Starting phenix.real_space_refine on Wed Sep 17 06:51:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blu_44677/09_2025/9blu_44677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blu_44677/09_2025/9blu_44677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9blu_44677/09_2025/9blu_44677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blu_44677/09_2025/9blu_44677.map" model { file = "/net/cci-nas-00/data/ceres_data/9blu_44677/09_2025/9blu_44677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blu_44677/09_2025/9blu_44677.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 22 5.16 5 C 4020 2.51 5 N 1102 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6377 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3848 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 20, 'TRANS': 490} Chain breaks: 1 Chain: "B" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1270 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1259 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 7, 'TRANS': 151} Time building chain proxies: 1.77, per 1000 atoms: 0.28 Number of scatterers: 6377 At special positions: 0 Unit cell: (76.44, 120.54, 111.72, 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 22 16.00 O 1233 8.00 N 1102 7.00 C 4020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 354.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 43.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.885A pdb=" N ILE A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 4.392A pdb=" N LYS A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.536A pdb=" N ILE A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.603A pdb=" N SER A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 294 removed outlier: 4.173A pdb=" N PHE A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.562A pdb=" N ILE A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 removed outlier: 4.046A pdb=" N LEU A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 102 Processing helix chain 'B' and resid 104 through 125 removed outlier: 5.056A pdb=" N GLU B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 removed outlier: 3.549A pdb=" N ASN B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 125 removed outlier: 3.581A pdb=" N VAL C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 158 removed outlier: 3.728A pdb=" N ASN C 139 " --> pdb=" O PRO C 135 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 140 " --> pdb=" O HIS C 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.703A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.703A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N MET A 70 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A 55 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A 56 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 192 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 58 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA A 189 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 219 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 191 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN A 221 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 193 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 270 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 335 removed outlier: 4.015A pdb=" N TYR A 331 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 340 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A 333 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY A 338 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 473 removed outlier: 3.607A pdb=" N LYS A 468 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 533 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A 532 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 545 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 179 removed outlier: 7.289A pdb=" N VAL B 213 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 210 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL B 194 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY B 212 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 201 removed outlier: 6.553A pdb=" N TYR B 199 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.563A pdb=" N GLY C 198 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR C 199 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 175 through 180 removed outlier: 7.299A pdb=" N VAL C 213 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS C 180 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU C 193 " --> pdb=" O GLY C 212 " (cutoff:3.500A) 326 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: 0.99 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2149 1.34 - 1.46: 1031 1.46 - 1.58: 3250 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 6466 Sorted by residual: bond pdb=" SD MET A 174 " pdb=" CE MET A 174 " ideal model delta sigma weight residual 1.791 1.768 0.023 2.50e-02 1.60e+03 8.39e-01 bond pdb=" CB GLU A 155 " pdb=" CG GLU A 155 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.01e-01 bond pdb=" CB ARG A 360 " pdb=" CG ARG A 360 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.85e-01 bond pdb=" CA PRO B 165 " pdb=" C PRO B 165 " ideal model delta sigma weight residual 1.527 1.518 0.009 1.07e-02 8.73e+03 7.20e-01 bond pdb=" N PRO B 165 " pdb=" CA PRO B 165 " ideal model delta sigma weight residual 1.479 1.467 0.013 1.71e-02 3.42e+03 5.67e-01 ... (remaining 6461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8630 1.61 - 3.21: 82 3.21 - 4.82: 14 4.82 - 6.43: 3 6.43 - 8.04: 2 Bond angle restraints: 8731 Sorted by residual: angle pdb=" CB MET A 46 " pdb=" CG MET A 46 " pdb=" SD MET A 46 " ideal model delta sigma weight residual 112.70 120.74 -8.04 3.00e+00 1.11e-01 7.18e+00 angle pdb=" CA ARG A 360 " pdb=" CB ARG A 360 " pdb=" CG ARG A 360 " ideal model delta sigma weight residual 114.10 119.03 -4.93 2.00e+00 2.50e-01 6.07e+00 angle pdb=" CB GLU A 155 " pdb=" CG GLU A 155 " pdb=" CD GLU A 155 " ideal model delta sigma weight residual 112.60 116.76 -4.16 1.70e+00 3.46e-01 6.00e+00 angle pdb=" CA GLU A 155 " pdb=" CB GLU A 155 " pdb=" CG GLU A 155 " ideal model delta sigma weight residual 114.10 118.71 -4.61 2.00e+00 2.50e-01 5.31e+00 angle pdb=" N MET A 174 " pdb=" CA MET A 174 " pdb=" CB MET A 174 " ideal model delta sigma weight residual 110.28 113.66 -3.38 1.55e+00 4.16e-01 4.76e+00 ... (remaining 8726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3339 17.93 - 35.87: 445 35.87 - 53.80: 165 53.80 - 71.74: 30 71.74 - 89.67: 10 Dihedral angle restraints: 3989 sinusoidal: 1614 harmonic: 2375 Sorted by residual: dihedral pdb=" CB GLU C 63 " pdb=" CG GLU C 63 " pdb=" CD GLU C 63 " pdb=" OE1 GLU C 63 " ideal model delta sinusoidal sigma weight residual 0.00 -89.67 89.67 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 513 " pdb=" CD ARG A 513 " pdb=" NE ARG A 513 " pdb=" CZ ARG A 513 " ideal model delta sinusoidal sigma weight residual 180.00 135.25 44.75 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASP A 556 " pdb=" CB ASP A 556 " pdb=" CG ASP A 556 " pdb=" OD1 ASP A 556 " ideal model delta sinusoidal sigma weight residual -30.00 -83.43 53.43 1 2.00e+01 2.50e-03 9.70e+00 ... (remaining 3986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 612 0.027 - 0.054: 249 0.054 - 0.080: 81 0.080 - 0.107: 58 0.107 - 0.134: 22 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CB ILE A 524 " pdb=" CA ILE A 524 " pdb=" CG1 ILE A 524 " pdb=" CG2 ILE A 524 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 144 " pdb=" N ILE A 144 " pdb=" C ILE A 144 " pdb=" CB ILE A 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE A 508 " pdb=" N ILE A 508 " pdb=" C ILE A 508 " pdb=" CB ILE A 508 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1019 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 103 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 104 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 125 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO C 126 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 392 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.43e-01 pdb=" N PRO A 393 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " -0.014 5.00e-02 4.00e+02 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 746 2.75 - 3.29: 5959 3.29 - 3.83: 10368 3.83 - 4.36: 11124 4.36 - 4.90: 20498 Nonbonded interactions: 48695 Sorted by model distance: nonbonded pdb=" O GLU A 352 " pdb=" OG1 THR A 356 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP B 110 " pdb=" NE2 HIS C 158 " model vdw 2.257 3.120 nonbonded pdb=" NH2 ARG A 391 " pdb=" OD2 ASP A 414 " model vdw 2.300 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" O LEU A 385 " model vdw 2.328 3.040 nonbonded pdb=" NH2 ARG A 202 " pdb=" OD1 ASN A 221 " model vdw 2.331 3.120 ... (remaining 48690 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 'B' and resid 59 through 217) selection = chain 'C' } 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: 3.890 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.810 Find NCS groups from input model: 0.050 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 0.027 6466 Z= 0.120 Angle : 0.453 8.036 8731 Z= 0.233 Chirality : 0.040 0.134 1022 Planarity : 0.003 0.041 1134 Dihedral : 18.948 89.669 2457 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.18 % Allowed : 29.91 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.31), residues: 823 helix: 2.54 (0.28), residues: 328 sheet: 0.69 (0.57), residues: 104 loop : -0.70 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 146 TYR 0.012 0.001 TYR C 78 PHE 0.007 0.001 PHE B 179 TRP 0.005 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6466) covalent geometry : angle 0.45276 ( 8731) hydrogen bonds : bond 0.17810 ( 323) hydrogen bonds : angle 6.18009 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 69 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 254 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 345 LYS cc_start: 0.7831 (tptp) cc_final: 0.6998 (mmtt) REVERT: A 508 ILE cc_start: -0.1736 (OUTLIER) cc_final: -0.2409 (tt) REVERT: B 201 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7747 (pp) REVERT: C 90 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.5915 (mt0) outliers start: 22 outliers final: 16 residues processed: 62 average time/residue: 0.0652 time to fit residues: 5.9874 Evaluate side-chains 64 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.205251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144009 restraints weight = 7120.985| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.96 r_work: 0.3491 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6466 Z= 0.148 Angle : 0.490 7.559 8731 Z= 0.257 Chirality : 0.042 0.140 1022 Planarity : 0.003 0.043 1134 Dihedral : 5.443 41.817 902 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.06 % Allowed : 28.18 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.30), residues: 823 helix: 2.72 (0.28), residues: 325 sheet: 0.62 (0.52), residues: 113 loop : -0.81 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.014 0.001 TYR A 243 PHE 0.008 0.001 PHE B 179 TRP 0.004 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6466) covalent geometry : angle 0.49023 ( 8731) hydrogen bonds : bond 0.04893 ( 323) hydrogen bonds : angle 4.71462 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 45 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7914 (tp) REVERT: A 159 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7824 (mtpp) REVERT: A 258 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.5451 (pm20) REVERT: A 300 LYS cc_start: 0.7862 (pttm) cc_final: 0.7250 (pttm) REVERT: A 345 LYS cc_start: 0.7578 (tptp) cc_final: 0.6985 (mptt) REVERT: A 424 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6217 (tp-100) REVERT: B 201 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7823 (pt) REVERT: C 90 GLN cc_start: 0.6308 (OUTLIER) cc_final: 0.5855 (mt0) outliers start: 35 outliers final: 17 residues processed: 77 average time/residue: 0.0593 time to fit residues: 6.6148 Evaluate side-chains 66 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 40.0000 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.205331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144725 restraints weight = 7024.558| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.07 r_work: 0.3485 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6466 Z= 0.137 Angle : 0.471 7.521 8731 Z= 0.246 Chirality : 0.042 0.168 1022 Planarity : 0.003 0.042 1134 Dihedral : 5.013 41.730 889 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.91 % Allowed : 28.90 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.30), residues: 823 helix: 2.53 (0.28), residues: 331 sheet: 0.57 (0.51), residues: 113 loop : -0.80 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 360 TYR 0.014 0.001 TYR C 78 PHE 0.007 0.001 PHE B 179 TRP 0.003 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6466) covalent geometry : angle 0.47093 ( 8731) hydrogen bonds : bond 0.04646 ( 323) hydrogen bonds : angle 4.52914 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7855 (tp) REVERT: A 191 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 300 LYS cc_start: 0.7870 (pttm) cc_final: 0.7253 (pttm) REVERT: A 345 LYS cc_start: 0.7569 (tptp) cc_final: 0.6974 (mptt) REVERT: A 356 THR cc_start: 0.7481 (m) cc_final: 0.7137 (m) REVERT: A 360 ARG cc_start: 0.6955 (tmm-80) cc_final: 0.6585 (ttp80) REVERT: B 201 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7825 (pt) REVERT: C 79 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6208 (pttt) REVERT: C 90 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5899 (mt0) outliers start: 34 outliers final: 22 residues processed: 74 average time/residue: 0.0710 time to fit residues: 7.4572 Evaluate side-chains 71 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.204773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143982 restraints weight = 7136.643| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.16 r_work: 0.3483 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6466 Z= 0.118 Angle : 0.451 7.348 8731 Z= 0.235 Chirality : 0.041 0.135 1022 Planarity : 0.003 0.040 1134 Dihedral : 4.928 41.649 889 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.20 % Allowed : 29.05 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.30), residues: 823 helix: 2.64 (0.28), residues: 331 sheet: 0.57 (0.51), residues: 113 loop : -0.79 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 360 TYR 0.016 0.001 TYR C 78 PHE 0.007 0.001 PHE B 179 TRP 0.003 0.000 TRP A 126 HIS 0.003 0.000 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6466) covalent geometry : angle 0.45144 ( 8731) hydrogen bonds : bond 0.04349 ( 323) hydrogen bonds : angle 4.34434 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 46 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7831 (tp) REVERT: A 258 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.5389 (pm20) REVERT: A 300 LYS cc_start: 0.7878 (pttm) cc_final: 0.7243 (pttm) REVERT: A 345 LYS cc_start: 0.7543 (tptp) cc_final: 0.7057 (mptt) REVERT: A 356 THR cc_start: 0.7497 (m) cc_final: 0.7122 (m) REVERT: A 360 ARG cc_start: 0.6969 (tmm-80) cc_final: 0.6492 (ttp80) REVERT: B 157 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8309 (ttmm) REVERT: B 201 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7825 (pt) REVERT: C 79 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6176 (pttt) REVERT: C 90 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5917 (mt0) outliers start: 36 outliers final: 19 residues processed: 77 average time/residue: 0.0798 time to fit residues: 8.4444 Evaluate side-chains 72 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.201015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143988 restraints weight = 7184.223| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.73 r_work: 0.3460 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6466 Z= 0.195 Angle : 0.531 7.819 8731 Z= 0.276 Chirality : 0.044 0.184 1022 Planarity : 0.003 0.043 1134 Dihedral : 5.234 42.789 888 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.92 % Allowed : 28.32 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.30), residues: 823 helix: 2.34 (0.28), residues: 331 sheet: 0.43 (0.51), residues: 113 loop : -0.87 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.019 0.002 TYR C 78 PHE 0.009 0.001 PHE B 179 TRP 0.004 0.001 TRP A 126 HIS 0.002 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6466) covalent geometry : angle 0.53108 ( 8731) hydrogen bonds : bond 0.05114 ( 323) hydrogen bonds : angle 4.44909 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 43 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8034 (tp) REVERT: A 345 LYS cc_start: 0.7808 (tptp) cc_final: 0.7145 (mptt) REVERT: A 356 THR cc_start: 0.7686 (m) cc_final: 0.7275 (m) REVERT: A 360 ARG cc_start: 0.7179 (tmm-80) cc_final: 0.6670 (ttp80) REVERT: A 424 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6475 (tp-100) REVERT: B 157 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8408 (ttmt) REVERT: B 201 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8066 (pt) REVERT: C 79 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6204 (pttt) REVERT: C 90 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6035 (mt0) outliers start: 41 outliers final: 29 residues processed: 78 average time/residue: 0.0691 time to fit residues: 7.6563 Evaluate side-chains 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.202195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143832 restraints weight = 7134.514| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.08 r_work: 0.3489 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6466 Z= 0.154 Angle : 0.505 7.704 8731 Z= 0.261 Chirality : 0.043 0.278 1022 Planarity : 0.003 0.044 1134 Dihedral : 5.189 42.835 888 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.20 % Allowed : 29.34 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.30), residues: 823 helix: 2.35 (0.27), residues: 331 sheet: 0.36 (0.51), residues: 113 loop : -0.88 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 360 TYR 0.018 0.002 TYR C 78 PHE 0.009 0.001 PHE B 179 TRP 0.003 0.001 TRP A 126 HIS 0.002 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6466) covalent geometry : angle 0.50477 ( 8731) hydrogen bonds : bond 0.04743 ( 323) hydrogen bonds : angle 4.35376 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 44 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7934 (tp) REVERT: A 345 LYS cc_start: 0.7795 (tptp) cc_final: 0.7122 (mptt) REVERT: A 356 THR cc_start: 0.7657 (m) cc_final: 0.7234 (m) REVERT: A 360 ARG cc_start: 0.7152 (tmm-80) cc_final: 0.6678 (ttp80) REVERT: A 508 ILE cc_start: -0.1828 (OUTLIER) cc_final: -0.2511 (tt) REVERT: B 157 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8345 (ttmt) REVERT: B 201 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8057 (pt) REVERT: C 79 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6205 (pttt) REVERT: C 90 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.6029 (mt0) outliers start: 36 outliers final: 23 residues processed: 77 average time/residue: 0.0682 time to fit residues: 7.4529 Evaluate side-chains 72 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.200821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140587 restraints weight = 7105.903| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.35 r_work: 0.3456 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6466 Z= 0.183 Angle : 0.538 7.806 8731 Z= 0.278 Chirality : 0.044 0.265 1022 Planarity : 0.003 0.046 1134 Dihedral : 5.309 44.672 888 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 6.21 % Allowed : 28.76 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.30), residues: 823 helix: 2.20 (0.27), residues: 331 sheet: 0.28 (0.50), residues: 113 loop : -0.94 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.020 0.002 TYR C 78 PHE 0.010 0.001 PHE A 278 TRP 0.004 0.001 TRP A 126 HIS 0.002 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 6466) covalent geometry : angle 0.53779 ( 8731) hydrogen bonds : bond 0.04975 ( 323) hydrogen bonds : angle 4.37613 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 42 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7974 (tp) REVERT: A 71 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6835 (tp30) REVERT: A 108 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8382 (pp30) REVERT: A 345 LYS cc_start: 0.7799 (tptp) cc_final: 0.7091 (mptt) REVERT: A 356 THR cc_start: 0.7611 (m) cc_final: 0.7175 (m) REVERT: A 508 ILE cc_start: -0.1904 (OUTLIER) cc_final: -0.2576 (tt) REVERT: B 157 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8326 (ttmt) REVERT: B 201 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7975 (pt) REVERT: C 79 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6198 (pttt) REVERT: C 90 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.5999 (mt0) outliers start: 43 outliers final: 30 residues processed: 80 average time/residue: 0.0779 time to fit residues: 8.7824 Evaluate side-chains 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 41 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 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 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.203445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145090 restraints weight = 7070.368| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.60 r_work: 0.3482 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6466 Z= 0.132 Angle : 0.498 7.608 8731 Z= 0.258 Chirality : 0.042 0.266 1022 Planarity : 0.003 0.046 1134 Dihedral : 5.130 43.179 888 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.91 % Allowed : 29.91 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.30), residues: 823 helix: 2.40 (0.28), residues: 331 sheet: 0.32 (0.50), residues: 113 loop : -0.91 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.019 0.002 TYR C 78 PHE 0.008 0.001 PHE B 179 TRP 0.004 0.001 TRP A 126 HIS 0.002 0.000 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6466) covalent geometry : angle 0.49770 ( 8731) hydrogen bonds : bond 0.04527 ( 323) hydrogen bonds : angle 4.25125 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7828 (tp) REVERT: A 71 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6932 (tp30) REVERT: A 345 LYS cc_start: 0.7701 (tptp) cc_final: 0.7063 (mptt) REVERT: A 356 THR cc_start: 0.7561 (m) cc_final: 0.7111 (m) REVERT: A 424 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.5630 (tp-100) REVERT: A 508 ILE cc_start: -0.1944 (OUTLIER) cc_final: -0.2602 (tt) REVERT: B 157 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8235 (ttmt) REVERT: B 201 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7866 (pt) REVERT: C 79 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6166 (pttt) REVERT: C 90 GLN cc_start: 0.6372 (OUTLIER) cc_final: 0.5878 (mt0) outliers start: 34 outliers final: 25 residues processed: 75 average time/residue: 0.0811 time to fit residues: 8.4845 Evaluate side-chains 77 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 44 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 0.0470 chunk 45 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.204279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147917 restraints weight = 7121.380| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.77 r_work: 0.3499 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6466 Z= 0.119 Angle : 0.489 7.486 8731 Z= 0.253 Chirality : 0.042 0.264 1022 Planarity : 0.003 0.045 1134 Dihedral : 5.017 43.042 887 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.06 % Allowed : 29.91 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.30), residues: 823 helix: 2.52 (0.28), residues: 331 sheet: 0.37 (0.50), residues: 113 loop : -0.88 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.018 0.001 TYR C 78 PHE 0.008 0.001 PHE B 179 TRP 0.004 0.001 TRP A 126 HIS 0.002 0.000 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6466) covalent geometry : angle 0.48943 ( 8731) hydrogen bonds : bond 0.04328 ( 323) hydrogen bonds : angle 4.18336 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 48 time to evaluate : 0.272 Fit side-chains REVERT: A 60 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 71 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7048 (tp30) REVERT: A 300 LYS cc_start: 0.7935 (pttm) cc_final: 0.7347 (pttm) REVERT: A 345 LYS cc_start: 0.7768 (tptp) cc_final: 0.7089 (mptt) REVERT: A 356 THR cc_start: 0.7606 (m) cc_final: 0.7164 (m) REVERT: A 424 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.5994 (tp-100) REVERT: A 508 ILE cc_start: -0.1860 (OUTLIER) cc_final: -0.2530 (tt) REVERT: B 157 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8288 (ttmt) REVERT: B 201 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8045 (pt) REVERT: C 79 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6212 (pttt) REVERT: C 90 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6070 (mt0) outliers start: 35 outliers final: 25 residues processed: 78 average time/residue: 0.0723 time to fit residues: 8.0133 Evaluate side-chains 81 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 48 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.205069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144766 restraints weight = 7008.853| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.37 r_work: 0.3509 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6466 Z= 0.112 Angle : 0.479 7.377 8731 Z= 0.247 Chirality : 0.041 0.260 1022 Planarity : 0.003 0.042 1134 Dihedral : 4.911 42.812 887 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.91 % Allowed : 30.20 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.30), residues: 823 helix: 2.76 (0.27), residues: 325 sheet: 0.40 (0.50), residues: 113 loop : -0.92 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.012 0.001 TYR A 243 PHE 0.007 0.001 PHE B 179 TRP 0.004 0.001 TRP A 126 HIS 0.002 0.000 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6466) covalent geometry : angle 0.47852 ( 8731) hydrogen bonds : bond 0.04179 ( 323) hydrogen bonds : angle 4.12389 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 0.264 Fit side-chains REVERT: A 60 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7833 (tp) REVERT: A 71 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6906 (tp30) REVERT: A 300 LYS cc_start: 0.7981 (pttm) cc_final: 0.7397 (pttm) REVERT: A 345 LYS cc_start: 0.7657 (tptp) cc_final: 0.7060 (mptt) REVERT: A 356 THR cc_start: 0.7485 (m) cc_final: 0.7043 (m) REVERT: A 508 ILE cc_start: -0.2011 (OUTLIER) cc_final: -0.2656 (tt) REVERT: B 157 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8183 (ttmt) REVERT: B 201 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7799 (pt) REVERT: C 79 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6168 (pttt) REVERT: C 90 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5896 (mt0) outliers start: 34 outliers final: 26 residues processed: 80 average time/residue: 0.0694 time to fit residues: 7.8845 Evaluate side-chains 81 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 48 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.205318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145141 restraints weight = 7056.465| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.30 r_work: 0.3506 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6466 Z= 0.116 Angle : 0.483 7.336 8731 Z= 0.249 Chirality : 0.041 0.255 1022 Planarity : 0.003 0.042 1134 Dihedral : 4.847 42.717 887 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.91 % Allowed : 30.49 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.30), residues: 823 helix: 2.82 (0.27), residues: 325 sheet: 0.42 (0.50), residues: 113 loop : -0.89 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 80 TYR 0.013 0.001 TYR A 243 PHE 0.007 0.001 PHE B 179 TRP 0.004 0.001 TRP A 126 HIS 0.002 0.000 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6466) covalent geometry : angle 0.48276 ( 8731) hydrogen bonds : bond 0.04117 ( 323) hydrogen bonds : angle 4.06796 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1944.60 seconds wall clock time: 34 minutes 3.57 seconds (2043.57 seconds total)