLU Chi-restraints excluded: chain D residue 161 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7520 Z= 0.190 Angle : 0.532 5.579 10264 Z= 0.277 Chirality : 0.037 0.114 1148 Planarity : 0.005 0.050 1292 Dihedral : 4.235 15.716 1028 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.47 % Allowed : 16.07 % Favored : 81.46 % 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: 1.15 (0.28), residues: 960 helix: 1.56 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.14 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 289 HIS 0.001 0.001 HIS A 283 PHE 0.014 0.001 PHE D 205 TYR 0.014 0.001 TYR D 206 ARG 0.002 0.000 ARG A 269 ********************** 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 181 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.6804 (m-80) cc_final: 0.6468 (m-80) REVERT: A 237 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5935 (mp0) REVERT: A 286 TYR cc_start: 0.7296 (m-10) cc_final: 0.6686 (m-80) REVERT: B 236 TYR cc_start: 0.8301 (p90) cc_final: 0.7881 (p90) REVERT: B 237 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5957 (mp0) REVERT: B 286 TYR cc_start: 0.7575 (m-80) cc_final: 0.7265 (m-80) REVERT: C 236 TYR cc_start: 0.8263 (p90) cc_final: 0.7868 (p90) REVERT: C 237 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: C 286 TYR cc_start: 0.7572 (m-80) cc_final: 0.7120 (m-80) REVERT: C 304 PHE cc_start: 0.8253 (t80) cc_final: 0.7968 (t80) REVERT: D 237 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5925 (mp0) outliers start: 18 outliers final: 14 residues processed: 169 average time/residue: 0.1544 time to fit residues: 37.6863 Evaluate side-chains 182 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 95 SER 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 95 SER Chi-restraints excluded: chain D residue 161 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.0270 chunk 78 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.143086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.118799 restraints weight = 8912.995| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.55 r_work: 0.3054 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3242 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= 0.172 Angle : 0.517 5.521 10264 Z= 0.269 Chirality : 0.037 0.112 1148 Planarity : 0.005 0.051 1292 Dihedral : 4.149 14.645 1028 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.20 % Allowed : 16.62 % Favored : 81.18 % 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: 1.25 (0.28), residues: 960 helix: 1.64 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.11 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 289 HIS 0.001 0.000 HIS D 283 PHE 0.018 0.001 PHE B 205 TYR 0.014 0.001 TYR B 287 ARG 0.001 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.42 seconds wall clock time: 35 minutes 18.31 seconds (2118.31 seconds total)