Starting phenix.real_space_refine on Thu Jul 2 06:06:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn9_52309/07_2026/9hn9_52309.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn9_52309/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hn9_52309/07_2026/9hn9_52309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn9_52309/07_2026/9hn9_52309.map" model { file = "/net/cci-nas-00/data/ceres_data/9hn9_52309/07_2026/9hn9_52309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn9_52309/07_2026/9hn9_52309.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 1.64, 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: 0.43 Conformation dependent library (CDL) restraints added in 294.5 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: 0.85 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: 0.87 Time building geometry restraints manager: 0.55 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: 9981 3.35 - 6.69: 100 6.69 - 10.04: 15 10.04 - 13.38: 2 13.38 - 16.73: 1 Bond angle restraints: 10099 Sorted by residual: 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=" CA ARG A 368 " pdb=" CB ARG A 368 " pdb=" CG ARG A 368 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.66e+01 angle pdb=" N9 G C 10 " pdb=" C4 G C 10 " pdb=" N3 G C 10 " ideal model delta sigma weight residual 126.00 128.40 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" CA TYR B 107 " pdb=" CB TYR B 107 " pdb=" CG TYR B 107 " ideal model delta sigma weight residual 113.90 120.69 -6.79 1.80e+00 3.09e-01 1.42e+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: 1168 0.114 - 0.228: 38 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: 2.010 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.820 ------------------------------------------------------------------------------- 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= 0.302 Angle : 0.904 16.728 10099 Z= 0.550 Chirality : 0.052 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 0.00571 / 0.30 ( 7192) covalent geometry : angle 0.90403 / 0.55 (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 : 0.136 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: 0.0701 time to fit residues: 8.9843 Evaluate side-chains 81 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 4.9990 chunk 74 optimal weight: 10.0000 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 = 0.141997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.124250 restraints weight = 20026.896| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.97 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.1134 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= 0.145 Angle : 0.659 11.117 10099 Z= 0.348 Chirality : 0.041 0.250 1210 Planarity : 0.005 0.049 1027 Dihedral : 19.794 83.242 1890 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.53 % Allowed : 7.99 % Favored : 91.47 % 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: -0.32 (0.27), residues: 336 sheet: -1.19 (0.59), residues: 68 loop : -1.24 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.033 0.003 TYR A 352 PHE 0.016 0.002 PHE B 170 TRP 0.010 0.002 TRP A 181 HIS 0.007 0.002 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 7192) covalent geometry : angle 0.65910 / 0.35 (10099) hydrogen bonds : bond 0.05801 / 4.22 ( 321) hydrogen bonds : angle 5.63525 / 4.09 ( 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 : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 GLN cc_start: 0.7779 (mm110) cc_final: 0.6564 (pt0) REVERT: A 368 ARG cc_start: 0.8921 (tmm-80) cc_final: 0.8501 (tmm-80) REVERT: B 222 PHE cc_start: 0.4271 (m-10) cc_final: 0.3760 (m-10) outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.0679 time to fit residues: 8.8307 Evaluate side-chains 84 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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: 6.9990 chunk 76 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.139665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.121688 restraints weight = 20104.841| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.94 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7192 Z= 0.179 Angle : 0.676 13.663 10099 Z= 0.355 Chirality : 0.043 0.363 1210 Planarity : 0.004 0.048 1027 Dihedral : 19.711 82.841 1890 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.53 % Allowed : 11.19 % Favored : 88.28 % 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: -1.01 (0.31), residues: 691 helix: 0.02 (0.27), residues: 337 sheet: -1.31 (0.60), residues: 72 loop : -1.22 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 177 TYR 0.027 0.003 TYR A 352 PHE 0.015 0.002 PHE B 170 TRP 0.021 0.003 TRP A 181 HIS 0.012 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 7192) covalent geometry : angle 0.67569 / 0.36 (10099) hydrogen bonds : bond 0.05829 / 4.22 ( 321) hydrogen bonds : angle 5.42185 / 3.94 ( 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 88 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 355 GLN cc_start: 0.7807 (mm110) cc_final: 0.6576 (pt0) outliers start: 3 outliers final: 3 residues processed: 86 average time/residue: 0.0636 time to fit residues: 7.4231 Evaluate side-chains 82 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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: 2.9990 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4575 r_free = 0.4575 target = 0.147310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.129742 restraints weight = 21797.295| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 4.01 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7192 Z= 0.134 Angle : 0.635 16.721 10099 Z= 0.329 Chirality : 0.041 0.335 1210 Planarity : 0.004 0.044 1027 Dihedral : 19.667 82.611 1890 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.60 % Allowed : 11.90 % Favored : 86.50 % 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: -0.79 (0.31), residues: 691 helix: 0.30 (0.28), residues: 338 sheet: -1.22 (0.56), residues: 76 loop : -1.26 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.023 0.002 TYR A 306 PHE 0.012 0.001 PHE B 170 TRP 0.011 0.002 TRP A 181 HIS 0.013 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7192) covalent geometry : angle 0.63549 / 0.33 (10099) hydrogen bonds : bond 0.05250 / 3.84 ( 321) hydrogen bonds : angle 5.12929 / 3.72 ( 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 94 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.7522 (tpt) cc_final: 0.7197 (tpp) REVERT: A 355 GLN cc_start: 0.7813 (mm110) cc_final: 0.6575 (pt0) REVERT: A 368 ARG cc_start: 0.8899 (tmm-80) cc_final: 0.8426 (tmm-80) REVERT: B 342 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7626 (pm20) REVERT: B 367 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7627 (tt) REVERT: B 381 MET cc_start: 0.7840 (mtt) cc_final: 0.7580 (mtt) outliers start: 9 outliers final: 3 residues processed: 90 average time/residue: 0.0581 time to fit residues: 7.2256 Evaluate side-chains 82 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL 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: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.140610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.122495 restraints weight = 20075.283| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.94 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7192 Z= 0.138 Angle : 0.617 11.176 10099 Z= 0.322 Chirality : 0.040 0.255 1210 Planarity : 0.004 0.045 1027 Dihedral : 19.602 82.601 1890 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.78 % Allowed : 13.14 % Favored : 85.08 % 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: -0.63 (0.31), residues: 691 helix: 0.47 (0.28), residues: 339 sheet: -1.27 (0.56), residues: 77 loop : -1.20 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.030 0.003 TYR A 352 PHE 0.012 0.001 PHE B 170 TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7192) covalent geometry : angle 0.61651 / 0.32 (10099) hydrogen bonds : bond 0.05079 / 3.69 ( 321) hydrogen bonds : angle 5.01937 / 3.63 ( 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 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.142 Fit side-chains REVERT: A 92 LEU cc_start: 0.4887 (mt) cc_final: 0.3951 (mp) REVERT: A 175 MET cc_start: 0.8475 (ppp) cc_final: 0.7828 (ppp) REVERT: A 249 MET cc_start: 0.7621 (tpt) cc_final: 0.7213 (tpp) REVERT: A 355 GLN cc_start: 0.7673 (mm110) cc_final: 0.6442 (pt0) REVERT: A 368 ARG cc_start: 0.8997 (tmm-80) cc_final: 0.8426 (tmm-80) REVERT: A 376 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6807 (p90) REVERT: B 367 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7667 (tt) REVERT: B 381 MET cc_start: 0.7718 (mtt) cc_final: 0.7445 (mtt) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.0643 time to fit residues: 8.4570 Evaluate side-chains 88 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 159 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.139757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.121590 restraints weight = 20248.345| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.95 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.2004 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 : 0.636 9.787 10099 Z= 0.333 Chirality : 0.041 0.222 1210 Planarity : 0.004 0.046 1027 Dihedral : 19.601 82.914 1890 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.02 % Allowed : 14.03 % Favored : 82.95 % 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: -0.55 (0.31), residues: 691 helix: 0.53 (0.28), residues: 338 sheet: -1.19 (0.56), residues: 75 loop : -1.17 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.034 0.003 TYR A 352 PHE 0.021 0.002 PHE B 391 TRP 0.008 0.002 TRP A 240 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7192) covalent geometry : angle 0.63639 / 0.33 (10099) hydrogen bonds : bond 0.05233 / 3.79 ( 321) hydrogen bonds : angle 5.02718 / 3.64 ( 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 101 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.5226 (mt) cc_final: 0.4235 (mp) REVERT: A 355 GLN cc_start: 0.7898 (mm110) cc_final: 0.6699 (pt0) REVERT: A 368 ARG cc_start: 0.8971 (tmm-80) cc_final: 0.8704 (ttp-110) REVERT: A 376 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6852 (p90) REVERT: B 367 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7618 (tt) REVERT: B 381 MET cc_start: 0.7791 (mtt) cc_final: 0.7540 (mtt) outliers start: 17 outliers final: 7 residues processed: 94 average time/residue: 0.0638 time to fit residues: 8.3134 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 217 MET 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 357 LYS 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: 0.0020 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 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 = 0.141434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.123260 restraints weight = 19845.265| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.98 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.2089 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= 0.129 Angle : 0.628 12.589 10099 Z= 0.325 Chirality : 0.041 0.288 1210 Planarity : 0.004 0.046 1027 Dihedral : 19.558 82.692 1890 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.31 % Allowed : 15.10 % Favored : 82.59 % 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: -0.49 (0.32), residues: 691 helix: 0.63 (0.28), residues: 338 sheet: -1.29 (0.55), residues: 77 loop : -1.17 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.035 0.002 TYR A 352 PHE 0.019 0.001 PHE B 391 TRP 0.007 0.001 TRP A 240 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 7192) covalent geometry : angle 0.62829 / 0.33 (10099) hydrogen bonds : bond 0.04920 / 3.58 ( 321) hydrogen bonds : angle 4.94389 / 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 102 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6356 (ptt90) cc_final: 0.6137 (ptm160) REVERT: A 249 MET cc_start: 0.7526 (tpt) cc_final: 0.7253 (tpp) REVERT: A 355 GLN cc_start: 0.7863 (mm110) cc_final: 0.6667 (pt0) REVERT: A 368 ARG cc_start: 0.8940 (tmm-80) cc_final: 0.8682 (ttp-110) REVERT: A 376 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6827 (p90) REVERT: B 340 TYR cc_start: 0.7170 (m-10) cc_final: 0.6939 (m-80) REVERT: B 367 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7515 (tt) outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.0680 time to fit residues: 9.0133 Evaluate side-chains 94 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 159 ASP 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 76 GLU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 357 LYS 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: 4.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 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 = 0.144955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.127255 restraints weight = 22145.460| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.95 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7192 Z= 0.192 Angle : 0.686 10.623 10099 Z= 0.357 Chirality : 0.043 0.362 1210 Planarity : 0.004 0.045 1027 Dihedral : 19.577 83.654 1890 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.49 % Allowed : 16.52 % Favored : 80.99 % 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: -0.58 (0.31), residues: 691 helix: 0.52 (0.28), residues: 338 sheet: -1.35 (0.55), residues: 75 loop : -1.13 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 177 TYR 0.042 0.003 TYR A 352 PHE 0.019 0.002 PHE B 391 TRP 0.013 0.003 TRP B 116 HIS 0.010 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 7192) covalent geometry : angle 0.68569 / 0.36 (10099) hydrogen bonds : bond 0.05639 / 4.06 ( 321) hydrogen bonds : angle 5.20725 / 3.78 ( 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 101 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.5067 (ttt) cc_final: 0.4502 (ttt) REVERT: A 175 MET cc_start: 0.8344 (ppp) cc_final: 0.8055 (ppp) REVERT: A 249 MET cc_start: 0.7607 (tpt) cc_final: 0.7297 (tpp) REVERT: A 355 GLN cc_start: 0.7970 (mm110) cc_final: 0.6809 (pt0) REVERT: A 368 ARG cc_start: 0.8913 (tmm-80) cc_final: 0.8675 (ttp-110) REVERT: A 376 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6995 (p90) REVERT: B 340 TYR cc_start: 0.7352 (m-10) cc_final: 0.7066 (m-80) REVERT: B 361 ARG cc_start: 0.6550 (ptp-170) cc_final: 0.6303 (ptp-170) REVERT: B 367 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7617 (tt) outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 0.0747 time to fit residues: 9.8661 Evaluate side-chains 98 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 159 ASP 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 76 GLU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 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 = 0.4572 r_free = 0.4572 target = 0.147059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.129473 restraints weight = 21744.297| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.96 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7192 Z= 0.141 Angle : 0.667 10.795 10099 Z= 0.344 Chirality : 0.041 0.341 1210 Planarity : 0.004 0.079 1027 Dihedral : 19.590 83.560 1890 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.13 % Allowed : 16.87 % Favored : 80.99 % 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: -0.59 (0.31), residues: 691 helix: 0.60 (0.28), residues: 337 sheet: -1.53 (0.53), residues: 77 loop : -1.20 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 15 TYR 0.040 0.003 TYR A 352 PHE 0.017 0.001 PHE B 391 TRP 0.006 0.001 TRP A 240 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7192) covalent geometry : angle 0.66674 / 0.34 (10099) hydrogen bonds : bond 0.05067 / 3.70 ( 321) hydrogen bonds : angle 5.05670 / 3.67 ( 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 101 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.8317 (ppp) cc_final: 0.8023 (ppp) REVERT: A 249 MET cc_start: 0.7625 (tpt) cc_final: 0.7323 (tpp) REVERT: A 259 MET cc_start: 0.6052 (ppp) cc_final: 0.5753 (ppp) REVERT: A 277 MET cc_start: 0.2625 (mmt) cc_final: 0.2129 (mmt) REVERT: A 311 SER cc_start: 0.7307 (m) cc_final: 0.7013 (p) REVERT: A 355 GLN cc_start: 0.7940 (mm110) cc_final: 0.6798 (pt0) REVERT: A 368 ARG cc_start: 0.8918 (tmm-80) cc_final: 0.8658 (ttp-110) REVERT: A 376 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6862 (p90) REVERT: B 77 TYR cc_start: 0.7349 (t80) cc_final: 0.6995 (t80) REVERT: B 340 TYR cc_start: 0.7333 (m-10) cc_final: 0.7046 (m-80) REVERT: B 361 ARG cc_start: 0.6471 (ptp-170) cc_final: 0.6119 (ptp-170) REVERT: B 367 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7470 (tt) outliers start: 12 outliers final: 10 residues processed: 97 average time/residue: 0.0702 time to fit residues: 9.1703 Evaluate side-chains 95 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 159 ASP 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 76 GLU 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 Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 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 = 0.4564 r_free = 0.4564 target = 0.146503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.128920 restraints weight = 21666.471| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.93 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.2443 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= 0.151 Angle : 0.692 16.482 10099 Z= 0.349 Chirality : 0.043 0.451 1210 Planarity : 0.004 0.050 1027 Dihedral : 19.549 83.619 1890 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.95 % Allowed : 17.94 % 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: -0.54 (0.31), residues: 691 helix: 0.72 (0.28), residues: 331 sheet: -1.53 (0.52), residues: 79 loop : -1.24 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 177 TYR 0.046 0.003 TYR A 352 PHE 0.016 0.001 PHE B 391 TRP 0.008 0.002 TRP A 240 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7192) covalent geometry : angle 0.69175 / 0.35 (10099) hydrogen bonds : bond 0.05123 / 3.72 ( 321) hydrogen bonds : angle 5.04600 / 3.67 ( 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 97 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8330 (ppp) cc_final: 0.8060 (ppp) REVERT: A 277 MET cc_start: 0.2937 (mmt) cc_final: 0.2498 (mmt) REVERT: A 311 SER cc_start: 0.7333 (m) cc_final: 0.7030 (p) REVERT: A 355 GLN cc_start: 0.7954 (mm110) cc_final: 0.6819 (pt0) REVERT: A 376 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6888 (p90) REVERT: B 77 TYR cc_start: 0.7501 (t80) cc_final: 0.6977 (t80) REVERT: B 340 TYR cc_start: 0.7367 (m-10) cc_final: 0.7078 (m-80) REVERT: B 361 ARG cc_start: 0.6490 (ptp-170) cc_final: 0.6257 (ptp-170) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.0683 time to fit residues: 8.6809 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 : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 159 ASP 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 76 GLU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 3 optimal weight: 0.2980 chunk 72 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 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 = 0.4513 r_free = 0.4513 target = 0.139907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.121660 restraints weight = 20060.333| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.94 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7192 Z= 0.156 Angle : 0.684 15.247 10099 Z= 0.348 Chirality : 0.043 0.415 1210 Planarity : 0.004 0.046 1027 Dihedral : 19.556 83.881 1890 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.13 % Allowed : 17.76 % 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: -0.59 (0.31), residues: 691 helix: 0.69 (0.28), residues: 331 sheet: -1.60 (0.52), residues: 78 loop : -1.27 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.043 0.003 TYR A 352 PHE 0.017 0.002 PHE B 391 TRP 0.008 0.002 TRP B 116 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7192) covalent geometry : angle 0.68359 / 0.35 (10099) hydrogen bonds : bond 0.05155 / 3.74 ( 321) hydrogen bonds : angle 5.07984 / 3.71 ( 854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.11 seconds wall clock time: 23 minutes 18.83 seconds (1398.83 seconds total)