Starting phenix.real_space_refine on Tue Aug 4 22:14:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn9_52309/08_2026/9hn9_52309.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn9_52309/08_2026/9hn9_52309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hn9_52309/08_2026/9hn9_52309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn9_52309/08_2026/9hn9_52309.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hn9_52309/08_2026/9hn9_52309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn9_52309/08_2026/9hn9_52309.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 5 Type Number sf(0) Gaussians P 73 5.49 5 S 46 5.16 5 C 4085 2.51 5 N 1194 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6897 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2883 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 359} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2455 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 310} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1548 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan': 1, ' G%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'9DG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.24 Number of scatterers: 6897 At special positions: 0 Unit cell: (73.08, 86.52, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 73 15.00 O 1499 8.00 N 1194 7.00 C 4085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 445.9 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 53.2% alpha, 9.6% beta 24 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.924A pdb=" N LEU A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.877A pdb=" N ARG A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.973A pdb=" N GLY A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.043A pdb=" N GLU A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.623A pdb=" N GLY A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.753A pdb=" N GLU A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 235 through 250 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 326 through 337 removed outlier: 3.966A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 366 removed outlier: 3.759A pdb=" N ALA A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.625A pdb=" N CYS A 387 " --> pdb=" O HIS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 399 removed outlier: 3.634A pdb=" N VAL A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 68 through 76 removed outlier: 3.798A pdb=" N GLU B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.489A pdb=" N SER B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.658A pdb=" N LEU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 198 through 211 removed outlier: 3.590A pdb=" N ARG B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.552A pdb=" N ALA B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.166A pdb=" N TYR B 340 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 341 " --> pdb=" O LYS B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 373 through 400 removed outlier: 3.837A pdb=" N VAL B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 45 removed outlier: 6.345A pdb=" N VAL A 44 " --> pdb=" O PHE A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.513A pdb=" N CYS A 70 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP A 105 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 72 " --> pdb=" O ASP A 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 156 removed outlier: 3.803A pdb=" N GLY A 224 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.269A pdb=" N LEU B 35 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR B 63 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR B 37 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ALA B 60 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 95 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU B 62 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 92 " --> pdb=" O TRP B 140 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLN B 142 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N CYS B 94 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 286 259 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 989 1.31 - 1.44: 2319 1.44 - 1.56: 3672 1.56 - 1.69: 144 1.69 - 1.81: 68 Bond restraints: 7192 Sorted by residual: bond pdb=" C2 9DG A 501 " pdb=" N3 9DG A 501 " ideal model delta sigma weight residual 1.298 1.461 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C4 9DG A 501 " pdb=" N3 9DG A 501 " ideal model delta sigma weight residual 1.363 1.486 -0.123 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C5 9DG A 501 " pdb=" C6 9DG A 501 " ideal model delta sigma weight residual 1.419 1.523 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C2 9DG A 501 " pdb=" N2 9DG A 501 " ideal model delta sigma weight residual 1.356 1.450 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C2 9DG A 501 " pdb=" N1 9DG A 501 " ideal model delta sigma weight residual 1.371 1.441 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 7187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 9977 3.35 - 6.69: 104 6.69 - 10.04: 15 10.04 - 13.38: 2 13.38 - 16.73: 1 Bond angle restraints: 10099 Sorted by residual: angle pdb=" O5' U C 12 " pdb=" C5' U C 12 " pdb=" C4' U C 12 " ideal model delta sigma weight residual 109.40 113.52 -4.12 8.00e-01 1.56e+00 2.65e+01 angle pdb=" C GLU A 216 " pdb=" N MET A 217 " pdb=" CA MET A 217 " ideal model delta sigma weight residual 122.38 113.15 9.23 1.81e+00 3.05e-01 2.60e+01 angle pdb=" CA LEU A 214 " pdb=" CB LEU A 214 " pdb=" CG LEU A 214 " ideal model delta sigma weight residual 116.30 133.03 -16.73 3.50e+00 8.16e-02 2.28e+01 angle pdb=" O5' G C 86 " pdb=" C5' G C 86 " pdb=" C4' G C 86 " ideal model delta sigma weight residual 109.40 113.02 -3.62 8.00e-01 1.56e+00 2.05e+01 angle pdb=" O5' G C 18 " pdb=" C5' G C 18 " pdb=" C4' G C 18 " ideal model delta sigma weight residual 109.40 112.89 -3.49 8.00e-01 1.56e+00 1.91e+01 ... (remaining 10094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3805 17.90 - 35.81: 343 35.81 - 53.71: 124 53.71 - 71.61: 94 71.61 - 89.51: 24 Dihedral angle restraints: 4390 sinusoidal: 2381 harmonic: 2009 Sorted by residual: dihedral pdb=" CA GLN A 90 " pdb=" C GLN A 90 " pdb=" N GLY A 91 " pdb=" CA GLY A 91 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA GLY A 91 " pdb=" C GLY A 91 " pdb=" N LEU A 92 " pdb=" CA LEU A 92 " ideal model delta harmonic sigma weight residual 180.00 -153.28 -26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA LEU A 19 " pdb=" C LEU A 19 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1108 0.114 - 0.228: 98 0.228 - 0.342: 3 0.342 - 0.456: 0 0.456 - 0.570: 1 Chirality restraints: 1210 Sorted by residual: chirality pdb=" CG LEU A 214 " pdb=" CB LEU A 214 " pdb=" CD1 LEU A 214 " pdb=" CD2 LEU A 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CB ILE B 189 " pdb=" CA ILE B 189 " pdb=" CG1 ILE B 189 " pdb=" CG2 ILE B 189 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" P C C 1 " pdb=" OP1 C C 1 " pdb=" OP2 C C 1 " pdb=" O5' C C 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.67 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1207 not shown) Planarity restraints: 1027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 170 " 0.022 2.00e-02 2.50e+03 1.78e-02 5.52e+00 pdb=" CG PHE B 170 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 170 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 170 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 170 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 11 " 0.027 2.00e-02 2.50e+03 1.41e-02 4.47e+00 pdb=" N1 C C 11 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C C 11 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C C 11 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 11 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C C 11 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C C 11 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C C 11 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 294 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO A 295 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.029 5.00e-02 4.00e+02 ... (remaining 1024 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 643 2.74 - 3.28: 6739 3.28 - 3.82: 13145 3.82 - 4.36: 15003 4.36 - 4.90: 23311 Nonbonded interactions: 58841 Sorted by model distance: nonbonded pdb=" O THR A 121 " pdb=" NH2 ARG A 177 " model vdw 2.196 3.120 nonbonded pdb=" O ALA A 207 " pdb=" OG1 THR A 211 " model vdw 2.216 3.040 nonbonded pdb=" OG SER B 255 " pdb=" OH TYR B 387 " model vdw 2.264 3.040 nonbonded pdb=" O2' A C 73 " pdb=" OP2 U C 75 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASP B 146 " pdb=" OG SER B 167 " model vdw 2.269 3.040 ... (remaining 58836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.090 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 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 : 0.006 0.163 7192 Z= 0.310 Angle : 0.966 16.728 10099 Z= 0.618 Chirality : 0.060 0.570 1210 Planarity : 0.006 0.052 1027 Dihedral : 18.719 89.515 3094 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.52 (0.30), residues: 691 helix: -0.77 (0.26), residues: 322 sheet: -0.90 (0.66), residues: 62 loop : -1.14 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 202 TYR 0.031 0.004 TYR B 363 PHE 0.040 0.003 PHE B 170 TRP 0.021 0.004 TRP B 116 HIS 0.017 0.002 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.31 ( 7192) covalent geometry : angle 0.96643 / 0.62 (10099) hydrogen bonds : bond 0.14244 / 10.74 ( 321) hydrogen bonds : angle 6.75716 / 4.90 ( 854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.7887 (pmm) cc_final: 0.7463 (pmm) REVERT: A 368 ARG cc_start: 0.8744 (tmm-80) cc_final: 0.8486 (tmm-80) REVERT: B 222 PHE cc_start: 0.4105 (m-10) cc_final: 0.3629 (m-10) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0781 time to fit residues: 10.0418 Evaluate side-chains 80 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.141883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.124293 restraints weight = 19686.465| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.93 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7192 Z= 0.144 Angle : 0.671 10.761 10099 Z= 0.351 Chirality : 0.042 0.247 1210 Planarity : 0.005 0.051 1027 Dihedral : 19.684 81.234 1890 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.53 % Allowed : 7.64 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.27 (0.30), residues: 691 helix: -0.31 (0.27), residues: 338 sheet: -1.21 (0.61), residues: 67 loop : -1.26 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 121 TYR 0.030 0.003 TYR A 352 PHE 0.016 0.002 PHE B 170 TRP 0.010 0.002 TRP A 181 HIS 0.010 0.002 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7192) covalent geometry : angle 0.67094 / 0.35 (10099) hydrogen bonds : bond 0.05918 / 4.28 ( 321) hydrogen bonds : angle 5.71302 / 4.15 ( 854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.7510 (tpt) cc_final: 0.7302 (tpp) REVERT: A 355 GLN cc_start: 0.7750 (mm110) cc_final: 0.6536 (pt0) REVERT: A 367 GLN cc_start: 0.7485 (mp10) cc_final: 0.7282 (mp10) REVERT: A 368 ARG cc_start: 0.8937 (tmm-80) cc_final: 0.8505 (tmm-80) REVERT: B 222 PHE cc_start: 0.4228 (m-10) cc_final: 0.3717 (m-10) REVERT: B 381 MET cc_start: 0.7059 (mtt) cc_final: 0.6765 (mtm) outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.0768 time to fit residues: 9.9718 Evaluate side-chains 86 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 7 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.0060 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.141963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.124342 restraints weight = 19641.477| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 3.91 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7192 Z= 0.132 Angle : 0.642 13.398 10099 Z= 0.334 Chirality : 0.041 0.333 1210 Planarity : 0.004 0.047 1027 Dihedral : 19.558 80.148 1890 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.53 % Allowed : 11.01 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.88 (0.31), residues: 691 helix: 0.12 (0.28), residues: 336 sheet: -1.15 (0.59), residues: 73 loop : -1.17 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 121 TYR 0.027 0.003 TYR A 352 PHE 0.014 0.001 PHE B 170 TRP 0.021 0.002 TRP A 181 HIS 0.009 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7192) covalent geometry : angle 0.64250 / 0.33 (10099) hydrogen bonds : bond 0.05309 / 3.87 ( 321) hydrogen bonds : angle 5.29156 / 3.85 ( 854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 277 MET cc_start: 0.2859 (mmt) cc_final: 0.2336 (mmt) REVERT: A 355 GLN cc_start: 0.7760 (mm110) cc_final: 0.6537 (pt0) REVERT: A 368 ARG cc_start: 0.9026 (tmm-80) cc_final: 0.8753 (ttp-110) REVERT: B 222 PHE cc_start: 0.4258 (m-10) cc_final: 0.3824 (m-10) outliers start: 3 outliers final: 3 residues processed: 86 average time/residue: 0.0884 time to fit residues: 10.1454 Evaluate side-chains 84 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.141684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.123838 restraints weight = 19731.969| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 3.93 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7192 Z= 0.134 Angle : 0.638 17.897 10099 Z= 0.328 Chirality : 0.041 0.368 1210 Planarity : 0.004 0.044 1027 Dihedral : 19.501 79.759 1890 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.60 % Allowed : 11.55 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.31), residues: 691 helix: 0.35 (0.28), residues: 338 sheet: -1.03 (0.60), residues: 71 loop : -1.21 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.025 0.003 TYR A 352 PHE 0.014 0.001 PHE A 376 TRP 0.009 0.001 TRP A 240 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7192) covalent geometry : angle 0.63842 / 0.33 (10099) hydrogen bonds : bond 0.05186 / 3.79 ( 321) hydrogen bonds : angle 5.08389 / 3.69 ( 854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.8293 (ppp) cc_final: 0.7918 (ppp) REVERT: A 213 CYS cc_start: 0.8068 (t) cc_final: 0.7755 (t) REVERT: A 355 GLN cc_start: 0.7750 (mm110) cc_final: 0.6511 (pt0) REVERT: A 368 ARG cc_start: 0.9013 (tmm-80) cc_final: 0.8813 (tmm-80) REVERT: B 367 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7586 (tt) outliers start: 9 outliers final: 4 residues processed: 88 average time/residue: 0.0810 time to fit residues: 9.8664 Evaluate side-chains 83 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 367 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 GLN B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.141621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.123421 restraints weight = 20108.375| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 4.02 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7192 Z= 0.131 Angle : 0.605 11.481 10099 Z= 0.314 Chirality : 0.040 0.261 1210 Planarity : 0.004 0.044 1027 Dihedral : 19.467 79.624 1890 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.95 % Allowed : 13.14 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.50 (0.32), residues: 691 helix: 0.61 (0.28), residues: 338 sheet: -1.18 (0.56), residues: 76 loop : -1.18 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.028 0.003 TYR A 352 PHE 0.013 0.001 PHE A 376 TRP 0.009 0.001 TRP A 240 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7192) covalent geometry : angle 0.60540 / 0.31 (10099) hydrogen bonds : bond 0.05015 / 3.65 ( 321) hydrogen bonds : angle 4.93165 / 3.57 ( 854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.7656 (tpt) cc_final: 0.7173 (tpp) REVERT: A 355 GLN cc_start: 0.7632 (mm110) cc_final: 0.6407 (pt0) REVERT: A 368 ARG cc_start: 0.9055 (tmm-80) cc_final: 0.8802 (tmm-80) REVERT: B 367 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7648 (tt) REVERT: B 381 MET cc_start: 0.7507 (mtt) cc_final: 0.7276 (mtt) outliers start: 11 outliers final: 4 residues processed: 90 average time/residue: 0.0840 time to fit residues: 10.3619 Evaluate side-chains 85 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 367 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.140359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.122221 restraints weight = 20184.020| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 3.95 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7192 Z= 0.156 Angle : 0.641 9.873 10099 Z= 0.332 Chirality : 0.041 0.222 1210 Planarity : 0.004 0.045 1027 Dihedral : 19.480 80.061 1890 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.49 % Allowed : 14.03 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.56 (0.31), residues: 691 helix: 0.56 (0.28), residues: 339 sheet: -1.25 (0.56), residues: 76 loop : -1.19 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 177 TYR 0.035 0.003 TYR A 352 PHE 0.012 0.001 PHE B 170 TRP 0.009 0.002 TRP A 240 HIS 0.014 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 7192) covalent geometry : angle 0.64064 / 0.33 (10099) hydrogen bonds : bond 0.05283 / 3.83 ( 321) hydrogen bonds : angle 5.03432 / 3.65 ( 854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.8275 (ppp) cc_final: 0.7949 (ppp) REVERT: A 277 MET cc_start: 0.2528 (mmt) cc_final: 0.2018 (mmt) REVERT: A 355 GLN cc_start: 0.7833 (mm110) cc_final: 0.6613 (pt0) REVERT: A 368 ARG cc_start: 0.9008 (tmm-80) cc_final: 0.8780 (tmm-80) REVERT: B 340 TYR cc_start: 0.7097 (m-10) cc_final: 0.6822 (m-80) REVERT: B 367 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7631 (tt) REVERT: B 381 MET cc_start: 0.7750 (mtt) cc_final: 0.7511 (mtt) outliers start: 14 outliers final: 5 residues processed: 91 average time/residue: 0.0746 time to fit residues: 9.4622 Evaluate side-chains 87 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 31 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.141565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.123486 restraints weight = 19724.327| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 3.95 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7192 Z= 0.129 Angle : 0.631 12.637 10099 Z= 0.325 Chirality : 0.041 0.282 1210 Planarity : 0.004 0.043 1027 Dihedral : 19.461 79.838 1890 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.78 % Allowed : 15.99 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.42 (0.32), residues: 691 helix: 0.73 (0.28), residues: 338 sheet: -1.28 (0.55), residues: 77 loop : -1.18 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.037 0.003 TYR A 352 PHE 0.018 0.001 PHE B 391 TRP 0.007 0.001 TRP A 240 HIS 0.009 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7192) covalent geometry : angle 0.63077 / 0.33 (10099) hydrogen bonds : bond 0.05002 / 3.63 ( 321) hydrogen bonds : angle 4.93171 / 3.58 ( 854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.7487 (tpt) cc_final: 0.7243 (tpp) REVERT: A 259 MET cc_start: 0.6175 (ppp) cc_final: 0.5901 (ppp) REVERT: A 277 MET cc_start: 0.3094 (mmt) cc_final: 0.2447 (mmt) REVERT: A 355 GLN cc_start: 0.7866 (mm110) cc_final: 0.6671 (pt0) REVERT: A 368 ARG cc_start: 0.8990 (tmm-80) cc_final: 0.8772 (tmm-80) REVERT: A 376 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6676 (p90) REVERT: B 340 TYR cc_start: 0.7092 (m-10) cc_final: 0.6862 (m-80) REVERT: B 361 ARG cc_start: 0.6457 (ptp-170) cc_final: 0.5983 (ptp-170) REVERT: B 367 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7562 (tt) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.0761 time to fit residues: 9.6445 Evaluate side-chains 90 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 50 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.147909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.130328 restraints weight = 21824.752| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 4.00 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7192 Z= 0.135 Angle : 0.657 14.731 10099 Z= 0.333 Chirality : 0.042 0.424 1210 Planarity : 0.004 0.043 1027 Dihedral : 19.428 79.759 1890 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.60 % Allowed : 17.58 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.42 (0.32), residues: 691 helix: 0.73 (0.28), residues: 338 sheet: -1.31 (0.54), residues: 77 loop : -1.16 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.028 0.003 TYR A 352 PHE 0.014 0.001 PHE B 391 TRP 0.008 0.001 TRP A 240 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7192) covalent geometry : angle 0.65709 / 0.33 (10099) hydrogen bonds : bond 0.04938 / 3.61 ( 321) hydrogen bonds : angle 4.96523 / 3.60 ( 854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8255 (ppp) cc_final: 0.7898 (ppp) REVERT: A 277 MET cc_start: 0.2961 (mmt) cc_final: 0.2300 (mmt) REVERT: A 355 GLN cc_start: 0.7915 (mm110) cc_final: 0.6736 (pt0) REVERT: A 376 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6604 (p90) REVERT: B 340 TYR cc_start: 0.7099 (m-10) cc_final: 0.6790 (m-80) REVERT: B 381 MET cc_start: 0.6972 (mtt) cc_final: 0.6579 (mtm) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.0812 time to fit residues: 9.8545 Evaluate side-chains 89 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 359 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.140607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.122378 restraints weight = 20110.445| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 3.93 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7192 Z= 0.152 Angle : 0.670 13.810 10099 Z= 0.340 Chirality : 0.043 0.386 1210 Planarity : 0.004 0.043 1027 Dihedral : 19.435 80.186 1890 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.60 % Allowed : 17.94 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.41 (0.32), residues: 691 helix: 0.76 (0.28), residues: 338 sheet: -1.41 (0.54), residues: 77 loop : -1.15 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.047 0.003 TYR A 352 PHE 0.019 0.002 PHE B 391 TRP 0.009 0.002 TRP B 116 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7192) covalent geometry : angle 0.66961 / 0.34 (10099) hydrogen bonds : bond 0.05178 / 3.76 ( 321) hydrogen bonds : angle 5.02095 / 3.65 ( 854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.8340 (ppp) cc_final: 0.8025 (ppp) REVERT: A 355 GLN cc_start: 0.7916 (mm110) cc_final: 0.6770 (pt0) REVERT: A 368 ARG cc_start: 0.8987 (tmm-80) cc_final: 0.8366 (tmm-80) REVERT: A 376 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6699 (p90) REVERT: B 340 TYR cc_start: 0.7203 (m-10) cc_final: 0.6989 (m-80) REVERT: B 361 ARG cc_start: 0.6537 (ptp-170) cc_final: 0.6116 (ptp-170) REVERT: B 367 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7491 (tt) REVERT: B 381 MET cc_start: 0.7002 (mtt) cc_final: 0.6596 (mtm) outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.0906 time to fit residues: 10.7769 Evaluate side-chains 90 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 28 optimal weight: 0.0030 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.141063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.123060 restraints weight = 19578.826| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 3.86 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7192 Z= 0.138 Angle : 0.676 13.658 10099 Z= 0.340 Chirality : 0.042 0.402 1210 Planarity : 0.004 0.044 1027 Dihedral : 19.446 80.238 1890 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.78 % Allowed : 18.12 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.43 (0.31), residues: 691 helix: 0.67 (0.28), residues: 344 sheet: -1.47 (0.60), residues: 60 loop : -1.13 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 368 TYR 0.046 0.003 TYR A 352 PHE 0.016 0.001 PHE B 391 TRP 0.007 0.001 TRP A 240 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 7192) covalent geometry : angle 0.67586 / 0.34 (10099) hydrogen bonds : bond 0.05022 / 3.66 ( 321) hydrogen bonds : angle 5.00156 / 3.63 ( 854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8373 (ppp) cc_final: 0.8071 (ppp) REVERT: A 249 MET cc_start: 0.7562 (tpt) cc_final: 0.7314 (tpp) REVERT: A 355 GLN cc_start: 0.7863 (mm110) cc_final: 0.6689 (pt0) REVERT: A 376 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6650 (p90) REVERT: B 77 TYR cc_start: 0.7513 (t80) cc_final: 0.6885 (t80) REVERT: B 340 TYR cc_start: 0.7239 (m-10) cc_final: 0.7019 (m-80) REVERT: B 361 ARG cc_start: 0.6527 (ptp-170) cc_final: 0.6101 (ptp-170) REVERT: B 367 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7448 (tt) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.0714 time to fit residues: 9.0052 Evaluate side-chains 90 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.147419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.129821 restraints weight = 21658.716| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 3.98 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7192 Z= 0.141 Angle : 0.673 13.159 10099 Z= 0.341 Chirality : 0.042 0.398 1210 Planarity : 0.004 0.045 1027 Dihedral : 19.436 80.259 1890 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.60 % Allowed : 17.94 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.47 (0.31), residues: 691 helix: 0.66 (0.28), residues: 344 sheet: -1.48 (0.56), residues: 69 loop : -1.16 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.043 0.003 TYR A 352 PHE 0.016 0.001 PHE B 391 TRP 0.008 0.002 TRP B 116 HIS 0.013 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7192) covalent geometry : angle 0.67262 / 0.34 (10099) hydrogen bonds : bond 0.05039 / 3.67 ( 321) hydrogen bonds : angle 5.06113 / 3.70 ( 854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.90 seconds wall clock time: 27 minutes 43.26 seconds (1663.26 seconds total)