Starting phenix.real_space_refine on Wed Feb 4 06:31:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6y_44292/02_2026/9b6y_44292.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6y_44292/02_2026/9b6y_44292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6y_44292/02_2026/9b6y_44292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6y_44292/02_2026/9b6y_44292.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6y_44292/02_2026/9b6y_44292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6y_44292/02_2026/9b6y_44292.cif" } resolution = 3.3 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= 0.001 sd= 0.018 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 63 5.16 5 C 5607 2.51 5 N 1548 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8955 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2985 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain: "B" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2985 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain: "C" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2985 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Time building chain proxies: 2.61, per 1000 atoms: 0.29 Number of scatterers: 8955 At special positions: 0 Unit cell: (103.2, 198.4, 73.6, 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 63 16.00 O 1737 8.00 N 1548 7.00 C 5607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.02 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 283 " 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: 0.74 Conformation dependent library (CDL) restraints added in 333.0 milliseconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 21 sheets defined 13.4% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.776A pdb=" N ILE A 6 " --> pdb=" O CYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.546A pdb=" N TRP A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.545A pdb=" N ILE B 6 " --> pdb=" O CYS B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'C' and resid 1 through 6 Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.706A pdb=" N PHE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 250 through 259 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.433A pdb=" N ASP A 8 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR A 32 " --> pdb=" O ASP A 8 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS A 29 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 45 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 138 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 48 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN A 136 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.433A pdb=" N ASP A 8 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR A 32 " --> pdb=" O ASP A 8 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS A 29 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 45 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 48 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET A 262 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 202 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 62 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER A 124 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS A 60 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER A 126 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS A 58 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE A 128 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA A 56 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 25 removed outlier: 3.696A pdb=" N THR A 179 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 73 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.531A pdb=" N GLN A 321 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN A 309 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 319 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 337 Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.379A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N MET B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 12 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA B 35 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL B 48 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET B 262 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 202 " --> pdb=" O VAL B 264 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 129 current: chain 'B' and resid 157 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 93 through 98 removed outlier: 3.914A pdb=" N SER B 202 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET B 262 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL B 48 " --> pdb=" O LEU B 276 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 51 current: chain 'B' and resid 217 through 219 Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 26 removed outlier: 3.573A pdb=" N GLY B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AB3, first strand: chain 'B' and resid 298 through 299 removed outlier: 6.894A pdb=" N LYS B 298 " --> pdb=" O ARG B 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 305 through 313 removed outlier: 6.400A pdb=" N GLN B 321 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASN B 309 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL B 319 " --> pdb=" O ASN B 309 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THR B 311 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 317 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 348 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 334 through 337 Processing sheet with id=AB6, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.461A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 48 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 202 " --> pdb=" O VAL C 264 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 109 through 129 current: chain 'C' and resid 157 through 162 Processing sheet with id=AB7, first strand: chain 'C' and resid 90 through 99 removed outlier: 3.825A pdb=" N SER C 202 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 48 " --> pdb=" O LEU C 276 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 41 through 51 current: chain 'C' and resid 217 through 219 Processing sheet with id=AB8, first strand: chain 'C' and resid 21 through 26 removed outlier: 3.907A pdb=" N THR C 179 " --> pdb=" O LYS C 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AC1, first strand: chain 'C' and resid 298 through 299 removed outlier: 7.027A pdb=" N LYS C 298 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.580A pdb=" N GLN C 321 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASN C 309 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 319 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 334 through 337 316 hydrogen bonds defined for protein. 780 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: 1.48 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2981 1.34 - 1.47: 2126 1.47 - 1.59: 3935 1.59 - 1.71: 0 1.71 - 1.84: 90 Bond restraints: 9132 Sorted by residual: bond pdb=" C ASP A 37 " pdb=" N LYS A 38 " ideal model delta sigma weight residual 1.331 1.257 0.074 3.12e-02 1.03e+03 5.56e+00 bond pdb=" CB TRP B 389 " pdb=" CG TRP B 389 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.89e+00 bond pdb=" CB VAL B 378 " pdb=" CG2 VAL B 378 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB CYS C 105 " pdb=" SG CYS C 105 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.52e+00 bond pdb=" CA GLN C 142 " pdb=" CB GLN C 142 " ideal model delta sigma weight residual 1.530 1.495 0.035 2.22e-02 2.03e+03 2.51e+00 ... (remaining 9127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11336 1.51 - 3.02: 906 3.02 - 4.53: 113 4.53 - 6.04: 17 6.04 - 7.55: 9 Bond angle restraints: 12381 Sorted by residual: angle pdb=" N ILE A 332 " pdb=" CA ILE A 332 " pdb=" C ILE A 332 " ideal model delta sigma weight residual 107.55 111.60 -4.05 9.90e-01 1.02e+00 1.67e+01 angle pdb=" N GLY B 52 " pdb=" CA GLY B 52 " pdb=" C GLY B 52 " ideal model delta sigma weight residual 112.34 119.83 -7.49 2.04e+00 2.40e-01 1.35e+01 angle pdb=" N ALA C 328 " pdb=" CA ALA C 328 " pdb=" C ALA C 328 " ideal model delta sigma weight residual 109.81 117.36 -7.55 2.21e+00 2.05e-01 1.17e+01 angle pdb=" N PRO B 75 " pdb=" CA PRO B 75 " pdb=" C PRO B 75 " ideal model delta sigma weight residual 112.47 119.04 -6.57 2.06e+00 2.36e-01 1.02e+01 angle pdb=" CA TYR A 194 " pdb=" CB TYR A 194 " pdb=" CG TYR A 194 " ideal model delta sigma weight residual 113.90 108.24 5.66 1.80e+00 3.09e-01 9.89e+00 ... (remaining 12376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5092 17.48 - 34.96: 299 34.96 - 52.44: 54 52.44 - 69.92: 17 69.92 - 87.40: 7 Dihedral angle restraints: 5469 sinusoidal: 2124 harmonic: 3345 Sorted by residual: dihedral pdb=" CA PRO C 329 " pdb=" C PRO C 329 " pdb=" N CYS C 330 " pdb=" CA CYS C 330 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU A 180 " pdb=" C LEU A 180 " pdb=" N GLU A 181 " pdb=" CA GLU A 181 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU C 26 " pdb=" C GLU C 26 " pdb=" N GLN C 27 " pdb=" CA GLN C 27 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 5466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 866 0.048 - 0.096: 397 0.096 - 0.144: 117 0.144 - 0.192: 21 0.192 - 0.240: 3 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA PRO B 75 " pdb=" N PRO B 75 " pdb=" C PRO B 75 " pdb=" CB PRO B 75 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASN B 67 " pdb=" N ASN B 67 " pdb=" C ASN B 67 " pdb=" CB ASN B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TYR B 61 " pdb=" N TYR B 61 " pdb=" C TYR B 61 " pdb=" CB TYR B 61 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1401 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.025 2.00e-02 2.50e+03 1.61e-02 5.19e+00 pdb=" CG TYR A 194 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 61 " -0.007 2.00e-02 2.50e+03 1.53e-02 4.69e+00 pdb=" CG TYR C 61 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 61 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 61 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 61 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 61 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 61 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 61 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 306 " -0.015 2.00e-02 2.50e+03 1.55e-02 4.22e+00 pdb=" CG PHE B 306 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 306 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 306 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 306 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 306 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 306 " -0.002 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2088 2.80 - 3.33: 8013 3.33 - 3.85: 13916 3.85 - 4.38: 16165 4.38 - 4.90: 28128 Nonbonded interactions: 68310 Sorted by model distance: nonbonded pdb=" NZ LYS A 69 " pdb=" OE2 GLU A 84 " model vdw 2.280 3.120 nonbonded pdb=" NZ LYS C 148 " pdb=" OE1 GLU C 362 " model vdw 2.341 3.120 nonbonded pdb=" NZ LYS C 266 " pdb=" O SER C 271 " model vdw 2.396 3.120 nonbonded pdb=" OE2 GLU B 169 " pdb=" NH1 ARG B 177 " model vdw 2.429 3.120 nonbonded pdb=" OE2 GLU A 169 " pdb=" NE ARG A 177 " model vdw 2.431 3.120 ... (remaining 68305 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 6.720 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.360 Find NCS groups from input model: 0.150 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 0.074 9136 Z= 0.366 Angle : 0.879 7.552 12389 Z= 0.514 Chirality : 0.057 0.240 1404 Planarity : 0.005 0.049 1593 Dihedral : 12.523 87.402 3309 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1167 helix: -2.75 (0.41), residues: 72 sheet: 0.41 (0.23), residues: 428 loop : -0.75 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 331 TYR 0.032 0.006 TYR A 194 PHE 0.036 0.004 PHE B 306 TRP 0.032 0.004 TRP A 203 HIS 0.006 0.002 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00809 ( 9132) covalent geometry : angle 0.87816 (12381) SS BOND : bond 0.00606 ( 4) SS BOND : angle 1.89699 ( 8) hydrogen bonds : bond 0.18275 ( 279) hydrogen bonds : angle 8.15542 ( 780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8504 (mt) cc_final: 0.8273 (mm) REVERT: A 31 VAL cc_start: 0.7741 (t) cc_final: 0.7443 (p) REVERT: A 46 GLU cc_start: 0.6650 (tt0) cc_final: 0.6326 (tt0) REVERT: A 57 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7501 (mtt180) REVERT: A 62 SER cc_start: 0.8148 (t) cc_final: 0.7731 (p) REVERT: A 69 LYS cc_start: 0.7627 (pttm) cc_final: 0.7350 (mtmm) REVERT: A 103 ASN cc_start: 0.7493 (m-40) cc_final: 0.7262 (m-40) REVERT: A 134 LYS cc_start: 0.7986 (mttt) cc_final: 0.7679 (mttt) REVERT: A 143 LEU cc_start: 0.7815 (mt) cc_final: 0.7518 (mm) REVERT: A 160 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7711 (mtpt) REVERT: A 201 GLU cc_start: 0.6475 (tt0) cc_final: 0.6123 (tt0) REVERT: A 208 GLN cc_start: 0.6973 (pm20) cc_final: 0.6650 (pm20) REVERT: A 215 LEU cc_start: 0.8090 (mp) cc_final: 0.7874 (mp) REVERT: A 232 VAL cc_start: 0.7665 (t) cc_final: 0.6963 (p) REVERT: A 236 PRO cc_start: 0.8583 (Cg_exo) cc_final: 0.8361 (Cg_endo) REVERT: A 273 LEU cc_start: 0.8455 (mt) cc_final: 0.8241 (mt) REVERT: A 275 LYS cc_start: 0.7386 (tttt) cc_final: 0.6890 (tttt) REVERT: A 298 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7691 (ptpt) REVERT: A 299 MET cc_start: 0.6609 (mmm) cc_final: 0.6347 (mmm) REVERT: A 348 ILE cc_start: 0.7446 (mt) cc_final: 0.7176 (mt) REVERT: A 368 ASN cc_start: 0.7907 (t0) cc_final: 0.7529 (t0) REVERT: B 26 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6531 (mt-10) REVERT: B 29 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7661 (mtmt) REVERT: B 70 ILE cc_start: 0.8404 (mp) cc_final: 0.8129 (mp) REVERT: B 71 ASN cc_start: 0.8367 (t0) cc_final: 0.7740 (t0) REVERT: B 82 LEU cc_start: 0.8314 (mt) cc_final: 0.7937 (mp) REVERT: B 85 GLU cc_start: 0.7569 (tt0) cc_final: 0.7349 (tt0) REVERT: B 164 LEU cc_start: 0.7862 (mt) cc_final: 0.7504 (mp) REVERT: B 205 VAL cc_start: 0.8117 (m) cc_final: 0.7719 (p) REVERT: B 207 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7423 (ttmt) REVERT: B 211 GLN cc_start: 0.8102 (mt0) cc_final: 0.7883 (mt0) REVERT: B 243 LYS cc_start: 0.7740 (pttt) cc_final: 0.7514 (pttt) REVERT: B 267 ASP cc_start: 0.7216 (t0) cc_final: 0.6899 (t0) REVERT: B 272 LYS cc_start: 0.7714 (mtmm) cc_final: 0.7351 (mtmm) REVERT: B 317 THR cc_start: 0.7920 (p) cc_final: 0.7713 (p) REVERT: B 321 GLN cc_start: 0.8186 (mt0) cc_final: 0.7953 (mt0) REVERT: B 340 LEU cc_start: 0.8241 (mt) cc_final: 0.7980 (mp) REVERT: B 388 GLN cc_start: 0.7669 (mt0) cc_final: 0.7392 (mt0) REVERT: C 26 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6831 (mt-10) REVERT: C 29 LYS cc_start: 0.7999 (mttt) cc_final: 0.7544 (mttt) REVERT: C 43 ILE cc_start: 0.8091 (tt) cc_final: 0.7793 (pt) REVERT: C 69 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7739 (mtmt) REVERT: C 71 ASN cc_start: 0.8264 (t0) cc_final: 0.7902 (t0) REVERT: C 84 GLU cc_start: 0.7996 (mp0) cc_final: 0.7066 (mp0) REVERT: C 89 ASP cc_start: 0.7417 (p0) cc_final: 0.7177 (p0) REVERT: C 132 GLN cc_start: 0.7784 (mm110) cc_final: 0.7354 (mm110) REVERT: C 154 THR cc_start: 0.7798 (p) cc_final: 0.7556 (p) REVERT: C 155 ASP cc_start: 0.7174 (m-30) cc_final: 0.6804 (m-30) REVERT: C 185 GLN cc_start: 0.5851 (pm20) cc_final: 0.5621 (pm20) REVERT: C 204 ILE cc_start: 0.8402 (tt) cc_final: 0.8186 (mt) REVERT: C 232 VAL cc_start: 0.8528 (t) cc_final: 0.8167 (m) REVERT: C 241 THR cc_start: 0.8467 (m) cc_final: 0.7976 (t) REVERT: C 250 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7203 (mm-40) REVERT: C 255 LYS cc_start: 0.8280 (mttt) cc_final: 0.8046 (mttp) REVERT: C 273 LEU cc_start: 0.7758 (mt) cc_final: 0.7512 (mt) REVERT: C 324 VAL cc_start: 0.8581 (t) cc_final: 0.8234 (m) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.0979 time to fit residues: 50.5204 Evaluate side-chains 363 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 144 HIS A 315 HIS A 321 GLN A 353 ASN C 27 GLN C 67 ASN C 353 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.115685 restraints weight = 13162.811| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.57 r_work: 0.3267 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9136 Z= 0.154 Angle : 0.621 7.573 12389 Z= 0.341 Chirality : 0.048 0.189 1404 Planarity : 0.004 0.044 1593 Dihedral : 6.291 25.561 1233 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.23 % Allowed : 9.74 % Favored : 89.03 % 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 are not related in a simple way. whole: -0.08 (0.24), residues: 1167 helix: -1.15 (0.57), residues: 79 sheet: 0.77 (0.23), residues: 429 loop : -0.43 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 177 TYR 0.016 0.002 TYR C 194 PHE 0.017 0.002 PHE B 119 TRP 0.016 0.002 TRP C 20 HIS 0.003 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9132) covalent geometry : angle 0.61986 (12381) SS BOND : bond 0.00517 ( 4) SS BOND : angle 1.72068 ( 8) hydrogen bonds : bond 0.03567 ( 279) hydrogen bonds : angle 5.96809 ( 780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 361 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7738 (t) cc_final: 0.7421 (p) REVERT: A 46 GLU cc_start: 0.7058 (tt0) cc_final: 0.6629 (tt0) REVERT: A 57 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7542 (mtt180) REVERT: A 69 LYS cc_start: 0.7864 (pttm) cc_final: 0.7620 (mtmm) REVERT: A 83 GLU cc_start: 0.7622 (mp0) cc_final: 0.7354 (mp0) REVERT: A 90 ASN cc_start: 0.7566 (m110) cc_final: 0.7365 (m-40) REVERT: A 103 ASN cc_start: 0.7704 (m-40) cc_final: 0.7484 (m-40) REVERT: A 118 LYS cc_start: 0.8171 (tttp) cc_final: 0.7969 (tttp) REVERT: A 125 MET cc_start: 0.7448 (mtm) cc_final: 0.7239 (mtp) REVERT: A 134 LYS cc_start: 0.8177 (mttt) cc_final: 0.7851 (mttt) REVERT: A 142 GLN cc_start: 0.7119 (mm110) cc_final: 0.6847 (mm110) REVERT: A 160 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7858 (mtpt) REVERT: A 201 GLU cc_start: 0.7109 (tt0) cc_final: 0.6612 (tt0) REVERT: A 227 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7121 (mm-30) REVERT: A 232 VAL cc_start: 0.7758 (t) cc_final: 0.7087 (p) REVERT: A 275 LYS cc_start: 0.7322 (tttt) cc_final: 0.6753 (tttt) REVERT: A 276 LEU cc_start: 0.7540 (tp) cc_final: 0.7122 (pp) REVERT: A 280 HIS cc_start: 0.7556 (p-80) cc_final: 0.7327 (p-80) REVERT: A 285 VAL cc_start: 0.8155 (t) cc_final: 0.7944 (p) REVERT: A 288 SER cc_start: 0.7685 (p) cc_final: 0.7452 (m) REVERT: A 298 LYS cc_start: 0.8064 (ptpt) cc_final: 0.7772 (ptpt) REVERT: A 308 LYS cc_start: 0.8261 (mtpp) cc_final: 0.8027 (mtpp) REVERT: A 324 VAL cc_start: 0.8632 (t) cc_final: 0.8365 (m) REVERT: A 368 ASN cc_start: 0.7980 (t0) cc_final: 0.7737 (t0) REVERT: B 6 ILE cc_start: 0.8133 (mt) cc_final: 0.7930 (mm) REVERT: B 29 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7575 (mtmt) REVERT: B 71 ASN cc_start: 0.8427 (t0) cc_final: 0.7852 (t0) REVERT: B 72 ASP cc_start: 0.7221 (p0) cc_final: 0.6973 (p0) REVERT: B 82 LEU cc_start: 0.8395 (mt) cc_final: 0.7999 (mp) REVERT: B 84 GLU cc_start: 0.7910 (mp0) cc_final: 0.7708 (mp0) REVERT: B 93 LYS cc_start: 0.7881 (tttt) cc_final: 0.7565 (tttp) REVERT: B 205 VAL cc_start: 0.8245 (m) cc_final: 0.7761 (p) REVERT: B 207 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7407 (tttt) REVERT: B 211 GLN cc_start: 0.8322 (mt0) cc_final: 0.8108 (mt0) REVERT: B 243 LYS cc_start: 0.7932 (pttt) cc_final: 0.7620 (pttt) REVERT: B 272 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7195 (mtmm) REVERT: B 305 SER cc_start: 0.8069 (t) cc_final: 0.7638 (p) REVERT: B 388 GLN cc_start: 0.7954 (mt0) cc_final: 0.7631 (mt0) REVERT: C 26 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 29 LYS cc_start: 0.8251 (mttt) cc_final: 0.7877 (mttt) REVERT: C 69 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7962 (mtmt) REVERT: C 89 ASP cc_start: 0.7557 (p0) cc_final: 0.7212 (p0) REVERT: C 132 GLN cc_start: 0.8110 (mm110) cc_final: 0.7646 (mm110) REVERT: C 155 ASP cc_start: 0.7365 (m-30) cc_final: 0.6990 (m-30) REVERT: C 185 GLN cc_start: 0.5953 (pm20) cc_final: 0.5723 (pm20) REVERT: C 202 SER cc_start: 0.8006 (m) cc_final: 0.7475 (t) REVERT: C 232 VAL cc_start: 0.8541 (t) cc_final: 0.8202 (m) REVERT: C 241 THR cc_start: 0.8412 (m) cc_final: 0.7988 (t) REVERT: C 250 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7449 (mm-40) REVERT: C 255 LYS cc_start: 0.8038 (mttt) cc_final: 0.7802 (mttp) REVERT: C 292 LEU cc_start: 0.7945 (mt) cc_final: 0.7517 (mp) REVERT: C 298 LYS cc_start: 0.7266 (pttm) cc_final: 0.6753 (pttm) REVERT: C 324 VAL cc_start: 0.8504 (t) cc_final: 0.8206 (m) outliers start: 12 outliers final: 8 residues processed: 366 average time/residue: 0.0907 time to fit residues: 44.7189 Evaluate side-chains 356 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 348 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 107 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 144 HIS A 321 GLN B 144 HIS B 151 ASN C 90 ASN C 353 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114516 restraints weight = 13115.510| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.56 r_work: 0.3255 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9136 Z= 0.180 Angle : 0.593 6.814 12389 Z= 0.320 Chirality : 0.047 0.164 1404 Planarity : 0.004 0.041 1593 Dihedral : 5.972 24.519 1233 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.46 % Allowed : 15.79 % Favored : 81.74 % 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 are not related in a simple way. whole: -0.07 (0.24), residues: 1167 helix: -0.83 (0.61), residues: 73 sheet: 0.82 (0.24), residues: 416 loop : -0.48 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 177 TYR 0.018 0.002 TYR C 194 PHE 0.012 0.002 PHE B 119 TRP 0.012 0.002 TRP C 209 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9132) covalent geometry : angle 0.59259 (12381) SS BOND : bond 0.00764 ( 4) SS BOND : angle 1.39496 ( 8) hydrogen bonds : bond 0.03533 ( 279) hydrogen bonds : angle 5.68740 ( 780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 353 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7765 (t) cc_final: 0.7459 (p) REVERT: A 57 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7567 (mtt180) REVERT: A 90 ASN cc_start: 0.7619 (m110) cc_final: 0.7412 (m-40) REVERT: A 110 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7635 (mtpp) REVERT: A 134 LYS cc_start: 0.8191 (mttt) cc_final: 0.7833 (mttt) REVERT: A 142 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6703 (mm-40) REVERT: A 160 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7872 (mtpt) REVERT: A 198 MET cc_start: 0.7705 (mtp) cc_final: 0.7438 (mtp) REVERT: A 201 GLU cc_start: 0.7090 (tt0) cc_final: 0.6615 (tt0) REVERT: A 227 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7182 (mm-30) REVERT: A 232 VAL cc_start: 0.7797 (t) cc_final: 0.7205 (p) REVERT: A 275 LYS cc_start: 0.7312 (tttt) cc_final: 0.6761 (tttt) REVERT: A 276 LEU cc_start: 0.7602 (tp) cc_final: 0.7053 (pp) REVERT: A 280 HIS cc_start: 0.7570 (p-80) cc_final: 0.7342 (p-80) REVERT: A 288 SER cc_start: 0.7586 (p) cc_final: 0.7362 (m) REVERT: A 298 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7816 (ptpt) REVERT: A 302 ASP cc_start: 0.8147 (m-30) cc_final: 0.7855 (m-30) REVERT: A 308 LYS cc_start: 0.8338 (mtpp) cc_final: 0.8092 (mtpp) REVERT: A 320 MET cc_start: 0.7779 (ptp) cc_final: 0.7567 (ptp) REVERT: A 324 VAL cc_start: 0.8643 (t) cc_final: 0.8280 (m) REVERT: A 368 ASN cc_start: 0.7986 (t0) cc_final: 0.7770 (t0) REVERT: B 29 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7552 (mtmt) REVERT: B 71 ASN cc_start: 0.8417 (t0) cc_final: 0.7763 (t0) REVERT: B 72 ASP cc_start: 0.7163 (p0) cc_final: 0.6903 (p0) REVERT: B 82 LEU cc_start: 0.8424 (mt) cc_final: 0.8054 (mp) REVERT: B 93 LYS cc_start: 0.7855 (tttt) cc_final: 0.7526 (tttt) REVERT: B 118 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7686 (ttpp) REVERT: B 169 GLU cc_start: 0.7730 (tt0) cc_final: 0.7372 (mt-10) REVERT: B 177 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7045 (mtm-85) REVERT: B 205 VAL cc_start: 0.8266 (m) cc_final: 0.7807 (p) REVERT: B 207 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7514 (tttt) REVERT: B 211 GLN cc_start: 0.8291 (mt0) cc_final: 0.8064 (mt0) REVERT: B 243 LYS cc_start: 0.7978 (pttt) cc_final: 0.7649 (pttt) REVERT: B 266 LYS cc_start: 0.8355 (tttp) cc_final: 0.8135 (tttp) REVERT: B 272 LYS cc_start: 0.7640 (mtmm) cc_final: 0.7195 (mtmm) REVERT: B 361 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: B 388 GLN cc_start: 0.7964 (mt0) cc_final: 0.7642 (mt0) REVERT: C 29 LYS cc_start: 0.8248 (mttt) cc_final: 0.7981 (mttt) REVERT: C 69 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7930 (mtmt) REVERT: C 89 ASP cc_start: 0.7547 (p0) cc_final: 0.6910 (p0) REVERT: C 90 ASN cc_start: 0.8067 (m-40) cc_final: 0.7763 (m110) REVERT: C 118 LYS cc_start: 0.8218 (tttp) cc_final: 0.7759 (ttmm) REVERT: C 132 GLN cc_start: 0.8135 (mm110) cc_final: 0.7668 (mm110) REVERT: C 143 LEU cc_start: 0.7931 (mt) cc_final: 0.7714 (mp) REVERT: C 202 SER cc_start: 0.7964 (m) cc_final: 0.7517 (t) REVERT: C 232 VAL cc_start: 0.8560 (t) cc_final: 0.8232 (m) REVERT: C 241 THR cc_start: 0.8424 (m) cc_final: 0.8029 (t) REVERT: C 250 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7375 (mm-40) REVERT: C 253 SER cc_start: 0.7952 (m) cc_final: 0.7537 (p) REVERT: C 255 LYS cc_start: 0.8131 (mttt) cc_final: 0.7865 (mttp) REVERT: C 273 LEU cc_start: 0.7937 (mt) cc_final: 0.7693 (mt) REVERT: C 292 LEU cc_start: 0.7949 (mt) cc_final: 0.7547 (mp) REVERT: C 324 VAL cc_start: 0.8499 (t) cc_final: 0.8228 (m) REVERT: C 390 HIS cc_start: 0.6756 (t70) cc_final: 0.6516 (t70) outliers start: 24 outliers final: 17 residues processed: 364 average time/residue: 0.0894 time to fit residues: 43.7038 Evaluate side-chains 365 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 347 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.0050 chunk 105 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 321 GLN B 90 ASN B 103 ASN B 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114964 restraints weight = 13165.304| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.56 r_work: 0.3258 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9136 Z= 0.143 Angle : 0.556 8.624 12389 Z= 0.297 Chirality : 0.046 0.162 1404 Planarity : 0.004 0.046 1593 Dihedral : 5.564 22.259 1233 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.79 % Allowed : 17.03 % Favored : 79.18 % 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 are not related in a simple way. whole: 0.04 (0.24), residues: 1167 helix: -0.69 (0.62), residues: 72 sheet: 0.91 (0.24), residues: 415 loop : -0.44 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 284 TYR 0.015 0.001 TYR C 194 PHE 0.011 0.002 PHE A 119 TRP 0.013 0.001 TRP C 20 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9132) covalent geometry : angle 0.55538 (12381) SS BOND : bond 0.00463 ( 4) SS BOND : angle 1.24847 ( 8) hydrogen bonds : bond 0.03060 ( 279) hydrogen bonds : angle 5.46128 ( 780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 357 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7707 (t) cc_final: 0.7412 (p) REVERT: A 57 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7595 (mtt180) REVERT: A 90 ASN cc_start: 0.7522 (m110) cc_final: 0.7289 (m-40) REVERT: A 110 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7588 (mtpp) REVERT: A 131 ASP cc_start: 0.7360 (t0) cc_final: 0.6967 (t0) REVERT: A 134 LYS cc_start: 0.8194 (mttt) cc_final: 0.7886 (mttt) REVERT: A 142 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6591 (mm-40) REVERT: A 160 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7869 (mtpt) REVERT: A 168 GLN cc_start: 0.6246 (mm-40) cc_final: 0.6022 (mm-40) REVERT: A 198 MET cc_start: 0.7736 (mtp) cc_final: 0.7492 (mtp) REVERT: A 201 GLU cc_start: 0.7092 (tt0) cc_final: 0.6574 (tt0) REVERT: A 227 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7157 (mm-30) REVERT: A 275 LYS cc_start: 0.7280 (tttt) cc_final: 0.6722 (tttt) REVERT: A 276 LEU cc_start: 0.7556 (tp) cc_final: 0.7135 (pp) REVERT: A 288 SER cc_start: 0.7658 (p) cc_final: 0.7423 (m) REVERT: A 298 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7877 (ptpt) REVERT: A 308 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8123 (mtpp) REVERT: A 320 MET cc_start: 0.7755 (ptp) cc_final: 0.7499 (ptp) REVERT: A 324 VAL cc_start: 0.8620 (t) cc_final: 0.8279 (m) REVERT: A 330 CYS cc_start: 0.8479 (m) cc_final: 0.8034 (p) REVERT: A 362 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 29 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7584 (mtmt) REVERT: B 71 ASN cc_start: 0.8446 (t0) cc_final: 0.8112 (t0) REVERT: B 82 LEU cc_start: 0.8410 (mt) cc_final: 0.8039 (mp) REVERT: B 83 GLU cc_start: 0.7816 (mp0) cc_final: 0.7345 (mp0) REVERT: B 84 GLU cc_start: 0.7983 (mp0) cc_final: 0.7593 (tp30) REVERT: B 93 LYS cc_start: 0.7904 (tttt) cc_final: 0.7640 (tttp) REVERT: B 116 CYS cc_start: 0.6437 (OUTLIER) cc_final: 0.6185 (m) REVERT: B 118 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7549 (ttpp) REVERT: B 169 GLU cc_start: 0.7764 (tt0) cc_final: 0.7433 (mt-10) REVERT: B 177 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7043 (mtm-85) REVERT: B 207 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7542 (tttt) REVERT: B 211 GLN cc_start: 0.8224 (mt0) cc_final: 0.7962 (mt0) REVERT: B 243 LYS cc_start: 0.7985 (pttt) cc_final: 0.7647 (pttt) REVERT: B 266 LYS cc_start: 0.8420 (tttp) cc_final: 0.8184 (tttp) REVERT: B 272 LYS cc_start: 0.7559 (mtmm) cc_final: 0.7102 (mtmm) REVERT: B 321 GLN cc_start: 0.8389 (mt0) cc_final: 0.8175 (mt0) REVERT: B 361 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: B 388 GLN cc_start: 0.7989 (mt0) cc_final: 0.7661 (mt0) REVERT: C 29 LYS cc_start: 0.8235 (mttt) cc_final: 0.7947 (mttt) REVERT: C 31 VAL cc_start: 0.8301 (t) cc_final: 0.8010 (p) REVERT: C 69 LYS cc_start: 0.8435 (mtmt) cc_final: 0.7855 (mtmt) REVERT: C 89 ASP cc_start: 0.7462 (p0) cc_final: 0.6895 (p0) REVERT: C 90 ASN cc_start: 0.7973 (m-40) cc_final: 0.7657 (m110) REVERT: C 118 LYS cc_start: 0.8194 (tttp) cc_final: 0.7736 (ttmm) REVERT: C 132 GLN cc_start: 0.8159 (mm110) cc_final: 0.7687 (mm110) REVERT: C 143 LEU cc_start: 0.7966 (mt) cc_final: 0.7724 (mp) REVERT: C 202 SER cc_start: 0.7965 (m) cc_final: 0.7524 (t) REVERT: C 232 VAL cc_start: 0.8570 (t) cc_final: 0.8254 (m) REVERT: C 241 THR cc_start: 0.8410 (m) cc_final: 0.8030 (t) REVERT: C 250 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7328 (mm-40) REVERT: C 253 SER cc_start: 0.7923 (m) cc_final: 0.7524 (p) REVERT: C 255 LYS cc_start: 0.8112 (mttt) cc_final: 0.7839 (mttp) REVERT: C 273 LEU cc_start: 0.7940 (mt) cc_final: 0.7686 (mt) REVERT: C 324 VAL cc_start: 0.8461 (t) cc_final: 0.8199 (m) REVERT: C 326 LYS cc_start: 0.8043 (mttp) cc_final: 0.7704 (mttp) REVERT: C 361 ASP cc_start: 0.7390 (t0) cc_final: 0.7126 (t0) REVERT: C 390 HIS cc_start: 0.6744 (t70) cc_final: 0.6514 (t70) outliers start: 37 outliers final: 22 residues processed: 372 average time/residue: 0.1054 time to fit residues: 52.5787 Evaluate side-chains 368 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 341 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 378 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 321 GLN B 90 ASN B 151 ASN C 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114179 restraints weight = 13064.325| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.56 r_work: 0.3245 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9136 Z= 0.193 Angle : 0.576 7.409 12389 Z= 0.308 Chirality : 0.047 0.170 1404 Planarity : 0.004 0.043 1593 Dihedral : 5.612 22.892 1233 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.90 % Allowed : 17.74 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1167 helix: -0.95 (0.59), residues: 73 sheet: 0.83 (0.24), residues: 420 loop : -0.58 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 284 TYR 0.017 0.002 TYR C 194 PHE 0.011 0.002 PHE B 128 TRP 0.014 0.002 TRP C 209 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9132) covalent geometry : angle 0.57533 (12381) SS BOND : bond 0.00506 ( 4) SS BOND : angle 1.40617 ( 8) hydrogen bonds : bond 0.03274 ( 279) hydrogen bonds : angle 5.43506 ( 780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 349 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7743 (t) cc_final: 0.7444 (p) REVERT: A 57 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7647 (mtt180) REVERT: A 90 ASN cc_start: 0.7570 (m110) cc_final: 0.7337 (m-40) REVERT: A 131 ASP cc_start: 0.7369 (t0) cc_final: 0.6958 (t0) REVERT: A 134 LYS cc_start: 0.8159 (mttt) cc_final: 0.7841 (mttt) REVERT: A 142 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6608 (mm-40) REVERT: A 160 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7934 (mtpt) REVERT: A 168 GLN cc_start: 0.6164 (mm-40) cc_final: 0.5951 (mm-40) REVERT: A 227 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7193 (mm-30) REVERT: A 275 LYS cc_start: 0.7342 (tttt) cc_final: 0.6828 (tttt) REVERT: A 276 LEU cc_start: 0.7515 (tp) cc_final: 0.7085 (pp) REVERT: A 288 SER cc_start: 0.7615 (p) cc_final: 0.7376 (m) REVERT: A 298 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7782 (ptpt) REVERT: A 312 ASP cc_start: 0.7835 (t0) cc_final: 0.7598 (t0) REVERT: A 320 MET cc_start: 0.7791 (ptp) cc_final: 0.7505 (ptp) REVERT: A 324 VAL cc_start: 0.8600 (t) cc_final: 0.8306 (m) REVERT: A 362 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7350 (mp0) REVERT: B 29 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7588 (mtmt) REVERT: B 43 ILE cc_start: 0.7696 (mt) cc_final: 0.7338 (mm) REVERT: B 71 ASN cc_start: 0.8499 (t0) cc_final: 0.8219 (t0) REVERT: B 83 GLU cc_start: 0.7805 (mp0) cc_final: 0.7374 (mp0) REVERT: B 84 GLU cc_start: 0.7971 (mp0) cc_final: 0.7616 (tp30) REVERT: B 93 LYS cc_start: 0.7992 (tttt) cc_final: 0.7749 (tttp) REVERT: B 116 CYS cc_start: 0.6390 (OUTLIER) cc_final: 0.6131 (m) REVERT: B 118 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7627 (ttpp) REVERT: B 169 GLU cc_start: 0.7775 (tt0) cc_final: 0.7484 (mt-10) REVERT: B 177 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7195 (mtm-85) REVERT: B 207 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7573 (tttt) REVERT: B 211 GLN cc_start: 0.8202 (mt0) cc_final: 0.7935 (mt0) REVERT: B 243 LYS cc_start: 0.7997 (pttt) cc_final: 0.7665 (pttt) REVERT: B 266 LYS cc_start: 0.8440 (tttp) cc_final: 0.8227 (tttp) REVERT: B 272 LYS cc_start: 0.7558 (mtmm) cc_final: 0.7112 (mtmm) REVERT: B 286 LYS cc_start: 0.7899 (tttt) cc_final: 0.7656 (tttm) REVERT: B 361 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7122 (m-30) REVERT: B 388 GLN cc_start: 0.8008 (mt0) cc_final: 0.7675 (mt0) REVERT: C 29 LYS cc_start: 0.8244 (mttt) cc_final: 0.7961 (mttt) REVERT: C 69 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7922 (mtmt) REVERT: C 89 ASP cc_start: 0.7437 (p0) cc_final: 0.6825 (p0) REVERT: C 90 ASN cc_start: 0.7939 (m-40) cc_final: 0.7554 (m-40) REVERT: C 118 LYS cc_start: 0.8193 (tttp) cc_final: 0.7734 (ttmm) REVERT: C 132 GLN cc_start: 0.8157 (mm110) cc_final: 0.7702 (mm110) REVERT: C 143 LEU cc_start: 0.7963 (mt) cc_final: 0.7691 (mp) REVERT: C 202 SER cc_start: 0.7981 (m) cc_final: 0.7575 (t) REVERT: C 232 VAL cc_start: 0.8608 (t) cc_final: 0.8299 (m) REVERT: C 241 THR cc_start: 0.8455 (m) cc_final: 0.8096 (t) REVERT: C 250 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7291 (mm-40) REVERT: C 253 SER cc_start: 0.8049 (m) cc_final: 0.7604 (p) REVERT: C 255 LYS cc_start: 0.8159 (mttt) cc_final: 0.7906 (mttp) REVERT: C 273 LEU cc_start: 0.7965 (mt) cc_final: 0.7694 (mt) REVERT: C 299 MET cc_start: 0.7826 (mmm) cc_final: 0.7405 (mmm) REVERT: C 324 VAL cc_start: 0.8440 (t) cc_final: 0.8160 (m) REVERT: C 326 LYS cc_start: 0.8038 (mttp) cc_final: 0.7679 (mttp) REVERT: C 361 ASP cc_start: 0.7524 (t0) cc_final: 0.7260 (t0) outliers start: 38 outliers final: 27 residues processed: 365 average time/residue: 0.0836 time to fit residues: 41.0834 Evaluate side-chains 372 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 341 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 378 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 321 GLN A 368 ASN B 90 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN C 211 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114152 restraints weight = 13124.451| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.55 r_work: 0.3255 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9136 Z= 0.195 Angle : 0.573 6.913 12389 Z= 0.306 Chirality : 0.047 0.165 1404 Planarity : 0.004 0.047 1593 Dihedral : 5.575 22.667 1233 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.51 % Allowed : 18.77 % Favored : 76.72 % 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 are not related in a simple way. whole: -0.24 (0.24), residues: 1167 helix: -1.01 (0.58), residues: 72 sheet: 0.86 (0.24), residues: 415 loop : -0.72 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 284 TYR 0.015 0.002 TYR C 194 PHE 0.012 0.002 PHE B 128 TRP 0.014 0.002 TRP A 209 HIS 0.004 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9132) covalent geometry : angle 0.57241 (12381) SS BOND : bond 0.00500 ( 4) SS BOND : angle 1.44062 ( 8) hydrogen bonds : bond 0.03212 ( 279) hydrogen bonds : angle 5.41503 ( 780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 343 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7749 (t) cc_final: 0.7441 (p) REVERT: A 57 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7681 (mtt180) REVERT: A 69 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7863 (mtmt) REVERT: A 90 ASN cc_start: 0.7566 (m110) cc_final: 0.7321 (m-40) REVERT: A 107 LEU cc_start: 0.8027 (mt) cc_final: 0.7571 (mt) REVERT: A 110 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7674 (mtpp) REVERT: A 131 ASP cc_start: 0.7451 (t0) cc_final: 0.6985 (t0) REVERT: A 134 LYS cc_start: 0.8189 (mttt) cc_final: 0.7834 (mttt) REVERT: A 142 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6604 (mm-40) REVERT: A 160 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7974 (mtpt) REVERT: A 275 LYS cc_start: 0.7337 (tttt) cc_final: 0.6837 (tttt) REVERT: A 276 LEU cc_start: 0.7516 (tp) cc_final: 0.7089 (pp) REVERT: A 288 SER cc_start: 0.7599 (p) cc_final: 0.7365 (m) REVERT: A 298 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7810 (ptpt) REVERT: A 312 ASP cc_start: 0.7839 (t0) cc_final: 0.7607 (t0) REVERT: A 320 MET cc_start: 0.7755 (ptp) cc_final: 0.7469 (ptp) REVERT: A 324 VAL cc_start: 0.8610 (t) cc_final: 0.8299 (m) REVERT: A 362 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7384 (mp0) REVERT: B 29 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7602 (mtmt) REVERT: B 83 GLU cc_start: 0.7823 (mp0) cc_final: 0.7373 (mp0) REVERT: B 84 GLU cc_start: 0.8002 (mp0) cc_final: 0.7661 (tp30) REVERT: B 93 LYS cc_start: 0.8015 (tttt) cc_final: 0.7754 (tttp) REVERT: B 116 CYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6206 (m) REVERT: B 118 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7610 (ttpp) REVERT: B 169 GLU cc_start: 0.7773 (tt0) cc_final: 0.7468 (mt-10) REVERT: B 177 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7184 (mtm-85) REVERT: B 207 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7577 (ttmt) REVERT: B 211 GLN cc_start: 0.8178 (mt0) cc_final: 0.7913 (mt0) REVERT: B 243 LYS cc_start: 0.8000 (pttt) cc_final: 0.7653 (pttt) REVERT: B 266 LYS cc_start: 0.8440 (tttp) cc_final: 0.8192 (tttp) REVERT: B 272 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7100 (mtmm) REVERT: B 303 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7738 (mttm) REVERT: B 321 GLN cc_start: 0.8359 (mt0) cc_final: 0.8152 (mt0) REVERT: B 361 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: C 19 THR cc_start: 0.6794 (OUTLIER) cc_final: 0.6462 (p) REVERT: C 29 LYS cc_start: 0.8238 (mttt) cc_final: 0.7948 (mttt) REVERT: C 31 VAL cc_start: 0.8392 (t) cc_final: 0.8038 (p) REVERT: C 69 LYS cc_start: 0.8462 (mtmt) cc_final: 0.7928 (mtmt) REVERT: C 89 ASP cc_start: 0.7405 (p0) cc_final: 0.6768 (p0) REVERT: C 90 ASN cc_start: 0.7926 (m-40) cc_final: 0.7535 (m-40) REVERT: C 118 LYS cc_start: 0.8183 (tttp) cc_final: 0.7730 (ttmm) REVERT: C 132 GLN cc_start: 0.8175 (mm110) cc_final: 0.7713 (mm110) REVERT: C 202 SER cc_start: 0.7981 (m) cc_final: 0.7567 (t) REVERT: C 232 VAL cc_start: 0.8615 (t) cc_final: 0.8303 (m) REVERT: C 241 THR cc_start: 0.8468 (m) cc_final: 0.8116 (t) REVERT: C 250 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7281 (mm-40) REVERT: C 253 SER cc_start: 0.8077 (m) cc_final: 0.7618 (p) REVERT: C 255 LYS cc_start: 0.8179 (mttt) cc_final: 0.7893 (mttm) REVERT: C 273 LEU cc_start: 0.7964 (mt) cc_final: 0.7696 (mt) REVERT: C 324 VAL cc_start: 0.8381 (t) cc_final: 0.8130 (m) REVERT: C 326 LYS cc_start: 0.8031 (mttp) cc_final: 0.7676 (mttp) REVERT: C 361 ASP cc_start: 0.7551 (t0) cc_final: 0.7315 (t0) outliers start: 44 outliers final: 32 residues processed: 362 average time/residue: 0.0865 time to fit residues: 42.2517 Evaluate side-chains 378 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 341 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 378 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 151 ASN C 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114829 restraints weight = 13174.778| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.58 r_work: 0.3255 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9136 Z= 0.135 Angle : 0.536 6.770 12389 Z= 0.284 Chirality : 0.046 0.162 1404 Planarity : 0.004 0.041 1593 Dihedral : 5.273 22.174 1233 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.59 % Allowed : 20.21 % Favored : 76.21 % 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 are not related in a simple way. whole: -0.08 (0.24), residues: 1167 helix: -0.90 (0.59), residues: 72 sheet: 1.01 (0.25), residues: 411 loop : -0.63 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.012 0.001 TYR C 194 PHE 0.010 0.001 PHE A 119 TRP 0.013 0.001 TRP A 209 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9132) covalent geometry : angle 0.53480 (12381) SS BOND : bond 0.00505 ( 4) SS BOND : angle 1.26509 ( 8) hydrogen bonds : bond 0.02884 ( 279) hydrogen bonds : angle 5.23985 ( 780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 340 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7717 (t) cc_final: 0.7404 (p) REVERT: A 46 GLU cc_start: 0.7116 (tt0) cc_final: 0.6680 (tt0) REVERT: A 57 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7716 (mtt180) REVERT: A 90 ASN cc_start: 0.7580 (m110) cc_final: 0.7317 (m-40) REVERT: A 110 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7638 (mtpp) REVERT: A 134 LYS cc_start: 0.8165 (mttt) cc_final: 0.7816 (mttt) REVERT: A 142 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6647 (mm-40) REVERT: A 160 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7962 (mtpt) REVERT: A 227 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 275 LYS cc_start: 0.7301 (tttt) cc_final: 0.6845 (tttt) REVERT: A 276 LEU cc_start: 0.7484 (tp) cc_final: 0.7149 (pp) REVERT: A 288 SER cc_start: 0.7585 (p) cc_final: 0.7350 (m) REVERT: A 298 LYS cc_start: 0.8145 (ptpt) cc_final: 0.7816 (ptpt) REVERT: A 312 ASP cc_start: 0.7833 (t0) cc_final: 0.7611 (t0) REVERT: A 320 MET cc_start: 0.7796 (ptp) cc_final: 0.7515 (ptp) REVERT: A 324 VAL cc_start: 0.8591 (t) cc_final: 0.8265 (m) REVERT: A 362 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7376 (mp0) REVERT: B 29 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7782 (mttp) REVERT: B 43 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7265 (mm) REVERT: B 69 LYS cc_start: 0.8477 (mttt) cc_final: 0.8132 (mtpp) REVERT: B 83 GLU cc_start: 0.7784 (mp0) cc_final: 0.7314 (mp0) REVERT: B 93 LYS cc_start: 0.8002 (tttt) cc_final: 0.7739 (tttp) REVERT: B 116 CYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6172 (m) REVERT: B 118 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7609 (ttpp) REVERT: B 169 GLU cc_start: 0.7786 (tt0) cc_final: 0.7471 (mt-10) REVERT: B 177 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7161 (mtm-85) REVERT: B 207 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7602 (tttt) REVERT: B 211 GLN cc_start: 0.8124 (mt0) cc_final: 0.7857 (mt0) REVERT: B 243 LYS cc_start: 0.7953 (pttt) cc_final: 0.7628 (pttt) REVERT: B 266 LYS cc_start: 0.8423 (tttp) cc_final: 0.8180 (tttp) REVERT: B 272 LYS cc_start: 0.7495 (mtmm) cc_final: 0.7046 (mtmm) REVERT: B 361 ASP cc_start: 0.7553 (t0) cc_final: 0.7153 (m-30) REVERT: C 29 LYS cc_start: 0.8237 (mttt) cc_final: 0.7933 (mttt) REVERT: C 31 VAL cc_start: 0.8351 (t) cc_final: 0.8028 (p) REVERT: C 69 LYS cc_start: 0.8440 (mtmt) cc_final: 0.7973 (mtmm) REVERT: C 89 ASP cc_start: 0.7385 (p0) cc_final: 0.6779 (p0) REVERT: C 118 LYS cc_start: 0.8160 (tttp) cc_final: 0.7703 (ttmm) REVERT: C 132 GLN cc_start: 0.8197 (mm110) cc_final: 0.7734 (mm110) REVERT: C 202 SER cc_start: 0.7909 (m) cc_final: 0.7529 (t) REVERT: C 232 VAL cc_start: 0.8616 (t) cc_final: 0.8293 (m) REVERT: C 241 THR cc_start: 0.8445 (m) cc_final: 0.7963 (p) REVERT: C 250 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7247 (mm-40) REVERT: C 253 SER cc_start: 0.7989 (m) cc_final: 0.7586 (p) REVERT: C 255 LYS cc_start: 0.8154 (mttt) cc_final: 0.7868 (mttp) REVERT: C 273 LEU cc_start: 0.7951 (mt) cc_final: 0.7681 (mt) REVERT: C 275 LYS cc_start: 0.7952 (mttt) cc_final: 0.7565 (mttp) REVERT: C 324 VAL cc_start: 0.8376 (t) cc_final: 0.8140 (m) REVERT: C 326 LYS cc_start: 0.8018 (mttp) cc_final: 0.7671 (mttp) REVERT: C 360 ASP cc_start: 0.8024 (m-30) cc_final: 0.7820 (m-30) REVERT: C 361 ASP cc_start: 0.7530 (t0) cc_final: 0.7292 (t0) outliers start: 35 outliers final: 25 residues processed: 353 average time/residue: 0.0902 time to fit residues: 42.6873 Evaluate side-chains 367 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 338 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 378 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 229 HIS B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110593 restraints weight = 13505.128| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.70 r_work: 0.3258 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9136 Z= 0.288 Angle : 0.641 7.175 12389 Z= 0.343 Chirality : 0.049 0.172 1404 Planarity : 0.005 0.045 1593 Dihedral : 5.863 23.066 1233 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.72 % Allowed : 20.10 % Favored : 75.18 % 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 are not related in a simple way. whole: -0.57 (0.24), residues: 1167 helix: -1.24 (0.57), residues: 73 sheet: 0.68 (0.24), residues: 423 loop : -1.00 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.017 0.002 TYR C 194 PHE 0.015 0.002 PHE A 119 TRP 0.016 0.003 TRP C 209 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 9132) covalent geometry : angle 0.63931 (12381) SS BOND : bond 0.00594 ( 4) SS BOND : angle 1.73678 ( 8) hydrogen bonds : bond 0.03664 ( 279) hydrogen bonds : angle 5.51506 ( 780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 363 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7776 (t) cc_final: 0.7468 (p) REVERT: A 57 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7713 (mtt180) REVERT: A 62 SER cc_start: 0.8321 (t) cc_final: 0.7780 (p) REVERT: A 83 GLU cc_start: 0.7700 (mp0) cc_final: 0.7409 (mp0) REVERT: A 90 ASN cc_start: 0.7565 (m110) cc_final: 0.7310 (m-40) REVERT: A 107 LEU cc_start: 0.8033 (mt) cc_final: 0.7573 (mt) REVERT: A 131 ASP cc_start: 0.7524 (t0) cc_final: 0.7069 (t0) REVERT: A 134 LYS cc_start: 0.8213 (mttt) cc_final: 0.7873 (mttt) REVERT: A 142 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6603 (mm-40) REVERT: A 160 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7991 (mtpt) REVERT: A 227 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 232 VAL cc_start: 0.7874 (t) cc_final: 0.7610 (m) REVERT: A 275 LYS cc_start: 0.7385 (tttt) cc_final: 0.6899 (tttt) REVERT: A 288 SER cc_start: 0.7648 (p) cc_final: 0.7423 (m) REVERT: A 298 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7844 (ptpt) REVERT: A 312 ASP cc_start: 0.7827 (t0) cc_final: 0.7625 (t0) REVERT: A 324 VAL cc_start: 0.8592 (t) cc_final: 0.8277 (m) REVERT: A 362 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7468 (mp0) REVERT: B 29 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7836 (mttp) REVERT: B 43 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7365 (mm) REVERT: B 83 GLU cc_start: 0.7845 (mp0) cc_final: 0.7422 (mp0) REVERT: B 93 LYS cc_start: 0.8127 (tttt) cc_final: 0.7873 (tttm) REVERT: B 118 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7590 (ttpp) REVERT: B 169 GLU cc_start: 0.7819 (tt0) cc_final: 0.7521 (mt-10) REVERT: B 177 ARG cc_start: 0.7620 (mtm110) cc_final: 0.7045 (mtm-85) REVERT: B 207 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7679 (tttt) REVERT: B 211 GLN cc_start: 0.8149 (mt0) cc_final: 0.7892 (mt0) REVERT: B 243 LYS cc_start: 0.8035 (pttt) cc_final: 0.7705 (pttt) REVERT: B 263 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7063 (mtt90) REVERT: B 266 LYS cc_start: 0.8439 (tttp) cc_final: 0.8154 (tttp) REVERT: B 272 LYS cc_start: 0.7608 (mtmm) cc_final: 0.7146 (mtmm) REVERT: B 361 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: C 19 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6552 (p) REVERT: C 26 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 69 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8002 (mtmt) REVERT: C 89 ASP cc_start: 0.7442 (p0) cc_final: 0.6801 (p0) REVERT: C 118 LYS cc_start: 0.8205 (tttp) cc_final: 0.7741 (ttmm) REVERT: C 132 GLN cc_start: 0.8251 (mm110) cc_final: 0.7775 (mm110) REVERT: C 202 SER cc_start: 0.8004 (m) cc_final: 0.7593 (t) REVERT: C 232 VAL cc_start: 0.8649 (t) cc_final: 0.8334 (m) REVERT: C 241 THR cc_start: 0.8509 (m) cc_final: 0.8163 (t) REVERT: C 250 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7298 (mm-40) REVERT: C 255 LYS cc_start: 0.8241 (mttt) cc_final: 0.7940 (mttp) REVERT: C 273 LEU cc_start: 0.8009 (mt) cc_final: 0.7771 (mt) REVERT: C 281 VAL cc_start: 0.7902 (t) cc_final: 0.7458 (p) REVERT: C 324 VAL cc_start: 0.8340 (t) cc_final: 0.8105 (m) REVERT: C 326 LYS cc_start: 0.8025 (mttp) cc_final: 0.7705 (mttp) REVERT: C 361 ASP cc_start: 0.7614 (t0) cc_final: 0.7397 (t0) outliers start: 46 outliers final: 34 residues processed: 384 average time/residue: 0.0936 time to fit residues: 47.2836 Evaluate side-chains 399 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 360 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 378 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 315 HIS B 321 GLN C 211 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109778 restraints weight = 13506.614| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.67 r_work: 0.3218 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9136 Z= 0.264 Angle : 0.637 7.338 12389 Z= 0.337 Chirality : 0.049 0.164 1404 Planarity : 0.005 0.045 1593 Dihedral : 5.866 23.272 1233 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.82 % Allowed : 20.51 % Favored : 74.67 % 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 are not related in a simple way. whole: -0.69 (0.24), residues: 1167 helix: -1.30 (0.57), residues: 73 sheet: 0.59 (0.24), residues: 423 loop : -1.08 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 284 TYR 0.018 0.002 TYR C 194 PHE 0.015 0.002 PHE A 161 TRP 0.016 0.002 TRP A 209 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 9132) covalent geometry : angle 0.63573 (12381) SS BOND : bond 0.00657 ( 4) SS BOND : angle 1.75934 ( 8) hydrogen bonds : bond 0.03487 ( 279) hydrogen bonds : angle 5.48090 ( 780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 356 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7716 (t) cc_final: 0.7396 (p) REVERT: A 57 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7655 (mtt180) REVERT: A 62 SER cc_start: 0.8259 (t) cc_final: 0.7722 (p) REVERT: A 83 GLU cc_start: 0.7712 (mp0) cc_final: 0.7417 (mp0) REVERT: A 90 ASN cc_start: 0.7551 (m110) cc_final: 0.7302 (m-40) REVERT: A 107 LEU cc_start: 0.8011 (mt) cc_final: 0.7554 (mt) REVERT: A 110 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7736 (mtpp) REVERT: A 131 ASP cc_start: 0.7568 (t0) cc_final: 0.7092 (t0) REVERT: A 134 LYS cc_start: 0.8212 (mttt) cc_final: 0.7851 (mttt) REVERT: A 142 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6596 (mm-40) REVERT: A 160 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7971 (mtpt) REVERT: A 227 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7386 (mm-30) REVERT: A 232 VAL cc_start: 0.7847 (t) cc_final: 0.7566 (m) REVERT: A 266 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7635 (tttm) REVERT: A 275 LYS cc_start: 0.7337 (tttt) cc_final: 0.6881 (tttt) REVERT: A 276 LEU cc_start: 0.7568 (tp) cc_final: 0.7141 (pp) REVERT: A 288 SER cc_start: 0.7622 (p) cc_final: 0.7385 (m) REVERT: A 298 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7800 (ptpt) REVERT: A 312 ASP cc_start: 0.7785 (t0) cc_final: 0.7585 (t0) REVERT: A 324 VAL cc_start: 0.8565 (t) cc_final: 0.8279 (m) REVERT: A 362 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7457 (mp0) REVERT: B 29 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7790 (mttp) REVERT: B 43 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7214 (mm) REVERT: B 83 GLU cc_start: 0.7846 (mp0) cc_final: 0.7406 (mp0) REVERT: B 84 GLU cc_start: 0.8008 (mp0) cc_final: 0.7669 (tp30) REVERT: B 93 LYS cc_start: 0.8057 (tttt) cc_final: 0.7776 (tttm) REVERT: B 118 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7511 (tttt) REVERT: B 169 GLU cc_start: 0.7815 (tt0) cc_final: 0.7567 (mt-10) REVERT: B 177 ARG cc_start: 0.7610 (mtm110) cc_final: 0.6914 (mtm-85) REVERT: B 207 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7648 (tttt) REVERT: B 211 GLN cc_start: 0.8148 (mt0) cc_final: 0.7887 (mt0) REVERT: B 243 LYS cc_start: 0.8042 (pttt) cc_final: 0.7711 (pttt) REVERT: B 266 LYS cc_start: 0.8441 (tttp) cc_final: 0.8155 (tttp) REVERT: B 267 ASP cc_start: 0.7626 (t0) cc_final: 0.7331 (t0) REVERT: B 272 LYS cc_start: 0.7526 (mtmm) cc_final: 0.7052 (mtmm) REVERT: B 361 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: C 19 THR cc_start: 0.6889 (OUTLIER) cc_final: 0.6552 (p) REVERT: C 69 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7973 (mtmt) REVERT: C 89 ASP cc_start: 0.7413 (p0) cc_final: 0.6819 (p0) REVERT: C 118 LYS cc_start: 0.8192 (tttp) cc_final: 0.7707 (ttmm) REVERT: C 132 GLN cc_start: 0.8273 (mm110) cc_final: 0.7804 (mm110) REVERT: C 202 SER cc_start: 0.7995 (m) cc_final: 0.7551 (t) REVERT: C 232 VAL cc_start: 0.8622 (t) cc_final: 0.8297 (m) REVERT: C 241 THR cc_start: 0.8484 (m) cc_final: 0.7999 (p) REVERT: C 250 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7239 (mm-40) REVERT: C 255 LYS cc_start: 0.8173 (mttt) cc_final: 0.7886 (mttp) REVERT: C 273 LEU cc_start: 0.8002 (mt) cc_final: 0.7747 (mt) REVERT: C 281 VAL cc_start: 0.7834 (t) cc_final: 0.7379 (p) REVERT: C 324 VAL cc_start: 0.8320 (t) cc_final: 0.8091 (m) REVERT: C 326 LYS cc_start: 0.8008 (mttp) cc_final: 0.7697 (mttp) REVERT: C 361 ASP cc_start: 0.7656 (t0) cc_final: 0.7426 (t0) outliers start: 47 outliers final: 38 residues processed: 377 average time/residue: 0.0919 time to fit residues: 46.5215 Evaluate side-chains 395 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 351 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 60 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 315 HIS B 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113599 restraints weight = 13175.047| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.69 r_work: 0.3247 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9136 Z= 0.119 Angle : 0.562 6.780 12389 Z= 0.297 Chirality : 0.046 0.163 1404 Planarity : 0.004 0.041 1593 Dihedral : 5.367 22.672 1233 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.69 % Allowed : 21.95 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1167 helix: -1.00 (0.59), residues: 72 sheet: 0.80 (0.25), residues: 410 loop : -0.87 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.012 0.001 TYR C 194 PHE 0.009 0.001 PHE A 119 TRP 0.015 0.001 TRP B 20 HIS 0.007 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9132) covalent geometry : angle 0.56107 (12381) SS BOND : bond 0.00541 ( 4) SS BOND : angle 1.46090 ( 8) hydrogen bonds : bond 0.02803 ( 279) hydrogen bonds : angle 5.20906 ( 780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 347 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7700 (t) cc_final: 0.7363 (p) REVERT: A 46 GLU cc_start: 0.7181 (tt0) cc_final: 0.6795 (tt0) REVERT: A 57 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7673 (mtt180) REVERT: A 90 ASN cc_start: 0.7568 (m110) cc_final: 0.7324 (m-40) REVERT: A 107 LEU cc_start: 0.8004 (mt) cc_final: 0.7546 (mt) REVERT: A 110 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7692 (mtpp) REVERT: A 134 LYS cc_start: 0.8162 (mttt) cc_final: 0.7813 (mttt) REVERT: A 142 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6616 (mm-40) REVERT: A 160 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7959 (mtpt) REVERT: A 227 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 232 VAL cc_start: 0.7844 (t) cc_final: 0.7570 (m) REVERT: A 276 LEU cc_start: 0.7554 (tp) cc_final: 0.7140 (pp) REVERT: A 288 SER cc_start: 0.7580 (p) cc_final: 0.7335 (m) REVERT: A 298 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7791 (ptpt) REVERT: A 299 MET cc_start: 0.8034 (mmm) cc_final: 0.7831 (mmm) REVERT: A 324 VAL cc_start: 0.8586 (t) cc_final: 0.8265 (m) REVERT: A 362 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7454 (mp0) REVERT: B 29 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7703 (mttm) REVERT: B 43 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7171 (mm) REVERT: B 83 GLU cc_start: 0.7818 (mp0) cc_final: 0.7375 (mp0) REVERT: B 84 GLU cc_start: 0.7960 (mp0) cc_final: 0.7441 (tp30) REVERT: B 93 LYS cc_start: 0.8004 (tttt) cc_final: 0.7748 (tttm) REVERT: B 118 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7482 (tttt) REVERT: B 169 GLU cc_start: 0.7792 (tt0) cc_final: 0.7485 (mt-10) REVERT: B 177 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7177 (mtm-85) REVERT: B 207 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7573 (tttt) REVERT: B 211 GLN cc_start: 0.8104 (mt0) cc_final: 0.7841 (mt0) REVERT: B 243 LYS cc_start: 0.7997 (pttt) cc_final: 0.7670 (pttt) REVERT: B 266 LYS cc_start: 0.8413 (tttp) cc_final: 0.8119 (tttp) REVERT: B 267 ASP cc_start: 0.7602 (t0) cc_final: 0.7297 (t0) REVERT: B 272 LYS cc_start: 0.7465 (mtmm) cc_final: 0.6991 (mtmm) REVERT: B 286 LYS cc_start: 0.7821 (tttm) cc_final: 0.7481 (tttm) REVERT: B 361 ASP cc_start: 0.7564 (t0) cc_final: 0.7197 (m-30) REVERT: C 19 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6507 (p) REVERT: C 31 VAL cc_start: 0.8342 (t) cc_final: 0.8008 (p) REVERT: C 69 LYS cc_start: 0.8459 (mtmt) cc_final: 0.7918 (mtmt) REVERT: C 89 ASP cc_start: 0.7370 (p0) cc_final: 0.6846 (p0) REVERT: C 118 LYS cc_start: 0.8193 (tttp) cc_final: 0.7726 (ttmm) REVERT: C 132 GLN cc_start: 0.8247 (mm110) cc_final: 0.7790 (mm110) REVERT: C 202 SER cc_start: 0.7893 (m) cc_final: 0.7531 (t) REVERT: C 232 VAL cc_start: 0.8631 (t) cc_final: 0.8293 (m) REVERT: C 241 THR cc_start: 0.8459 (m) cc_final: 0.7990 (p) REVERT: C 250 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7183 (mm-40) REVERT: C 253 SER cc_start: 0.8039 (m) cc_final: 0.7635 (p) REVERT: C 255 LYS cc_start: 0.8130 (mttt) cc_final: 0.7840 (mttp) REVERT: C 273 LEU cc_start: 0.7966 (mt) cc_final: 0.7684 (mt) REVERT: C 281 VAL cc_start: 0.7783 (t) cc_final: 0.7318 (p) REVERT: C 324 VAL cc_start: 0.8303 (t) cc_final: 0.8090 (m) REVERT: C 326 LYS cc_start: 0.7982 (mttp) cc_final: 0.7666 (mttp) REVERT: C 361 ASP cc_start: 0.7605 (t0) cc_final: 0.7380 (t0) outliers start: 36 outliers final: 30 residues processed: 361 average time/residue: 0.0914 time to fit residues: 44.2370 Evaluate side-chains 379 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 345 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 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 71 ASN B 151 ASN B 315 HIS B 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111004 restraints weight = 13378.395| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.68 r_work: 0.3239 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9136 Z= 0.178 Angle : 0.587 7.645 12389 Z= 0.309 Chirality : 0.047 0.167 1404 Planarity : 0.004 0.042 1593 Dihedral : 5.422 22.164 1233 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.79 % Allowed : 23.08 % Favored : 73.13 % 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 are not related in a simple way. whole: -0.45 (0.24), residues: 1167 helix: -1.05 (0.59), residues: 72 sheet: 0.76 (0.25), residues: 412 loop : -0.90 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.014 0.001 TYR C 194 PHE 0.011 0.002 PHE A 119 TRP 0.015 0.002 TRP A 209 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9132) covalent geometry : angle 0.58568 (12381) SS BOND : bond 0.00599 ( 4) SS BOND : angle 1.48057 ( 8) hydrogen bonds : bond 0.03047 ( 279) hydrogen bonds : angle 5.23698 ( 780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.03 seconds wall clock time: 37 minutes 24.01 seconds (2244.01 seconds total)