Starting phenix.real_space_refine on Tue Feb 3 21:16:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn9_52309/02_2026/9hn9_52309.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn9_52309/02_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_52309/02_2026/9hn9_52309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn9_52309/02_2026/9hn9_52309.map" model { file = "/net/cci-nas-00/data/ceres_data/9hn9_52309/02_2026/9hn9_52309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn9_52309/02_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.17, per 1000 atoms: 0.17 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: 0.79 Conformation dependent library (CDL) restraints added in 203.7 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: 0.81 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: 1.02 Time building geometry restraints manager: 0.94 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=" 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 angle pdb=" CB MET B 380 " pdb=" CG MET B 380 " pdb=" SD MET B 380 " ideal model delta sigma weight residual 112.70 102.22 10.48 3.00e+00 1.11e-01 1.22e+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: 1.810 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.260 Find NCS groups from input model: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 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= 0.269 Angle : 0.904 16.728 10099 Z= 0.451 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 covalent geometry : bond 0.00571 ( 7192) covalent geometry : angle 0.90390 (10099) hydrogen bonds : bond 0.14244 ( 321) hydrogen bonds : angle 6.75716 ( 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 : 0.146 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: 0.0760 time to fit residues: 9.7064 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 : 0.130 ------------------------------------------------------------------------------- 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: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.142210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.124498 restraints weight = 19627.095| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 3.90 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7192 Z= 0.132 Angle : 0.633 9.243 10099 Z= 0.323 Chirality : 0.039 0.244 1210 Planarity : 0.004 0.048 1027 Dihedral : 19.579 81.447 1890 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.89 % Allowed : 8.35 % Favored : 90.76 % 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: -1.09 (0.30), residues: 691 helix: -0.15 (0.27), residues: 340 sheet: -1.37 (0.59), residues: 67 loop : -1.14 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.031 0.003 TYR A 306 PHE 0.018 0.001 PHE B 170 TRP 0.010 0.002 TRP A 240 HIS 0.005 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7192) covalent geometry : angle 0.63321 (10099) hydrogen bonds : bond 0.04625 ( 321) hydrogen bonds : angle 5.10284 ( 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 98 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 201 ILE cc_start: 0.7937 (mp) cc_final: 0.7693 (mp) REVERT: A 277 MET cc_start: 0.2324 (mmt) cc_final: 0.1841 (mmt) REVERT: A 355 GLN cc_start: 0.7763 (mm110) cc_final: 0.6573 (pt0) REVERT: A 367 GLN cc_start: 0.7491 (mp10) cc_final: 0.7232 (mp10) REVERT: A 368 ARG cc_start: 0.8960 (tmm-80) cc_final: 0.8486 (tmm-80) REVERT: B 64 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6200 (tt) REVERT: B 222 PHE cc_start: 0.4337 (m-10) cc_final: 0.3846 (m-10) outliers start: 5 outliers final: 2 residues processed: 93 average time/residue: 0.0785 time to fit residues: 9.8417 Evaluate side-chains 83 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 MET 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: 0.0570 chunk 76 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.0370 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.143725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.125831 restraints weight = 19434.351| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 3.89 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7192 Z= 0.115 Angle : 0.606 10.111 10099 Z= 0.307 Chirality : 0.038 0.200 1210 Planarity : 0.004 0.069 1027 Dihedral : 19.432 80.713 1890 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.60 % Allowed : 10.30 % Favored : 88.10 % 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: -0.62 (0.31), residues: 691 helix: 0.42 (0.28), residues: 340 sheet: -1.41 (0.57), residues: 66 loop : -1.09 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 177 TYR 0.025 0.002 TYR A 306 PHE 0.015 0.001 PHE B 170 TRP 0.024 0.002 TRP A 181 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7192) covalent geometry : angle 0.60574 (10099) hydrogen bonds : bond 0.04284 ( 321) hydrogen bonds : angle 4.75921 ( 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 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.201 Fit side-chains REVERT: A 355 GLN cc_start: 0.7782 (mm110) cc_final: 0.6561 (pt0) REVERT: A 367 GLN cc_start: 0.7457 (mp10) cc_final: 0.7176 (mp10) REVERT: A 368 ARG cc_start: 0.8932 (tmm-80) cc_final: 0.8528 (tmm-80) REVERT: B 64 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6224 (tt) outliers start: 9 outliers final: 3 residues processed: 94 average time/residue: 0.0682 time to fit residues: 9.0002 Evaluate side-chains 89 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU 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: 4.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.148416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.130526 restraints weight = 21324.622| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.99 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7192 Z= 0.128 Angle : 0.609 11.680 10099 Z= 0.307 Chirality : 0.039 0.175 1210 Planarity : 0.004 0.042 1027 Dihedral : 19.414 81.191 1890 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.49 % Allowed : 12.61 % 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: -0.36 (0.32), residues: 691 helix: 0.69 (0.28), residues: 340 sheet: -1.26 (0.58), residues: 71 loop : -1.04 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.027 0.002 TYR A 352 PHE 0.016 0.001 PHE B 384 TRP 0.009 0.002 TRP A 240 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7192) covalent geometry : angle 0.60929 (10099) hydrogen bonds : bond 0.04411 ( 321) hydrogen bonds : angle 4.73065 ( 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 103 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.8118 (ppp) cc_final: 0.7860 (ppp) REVERT: A 355 GLN cc_start: 0.7871 (mm110) cc_final: 0.6670 (pt0) REVERT: A 368 ARG cc_start: 0.8894 (tmm-80) cc_final: 0.8691 (ttp-110) REVERT: A 376 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6970 (p90) REVERT: B 381 MET cc_start: 0.7215 (mtt) cc_final: 0.6727 (mtm) outliers start: 14 outliers final: 3 residues processed: 98 average time/residue: 0.0682 time to fit residues: 9.0728 Evaluate side-chains 84 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 26 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS B 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.145022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.127306 restraints weight = 21793.241| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 3.89 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7192 Z= 0.175 Angle : 0.656 10.533 10099 Z= 0.332 Chirality : 0.041 0.178 1210 Planarity : 0.004 0.050 1027 Dihedral : 19.607 84.261 1890 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.84 % Allowed : 13.50 % Favored : 83.66 % 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 (0.31), residues: 691 helix: 0.63 (0.27), residues: 340 sheet: -1.35 (0.57), residues: 70 loop : -1.18 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 121 TYR 0.027 0.002 TYR A 352 PHE 0.014 0.002 PHE B 391 TRP 0.011 0.002 TRP A 181 HIS 0.013 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 7192) covalent geometry : angle 0.65614 (10099) hydrogen bonds : bond 0.05264 ( 321) hydrogen bonds : angle 5.03948 ( 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 106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 GLN cc_start: 0.7929 (mm110) cc_final: 0.6692 (pt0) REVERT: A 376 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7088 (p90) REVERT: B 64 LEU cc_start: 0.6586 (tp) cc_final: 0.5870 (tt) REVERT: B 77 TYR cc_start: 0.7472 (t80) cc_final: 0.6876 (t80) REVERT: B 340 TYR cc_start: 0.7258 (m-10) cc_final: 0.6976 (m-80) REVERT: B 361 ARG cc_start: 0.6456 (ptp-170) cc_final: 0.6212 (ptp-170) REVERT: B 367 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7404 (tt) outliers start: 16 outliers final: 6 residues processed: 101 average time/residue: 0.0774 time to fit residues: 10.4619 Evaluate side-chains 92 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.141066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.122845 restraints weight = 19976.266| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.87 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.2590 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= 0.131 Angle : 0.637 13.266 10099 Z= 0.319 Chirality : 0.040 0.195 1210 Planarity : 0.004 0.045 1027 Dihedral : 19.507 83.531 1890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.13 % Allowed : 15.81 % Favored : 82.06 % 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: -0.36 (0.32), residues: 691 helix: 0.78 (0.28), residues: 340 sheet: -1.41 (0.56), residues: 74 loop : -1.11 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 177 TYR 0.027 0.002 TYR A 352 PHE 0.013 0.001 PHE B 170 TRP 0.008 0.002 TRP A 240 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7192) covalent geometry : angle 0.63749 (10099) hydrogen bonds : bond 0.04418 ( 321) hydrogen bonds : angle 4.86955 ( 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: 12 poor density : 86 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.2911 (mmt) cc_final: 0.2532 (mmt) REVERT: A 355 GLN cc_start: 0.7883 (mm110) cc_final: 0.6678 (pt0) REVERT: A 368 ARG cc_start: 0.8980 (tmm-80) cc_final: 0.8476 (tmm-80) REVERT: A 376 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6943 (p90) REVERT: B 340 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: B 361 ARG cc_start: 0.6448 (ptp-170) cc_final: 0.6134 (ptp-170) REVERT: B 367 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7298 (tt) outliers start: 12 outliers final: 5 residues processed: 92 average time/residue: 0.0748 time to fit residues: 9.3677 Evaluate side-chains 92 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 340 TYR 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.145266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.127427 restraints weight = 21541.295| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 3.94 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7192 Z= 0.168 Angle : 0.679 12.252 10099 Z= 0.337 Chirality : 0.041 0.193 1210 Planarity : 0.004 0.048 1027 Dihedral : 19.598 84.900 1890 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.13 % Allowed : 17.23 % Favored : 80.64 % 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: 340 sheet: -1.38 (0.57), residues: 72 loop : -1.14 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 121 TYR 0.028 0.002 TYR A 352 PHE 0.015 0.002 PHE B 391 TRP 0.010 0.002 TRP B 116 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7192) covalent geometry : angle 0.67889 (10099) hydrogen bonds : bond 0.05063 ( 321) hydrogen bonds : angle 5.08594 ( 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 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 SER cc_start: 0.7263 (m) cc_final: 0.6930 (p) REVERT: A 355 GLN cc_start: 0.7876 (mm110) cc_final: 0.6649 (pt0) REVERT: A 368 ARG cc_start: 0.8967 (tmm-80) cc_final: 0.8545 (tmm-80) REVERT: A 376 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.7048 (p90) REVERT: B 77 TYR cc_start: 0.7543 (t80) cc_final: 0.6988 (t80) REVERT: B 340 TYR cc_start: 0.7296 (m-10) cc_final: 0.7026 (m-80) REVERT: B 361 ARG cc_start: 0.6497 (ptp-170) cc_final: 0.6192 (ptp-170) REVERT: B 367 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7419 (tt) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.0810 time to fit residues: 10.7171 Evaluate side-chains 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 87 MET Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 357 LYS 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: 6.9990 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.118139 restraints weight = 20367.955| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 3.95 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7192 Z= 0.202 Angle : 0.723 13.059 10099 Z= 0.363 Chirality : 0.043 0.193 1210 Planarity : 0.004 0.049 1027 Dihedral : 19.792 87.664 1890 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.13 % Allowed : 18.12 % Favored : 79.75 % 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: -0.81 (0.31), residues: 691 helix: 0.31 (0.27), residues: 339 sheet: -1.59 (0.59), residues: 68 loop : -1.21 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 121 TYR 0.028 0.003 TYR A 352 PHE 0.017 0.002 PHE B 391 TRP 0.014 0.003 TRP B 116 HIS 0.011 0.002 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7192) covalent geometry : angle 0.72258 (10099) hydrogen bonds : bond 0.05644 ( 321) hydrogen bonds : angle 5.38814 ( 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 106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8360 (ppp) cc_final: 0.8157 (ppp) REVERT: A 311 SER cc_start: 0.7305 (m) cc_final: 0.6902 (p) REVERT: A 355 GLN cc_start: 0.7816 (mm110) cc_final: 0.6571 (pt0) REVERT: A 368 ARG cc_start: 0.9048 (tmm-80) cc_final: 0.8582 (tmm-80) REVERT: B 77 TYR cc_start: 0.7644 (t80) cc_final: 0.7034 (t80) REVERT: B 340 TYR cc_start: 0.7455 (m-10) cc_final: 0.7210 (m-80) REVERT: B 367 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7422 (tt) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.0745 time to fit residues: 10.0520 Evaluate side-chains 95 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 0.0020 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.4286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 325 HIS ** 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 = 0.4588 r_free = 0.4588 target = 0.148002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.130218 restraints weight = 21678.597| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 4.01 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.3126 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= 0.126 Angle : 0.675 14.321 10099 Z= 0.333 Chirality : 0.040 0.197 1210 Planarity : 0.004 0.049 1027 Dihedral : 19.563 84.440 1890 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.42 % Allowed : 20.25 % Favored : 78.33 % 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: -0.48 (0.32), residues: 691 helix: 0.75 (0.28), residues: 338 sheet: -1.57 (0.58), residues: 68 loop : -1.24 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 121 TYR 0.042 0.003 TYR A 352 PHE 0.017 0.001 PHE B 170 TRP 0.007 0.001 TRP A 181 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7192) covalent geometry : angle 0.67482 (10099) hydrogen bonds : bond 0.04330 ( 321) hydrogen bonds : angle 4.95735 ( 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 98 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.214 Fit side-chains REVERT: A 175 MET cc_start: 0.8202 (ppp) cc_final: 0.7970 (ppp) REVERT: A 249 MET cc_start: 0.7417 (tpp) cc_final: 0.7156 (tpp) REVERT: A 277 MET cc_start: 0.2534 (mmt) cc_final: 0.2068 (mmt) REVERT: A 311 SER cc_start: 0.7358 (m) cc_final: 0.7009 (p) REVERT: A 355 GLN cc_start: 0.7813 (mm110) cc_final: 0.6616 (pt0) REVERT: A 368 ARG cc_start: 0.8973 (tmm-80) cc_final: 0.8601 (tmm-80) REVERT: A 376 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.6539 (p90) REVERT: B 77 TYR cc_start: 0.7458 (t80) cc_final: 0.6932 (t80) REVERT: B 340 TYR cc_start: 0.7262 (m-10) cc_final: 0.6849 (m-80) REVERT: B 367 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7292 (tt) outliers start: 8 outliers final: 6 residues processed: 94 average time/residue: 0.0892 time to fit residues: 11.1152 Evaluate side-chains 92 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.140225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.121933 restraints weight = 19811.397| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 3.92 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.3180 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= 0.143 Angle : 0.677 13.885 10099 Z= 0.336 Chirality : 0.040 0.195 1210 Planarity : 0.004 0.052 1027 Dihedral : 19.554 84.305 1890 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.60 % Allowed : 19.89 % Favored : 78.51 % 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: -0.39 (0.31), residues: 691 helix: 0.85 (0.28), residues: 334 sheet: -1.46 (0.59), residues: 73 loop : -1.22 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 29 TYR 0.021 0.002 TYR A 352 PHE 0.014 0.001 PHE B 170 TRP 0.009 0.002 TRP B 116 HIS 0.007 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7192) covalent geometry : angle 0.67711 (10099) hydrogen bonds : bond 0.04611 ( 321) hydrogen bonds : angle 4.99902 ( 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 96 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8274 (ppp) cc_final: 0.8035 (ppp) REVERT: A 311 SER cc_start: 0.7389 (m) cc_final: 0.7021 (p) REVERT: A 355 GLN cc_start: 0.7790 (mm110) cc_final: 0.6547 (pt0) REVERT: A 368 ARG cc_start: 0.9007 (tmm-80) cc_final: 0.8597 (tmm-80) REVERT: A 376 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6572 (p90) REVERT: B 39 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8564 (p) REVERT: B 77 TYR cc_start: 0.7523 (t80) cc_final: 0.6977 (t80) REVERT: B 340 TYR cc_start: 0.7331 (m-10) cc_final: 0.6949 (m-80) REVERT: B 367 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7348 (tt) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.0697 time to fit residues: 8.8901 Evaluate side-chains 96 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 3 optimal weight: 0.0470 chunk 72 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.148729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.130852 restraints weight = 21674.433| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 4.03 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.3240 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= 0.126 Angle : 0.663 14.075 10099 Z= 0.328 Chirality : 0.040 0.195 1210 Planarity : 0.004 0.051 1027 Dihedral : 19.476 83.275 1890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.60 % Allowed : 20.25 % Favored : 78.15 % 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: -0.30 (0.32), residues: 691 helix: 0.98 (0.28), residues: 332 sheet: -1.51 (0.55), residues: 80 loop : -1.18 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 177 TYR 0.021 0.002 TYR A 352 PHE 0.015 0.001 PHE B 170 TRP 0.008 0.001 TRP A 181 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7192) covalent geometry : angle 0.66284 (10099) hydrogen bonds : bond 0.04308 ( 321) hydrogen bonds : angle 4.90407 ( 854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1406.17 seconds wall clock time: 24 minutes 51.23 seconds (1491.23 seconds total)