Starting phenix.real_space_refine on Sat May 10 22:36:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chu_45602/05_2025/9chu_45602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chu_45602/05_2025/9chu_45602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chu_45602/05_2025/9chu_45602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chu_45602/05_2025/9chu_45602.map" model { file = "/net/cci-nas-00/data/ceres_data/9chu_45602/05_2025/9chu_45602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chu_45602/05_2025/9chu_45602.cif" } resolution = 3.49 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= 0.054 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 48 5.16 5 C 4555 2.51 5 N 1151 2.21 5 O 1255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7009 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3326 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 418} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2806 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.42, per 1000 atoms: 0.77 Number of scatterers: 7009 At special positions: 0 Unit cell: (64.6, 84.15, 152.15, 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 48 16.00 O 1255 8.00 N 1151 7.00 C 4555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 190 " distance=2.03 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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 52.3% alpha, 5.5% 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 32 through 61 removed outlier: 3.891A pdb=" N PHE A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 97 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 102 through 137 removed outlier: 3.543A pdb=" N CYS A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 146 through 171 Proline residue: A 168 - end of helix removed outlier: 3.522A pdb=" N MET A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.581A pdb=" N VAL A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.736A pdb=" N ILE A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.561A pdb=" N ILE A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.797A pdb=" N LEU A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 395 through 421 Proline residue: A 411 - end of helix removed outlier: 4.711A pdb=" N ILE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.536A pdb=" N ASN A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 4.183A pdb=" N LEU A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 73 removed outlier: 3.829A pdb=" N GLN B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 4.194A pdb=" N LYS B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.713A pdb=" N GLU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.719A pdb=" N TYR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 347 through 368 Proline residue: B 354 - end of helix Processing helix chain 'C' and resid 56 through 61 Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.142A pdb=" N LEU B 195 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 276 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE B 304 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG B 278 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.591A pdb=" N LEU B 113 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 112 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 324 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.607A pdb=" N THR C 21 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 106 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C 23 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 35 through 38 removed outlier: 6.549A pdb=" N LYS C 35 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 37 " --> pdb=" O GLY C 28 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 942 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: 1.90 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1848 1.33 - 1.45: 1331 1.45 - 1.57: 3925 1.57 - 1.69: 1 1.69 - 1.81: 73 Bond restraints: 7178 Sorted by residual: bond pdb=" C9 FK5 C 201 " pdb=" O4 FK5 C 201 " ideal model delta sigma weight residual 1.206 1.407 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C1 FK5 C 201 " pdb=" O2 FK5 C 201 " ideal model delta sigma weight residual 1.211 1.410 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C22 FK5 C 201 " pdb=" O9 FK5 C 201 " ideal model delta sigma weight residual 1.215 1.408 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" C8 FK5 C 201 " pdb=" O3 FK5 C 201 " ideal model delta sigma weight residual 1.232 1.408 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C8 FK5 C 201 " pdb=" C9 FK5 C 201 " ideal model delta sigma weight residual 1.537 1.395 0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 7173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 9446 2.32 - 4.64: 233 4.64 - 6.95: 46 6.95 - 9.27: 15 9.27 - 11.59: 3 Bond angle restraints: 9743 Sorted by residual: angle pdb=" N VAL A 206 " pdb=" CA VAL A 206 " pdb=" C VAL A 206 " ideal model delta sigma weight residual 113.20 101.61 11.59 9.60e-01 1.09e+00 1.46e+02 angle pdb=" N VAL A 420 " pdb=" CA VAL A 420 " pdb=" C VAL A 420 " ideal model delta sigma weight residual 110.30 103.53 6.77 9.70e-01 1.06e+00 4.87e+01 angle pdb=" N ASP A 423 " pdb=" CA ASP A 423 " pdb=" C ASP A 423 " ideal model delta sigma weight residual 111.33 103.40 7.93 1.21e+00 6.83e-01 4.30e+01 angle pdb=" N SER A 203 " pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta sigma weight residual 110.20 119.73 -9.53 1.49e+00 4.50e-01 4.09e+01 angle pdb=" N GLN A 422 " pdb=" CA GLN A 422 " pdb=" C GLN A 422 " ideal model delta sigma weight residual 113.15 105.90 7.25 1.19e+00 7.06e-01 3.71e+01 ... (remaining 9738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 4221 35.78 - 71.56: 80 71.56 - 107.34: 8 107.34 - 143.13: 0 143.13 - 178.91: 4 Dihedral angle restraints: 4313 sinusoidal: 1734 harmonic: 2579 Sorted by residual: dihedral pdb=" CB CYS A 106 " pdb=" SG CYS A 106 " pdb=" SG CYS A 191 " pdb=" CB CYS A 191 " ideal model delta sinusoidal sigma weight residual -86.00 -174.25 88.25 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" N SER A 203 " pdb=" C SER A 203 " pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta harmonic sigma weight residual 122.80 137.79 -14.99 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" C ARG A 175 " pdb=" N ARG A 175 " pdb=" CA ARG A 175 " pdb=" CB ARG A 175 " ideal model delta harmonic sigma weight residual -122.60 -136.04 13.44 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 4310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1075 0.132 - 0.264: 22 0.264 - 0.396: 3 0.396 - 0.529: 2 0.529 - 0.661: 1 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA SER A 203 " pdb=" N SER A 203 " pdb=" C SER A 203 " pdb=" CB SER A 203 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA ARG A 175 " pdb=" N ARG A 175 " pdb=" C ARG A 175 " pdb=" CB ARG A 175 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CAL E5E A 501 " pdb=" CAH E5E A 501 " pdb=" CAK E5E A 501 " pdb=" OAD E5E A 501 " both_signs ideal model delta sigma weight residual False -2.31 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1100 not shown) Planarity restraints: 1231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 FK5 C 201 " 0.111 2.00e-02 2.50e+03 1.22e-01 1.87e+02 pdb=" C27 FK5 C 201 " -0.039 2.00e-02 2.50e+03 pdb=" C28 FK5 C 201 " -0.193 2.00e-02 2.50e+03 pdb=" C29 FK5 C 201 " 0.151 2.00e-02 2.50e+03 pdb=" C42 FK5 C 201 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 FK5 C 201 " -0.052 2.00e-02 2.50e+03 5.92e-02 4.38e+01 pdb=" C19 FK5 C 201 " 0.014 2.00e-02 2.50e+03 pdb=" C20 FK5 C 201 " 0.095 2.00e-02 2.50e+03 pdb=" C21 FK5 C 201 " -0.072 2.00e-02 2.50e+03 pdb=" C37 FK5 C 201 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 430 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C VAL A 430 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A 430 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR A 431 " -0.022 2.00e-02 2.50e+03 ... (remaining 1228 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 282 2.71 - 3.26: 7155 3.26 - 3.81: 10761 3.81 - 4.35: 12971 4.35 - 4.90: 22172 Nonbonded interactions: 53341 Sorted by model distance: nonbonded pdb=" OH TYR C 82 " pdb=" O3 FK5 C 201 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 219 " pdb=" O LEU A 395 " model vdw 2.212 3.040 nonbonded pdb=" O GLY B 105 " pdb=" OH TYR B 112 " model vdw 2.221 3.040 nonbonded pdb=" O SER C 39 " pdb=" OG SER C 39 " model vdw 2.260 3.040 nonbonded pdb=" O PHE B 238 " pdb=" NH1 ARG B 291 " model vdw 2.279 3.120 ... (remaining 53336 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.180 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:4.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.008 0.201 7180 Z= 0.415 Angle : 0.893 11.588 9747 Z= 0.519 Chirality : 0.060 0.661 1103 Planarity : 0.006 0.122 1231 Dihedral : 16.113 178.907 2643 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.41 % Allowed : 1.22 % Favored : 98.37 % Cbeta Deviations : 0.36 % 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: -1.06 (0.29), residues: 877 helix: 0.22 (0.25), residues: 435 sheet: -2.37 (0.60), residues: 66 loop : -1.43 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 59 HIS 0.014 0.001 HIS B 280 PHE 0.025 0.002 PHE A 223 TYR 0.018 0.002 TYR A 449 ARG 0.004 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.14401 ( 324) hydrogen bonds : angle 5.87809 ( 942) SS BOND : bond 0.00204 ( 2) SS BOND : angle 2.56779 ( 4) covalent geometry : bond 0.00834 ( 7178) covalent geometry : angle 0.89204 ( 9743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 193 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 315 ASN cc_start: 0.8603 (t0) cc_final: 0.8339 (t0) REVERT: C 11 ASP cc_start: 0.8247 (t70) cc_final: 0.7864 (t70) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.1909 time to fit residues: 32.1324 Evaluate side-chains 99 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 435 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147403 restraints weight = 8461.697| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.63 r_work: 0.3617 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7180 Z= 0.141 Angle : 0.599 6.098 9747 Z= 0.310 Chirality : 0.042 0.171 1103 Planarity : 0.004 0.032 1231 Dihedral : 13.778 176.083 1064 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.04 % Allowed : 8.42 % Favored : 89.54 % 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: -0.63 (0.30), residues: 877 helix: 0.67 (0.26), residues: 439 sheet: -2.32 (0.56), residues: 75 loop : -1.30 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 59 HIS 0.005 0.001 HIS B 280 PHE 0.014 0.001 PHE A 242 TYR 0.015 0.001 TYR B 261 ARG 0.003 0.000 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 324) hydrogen bonds : angle 4.45126 ( 942) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.83044 ( 4) covalent geometry : bond 0.00326 ( 7178) covalent geometry : angle 0.59885 ( 9743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.737 Fit side-chains REVERT: A 72 ILE cc_start: 0.8383 (mm) cc_final: 0.8129 (mm) REVERT: A 193 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7452 (t80) REVERT: A 259 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7308 (mpp) REVERT: B 315 ASN cc_start: 0.8821 (t0) cc_final: 0.8586 (t0) REVERT: C 5 GLU cc_start: 0.7416 (pm20) cc_final: 0.7169 (pm20) REVERT: C 11 ASP cc_start: 0.8244 (t70) cc_final: 0.7798 (t70) outliers start: 15 outliers final: 9 residues processed: 114 average time/residue: 0.1509 time to fit residues: 24.5224 Evaluate side-chains 106 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 269 GLN B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139487 restraints weight = 8827.908| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.83 r_work: 0.3478 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7180 Z= 0.160 Angle : 0.599 7.692 9747 Z= 0.308 Chirality : 0.042 0.133 1103 Planarity : 0.004 0.029 1231 Dihedral : 13.501 175.205 1064 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.72 % Allowed : 12.50 % Favored : 84.78 % 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: -0.53 (0.30), residues: 877 helix: 0.76 (0.26), residues: 441 sheet: -2.31 (0.56), residues: 75 loop : -1.26 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 173 HIS 0.002 0.001 HIS B 26 PHE 0.016 0.001 PHE B 333 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 324) hydrogen bonds : angle 4.22580 ( 942) SS BOND : bond 0.00086 ( 2) SS BOND : angle 0.52916 ( 4) covalent geometry : bond 0.00387 ( 7178) covalent geometry : angle 0.59947 ( 9743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.761 Fit side-chains REVERT: A 72 ILE cc_start: 0.8284 (mm) cc_final: 0.8028 (mm) REVERT: A 99 TRP cc_start: 0.6742 (OUTLIER) cc_final: 0.5730 (t60) REVERT: A 193 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7472 (t80) REVERT: A 379 LYS cc_start: 0.8357 (pptt) cc_final: 0.8132 (pptt) REVERT: B 98 MET cc_start: 0.7720 (mmm) cc_final: 0.7439 (mmm) REVERT: B 102 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: B 298 PHE cc_start: 0.7315 (m-80) cc_final: 0.6751 (t80) REVERT: B 315 ASN cc_start: 0.8755 (t0) cc_final: 0.8531 (t0) REVERT: C 11 ASP cc_start: 0.8255 (t70) cc_final: 0.7832 (t70) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 0.1587 time to fit residues: 24.2263 Evaluate side-chains 108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 78 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.171922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144728 restraints weight = 8738.709| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.92 r_work: 0.3525 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7180 Z= 0.114 Angle : 0.543 8.489 9747 Z= 0.281 Chirality : 0.040 0.129 1103 Planarity : 0.003 0.030 1231 Dihedral : 13.215 174.802 1064 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.72 % Allowed : 14.13 % Favored : 83.15 % 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: -0.22 (0.30), residues: 877 helix: 1.04 (0.26), residues: 439 sheet: -2.21 (0.56), residues: 75 loop : -1.12 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 173 HIS 0.002 0.000 HIS B 280 PHE 0.010 0.001 PHE B 258 TYR 0.010 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 324) hydrogen bonds : angle 3.98366 ( 942) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.40636 ( 4) covalent geometry : bond 0.00257 ( 7178) covalent geometry : angle 0.54288 ( 9743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.801 Fit side-chains REVERT: A 72 ILE cc_start: 0.8240 (mm) cc_final: 0.7983 (mm) REVERT: A 193 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7489 (t80) REVERT: A 435 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7530 (t0) REVERT: B 102 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: C 5 GLU cc_start: 0.7125 (pm20) cc_final: 0.6840 (pm20) REVERT: C 11 ASP cc_start: 0.8216 (t70) cc_final: 0.7827 (t70) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.1592 time to fit residues: 27.1536 Evaluate side-chains 109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 34 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 150 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.170740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143694 restraints weight = 8696.010| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.82 r_work: 0.3499 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7180 Z= 0.132 Angle : 0.573 13.485 9747 Z= 0.289 Chirality : 0.041 0.127 1103 Planarity : 0.003 0.030 1231 Dihedral : 13.196 175.091 1064 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.40 % Allowed : 15.22 % Favored : 81.39 % 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: -0.19 (0.30), residues: 877 helix: 1.06 (0.26), residues: 439 sheet: -2.19 (0.56), residues: 75 loop : -1.09 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 173 HIS 0.002 0.000 HIS B 280 PHE 0.013 0.001 PHE B 333 TYR 0.017 0.001 TYR B 287 ARG 0.003 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 324) hydrogen bonds : angle 3.95144 ( 942) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.40945 ( 4) covalent geometry : bond 0.00311 ( 7178) covalent geometry : angle 0.57296 ( 9743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.754 Fit side-chains REVERT: A 72 ILE cc_start: 0.8288 (mm) cc_final: 0.8029 (mm) REVERT: A 193 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7657 (t80) REVERT: A 435 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7591 (t0) REVERT: B 50 MET cc_start: 0.7838 (ttm) cc_final: 0.7598 (mmm) REVERT: B 102 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: B 151 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: B 298 PHE cc_start: 0.7337 (m-80) cc_final: 0.6844 (t80) REVERT: C 5 GLU cc_start: 0.7366 (pm20) cc_final: 0.6909 (pm20) REVERT: C 11 ASP cc_start: 0.8227 (t70) cc_final: 0.7795 (t70) outliers start: 25 outliers final: 16 residues processed: 117 average time/residue: 0.1515 time to fit residues: 25.5421 Evaluate side-chains 114 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141724 restraints weight = 8672.083| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.79 r_work: 0.3463 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7180 Z= 0.145 Angle : 0.595 13.856 9747 Z= 0.298 Chirality : 0.041 0.125 1103 Planarity : 0.003 0.030 1231 Dihedral : 13.197 175.282 1064 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.99 % Allowed : 15.76 % Favored : 81.25 % 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: -0.22 (0.30), residues: 877 helix: 1.02 (0.26), residues: 439 sheet: -2.06 (0.57), residues: 75 loop : -1.12 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 173 HIS 0.002 0.001 HIS B 280 PHE 0.016 0.001 PHE B 333 TYR 0.013 0.001 TYR B 287 ARG 0.003 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 324) hydrogen bonds : angle 3.96291 ( 942) SS BOND : bond 0.00033 ( 2) SS BOND : angle 0.40519 ( 4) covalent geometry : bond 0.00348 ( 7178) covalent geometry : angle 0.59505 ( 9743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.733 Fit side-chains REVERT: A 72 ILE cc_start: 0.8298 (mm) cc_final: 0.8028 (mm) REVERT: A 193 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7679 (t80) REVERT: A 259 MET cc_start: 0.7802 (tmm) cc_final: 0.7370 (mmt) REVERT: A 435 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7690 (t0) REVERT: B 50 MET cc_start: 0.7840 (ttm) cc_final: 0.7605 (mmm) REVERT: B 70 ILE cc_start: 0.8139 (tp) cc_final: 0.7825 (tt) REVERT: B 98 MET cc_start: 0.7757 (mmm) cc_final: 0.7234 (mmm) REVERT: B 102 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: B 151 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: B 298 PHE cc_start: 0.7404 (m-80) cc_final: 0.6886 (t80) REVERT: C 5 GLU cc_start: 0.7374 (pm20) cc_final: 0.6979 (pm20) REVERT: C 11 ASP cc_start: 0.8250 (t70) cc_final: 0.7799 (t70) outliers start: 22 outliers final: 17 residues processed: 116 average time/residue: 0.1487 time to fit residues: 24.7323 Evaluate side-chains 120 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 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 = 0.3980 r_free = 0.3980 target = 0.169293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142265 restraints weight = 8654.516| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.81 r_work: 0.3490 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7180 Z= 0.159 Angle : 0.607 13.968 9747 Z= 0.305 Chirality : 0.042 0.125 1103 Planarity : 0.003 0.030 1231 Dihedral : 13.205 174.978 1064 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.85 % Allowed : 17.26 % Favored : 79.89 % 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: -0.30 (0.30), residues: 877 helix: 0.93 (0.26), residues: 440 sheet: -2.04 (0.57), residues: 75 loop : -1.14 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 173 HIS 0.006 0.001 HIS B 150 PHE 0.019 0.001 PHE B 333 TYR 0.012 0.001 TYR B 174 ARG 0.002 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 324) hydrogen bonds : angle 3.98297 ( 942) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.43601 ( 4) covalent geometry : bond 0.00388 ( 7178) covalent geometry : angle 0.60689 ( 9743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.727 Fit side-chains REVERT: A 72 ILE cc_start: 0.8287 (mm) cc_final: 0.7995 (mm) REVERT: A 193 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7630 (t80) REVERT: A 379 LYS cc_start: 0.8329 (pptt) cc_final: 0.8097 (pptt) REVERT: B 70 ILE cc_start: 0.8135 (tp) cc_final: 0.7801 (tt) REVERT: B 98 MET cc_start: 0.7623 (mmm) cc_final: 0.7154 (mmm) REVERT: B 102 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: B 298 PHE cc_start: 0.7205 (m-80) cc_final: 0.6765 (t80) REVERT: B 328 MET cc_start: 0.7289 (ttp) cc_final: 0.7048 (ttp) REVERT: C 5 GLU cc_start: 0.7275 (pm20) cc_final: 0.7053 (pm20) REVERT: C 11 ASP cc_start: 0.8345 (t70) cc_final: 0.7949 (t70) outliers start: 21 outliers final: 19 residues processed: 116 average time/residue: 0.1771 time to fit residues: 29.1604 Evaluate side-chains 119 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.7758 > 50: distance: 43 - 60: 27.545 distance: 47 - 66: 32.571 distance: 52 - 70: 18.944 distance: 55 - 60: 28.606 distance: 56 - 78: 22.160 distance: 60 - 61: 26.899 distance: 61 - 62: 27.441 distance: 61 - 64: 24.850 distance: 62 - 63: 24.106 distance: 62 - 66: 44.851 distance: 63 - 85: 43.622 distance: 64 - 65: 50.129 distance: 66 - 67: 37.881 distance: 67 - 68: 29.940 distance: 68 - 69: 32.926 distance: 68 - 70: 11.827 distance: 69 - 91: 48.165 distance: 70 - 71: 20.056 distance: 71 - 72: 14.233 distance: 71 - 74: 34.490 distance: 72 - 73: 34.113 distance: 72 - 78: 31.914 distance: 73 - 102: 42.191 distance: 74 - 75: 45.145 distance: 75 - 76: 36.496 distance: 75 - 77: 26.187 distance: 78 - 79: 22.372 distance: 79 - 80: 16.092 distance: 79 - 82: 38.305 distance: 80 - 81: 32.016 distance: 80 - 85: 47.213 distance: 82 - 83: 31.841 distance: 82 - 84: 45.082 distance: 85 - 86: 52.230 distance: 86 - 89: 13.209 distance: 87 - 88: 5.530 distance: 87 - 91: 13.688 distance: 89 - 90: 12.057 distance: 91 - 92: 20.699 distance: 92 - 93: 17.881 distance: 92 - 95: 28.100 distance: 93 - 94: 9.159 distance: 93 - 102: 53.554 distance: 95 - 96: 28.347 distance: 96 - 97: 19.356 distance: 96 - 98: 32.600 distance: 97 - 99: 20.058 distance: 98 - 100: 30.921 distance: 99 - 101: 14.404 distance: 100 - 101: 11.654 distance: 102 - 103: 46.727 distance: 103 - 104: 35.869 distance: 103 - 106: 47.455 distance: 104 - 105: 46.803 distance: 104 - 110: 27.036 distance: 106 - 107: 13.237 distance: 107 - 108: 17.879 distance: 107 - 109: 19.305 distance: 110 - 111: 38.354 distance: 110 - 116: 38.299 distance: 111 - 112: 37.024 distance: 111 - 114: 16.403 distance: 112 - 113: 11.352 distance: 112 - 117: 23.291 distance: 115 - 116: 18.249 distance: 117 - 118: 28.566 distance: 118 - 119: 34.314 distance: 118 - 121: 38.121 distance: 119 - 120: 18.873 distance: 119 - 125: 33.086 distance: 121 - 122: 39.106 distance: 121 - 123: 20.900 distance: 122 - 124: 21.761 distance: 125 - 126: 21.050 distance: 126 - 127: 11.991 distance: 126 - 129: 18.324 distance: 127 - 128: 9.680 distance: 127 - 134: 22.675 distance: 129 - 130: 15.211 distance: 130 - 131: 20.476 distance: 131 - 132: 12.875 distance: 131 - 133: 9.649