Starting phenix.real_space_refine on Thu Jul 2 16:14:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzo_49954/07_2026/9nzo_49954.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzo_49954/07_2026/9nzo_49954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nzo_49954/07_2026/9nzo_49954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzo_49954/07_2026/9nzo_49954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nzo_49954/07_2026/9nzo_49954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzo_49954/07_2026/9nzo_49954.map" } resolution = 3.2 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= 0.029 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 168 5.49 5 S 13 5.16 5 C 5078 2.51 5 N 1642 2.21 5 O 2123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 9024 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1994 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 9, 'TRANS': 239} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 668 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2556 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 4, 'rna3p_pur': 61, 'rna3p_pyr': 45} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain breaks: 3 Chain: "A" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3461 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 13, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 9, 'TYR:plan': 2, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 142 Time building chain proxies: 1.69, per 1000 atoms: 0.19 Number of scatterers: 9024 At special positions: 0 Unit cell: (120.357, 121.29, 102.63, 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 13 16.00 P 168 15.00 O 2123 8.00 N 1642 7.00 C 5078 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: 0.82 Conformation dependent library (CDL) restraints added in 256.0 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1310 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 52.3% alpha, 15.9% beta 64 base pairs and 111 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 24 through 68 removed outlier: 4.877A pdb=" N TYR B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 removed outlier: 3.589A pdb=" N TYR B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 113 Processing helix chain 'B' and resid 128 through 137 Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.837A pdb=" N ASN B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.686A pdb=" N ILE B 223 " --> pdb=" O ASN B 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 41 Processing helix chain 'A' and resid 42 through 68 removed outlier: 3.699A pdb=" N GLU A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 80 removed outlier: 3.917A pdb=" N TYR A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.698A pdb=" N ASN A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 115 Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.730A pdb=" N TYR A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.925A pdb=" N ASN A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 299 through 308 removed outlier: 4.223A pdb=" N MET A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.955A pdb=" N GLN A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 362 removed outlier: 3.523A pdb=" N GLY A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 467 through 478 Processing sheet with id=AA1, first strand: chain 'B' and resid 179 through 180 removed outlier: 4.858A pdb=" N ARG B 247 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE B 199 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.816A pdb=" N SER A 237 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 238 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 247 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 251 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 13 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE A 199 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.816A pdb=" N SER A 237 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 238 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 281 removed outlier: 7.407A pdb=" N ALA A 364 " --> pdb=" O PRO A 264 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG A 266 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 370 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY A 365 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ARG A 415 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 367 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 417 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET A 369 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 439 removed outlier: 6.560A pdb=" N THR A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 158 hydrogen bonds 288 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 111 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1960 1.33 - 1.45: 2974 1.45 - 1.57: 4270 1.57 - 1.69: 331 1.69 - 1.81: 19 Bond restraints: 9554 Sorted by residual: bond pdb=" C1' DT D 12 " pdb=" N1 DT D 12 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.06e+01 bond pdb=" C3' DT D 1 " pdb=" O3' DT D 1 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" C3' DC E 5 " pdb=" C2' DC E 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.62e+00 bond pdb=" C3' DT E 12 " pdb=" C2' DT E 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.34e+00 bond pdb=" C1' DC D 6 " pdb=" N1 DC D 6 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.26e+00 ... (remaining 9549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 13224 2.16 - 4.31: 409 4.31 - 6.47: 57 6.47 - 8.62: 15 8.62 - 10.78: 5 Bond angle restraints: 13710 Sorted by residual: angle pdb=" O4' DA E 16 " pdb=" C4' DA E 16 " pdb=" C3' DA E 16 " ideal model delta sigma weight residual 106.00 102.62 3.38 6.00e-01 2.78e+00 3.17e+01 angle pdb=" O4' DG E 15 " pdb=" C4' DG E 15 " pdb=" C3' DG E 15 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.81e+01 angle pdb=" CA GLU A 296 " pdb=" CB GLU A 296 " pdb=" CG GLU A 296 " ideal model delta sigma weight residual 114.10 124.55 -10.45 2.00e+00 2.50e-01 2.73e+01 angle pdb=" C1' U C 71 " pdb=" N1 U C 71 " pdb=" C2 U C 71 " ideal model delta sigma weight residual 117.70 123.22 -5.52 1.20e+00 6.94e-01 2.12e+01 angle pdb=" O4' DC D 20 " pdb=" C4' DC D 20 " pdb=" C3' DC D 20 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.03e+01 ... (remaining 13705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 5118 33.91 - 67.82: 550 67.82 - 101.73: 43 101.73 - 135.64: 5 135.64 - 169.55: 2 Dihedral angle restraints: 5718 sinusoidal: 3687 harmonic: 2031 Sorted by residual: dihedral pdb=" O4' G C 75 " pdb=" C1' G C 75 " pdb=" N9 G C 75 " pdb=" C4 G C 75 " ideal model delta sinusoidal sigma weight residual -106.00 -169.84 63.84 1 1.70e+01 3.46e-03 1.86e+01 dihedral pdb=" C ASP A 216 " pdb=" N ASP A 216 " pdb=" CA ASP A 216 " pdb=" CB ASP A 216 " ideal model delta harmonic sigma weight residual -122.60 -133.16 10.56 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" CA ARG B 217 " pdb=" C ARG B 217 " pdb=" N SER B 218 " pdb=" CA SER B 218 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1558 0.116 - 0.232: 51 0.232 - 0.348: 4 0.348 - 0.464: 0 0.464 - 0.580: 2 Chirality restraints: 1615 Sorted by residual: chirality pdb=" P DT D 17 " pdb=" OP1 DT D 17 " pdb=" OP2 DT D 17 " pdb=" O5' DT D 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" P DC D 16 " pdb=" OP1 DC D 16 " pdb=" OP2 DC D 16 " pdb=" O5' DC D 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CA ASP A 216 " pdb=" N ASP A 216 " pdb=" C ASP A 216 " pdb=" CB ASP A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 1612 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 263 " 0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO A 264 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G C 45 " 0.040 2.00e-02 2.50e+03 1.68e-02 8.49e+00 pdb=" N9 G C 45 " -0.036 2.00e-02 2.50e+03 pdb=" C8 G C 45 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G C 45 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 45 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G C 45 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G C 45 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G C 45 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G C 45 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 45 " -0.009 2.00e-02 2.50e+03 pdb=" N3 G C 45 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G C 45 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 331 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C GLN A 331 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN A 331 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 332 " -0.017 2.00e-02 2.50e+03 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 933 2.75 - 3.29: 8143 3.29 - 3.82: 16982 3.82 - 4.36: 19623 4.36 - 4.90: 29294 Nonbonded interactions: 74975 Sorted by model distance: nonbonded pdb=" O LEU B 29 " pdb=" CD2 TYR B 33 " model vdw 2.210 3.340 nonbonded pdb=" N2 DG D 32 " pdb=" O2 DC E 2 " model vdw 2.253 2.496 nonbonded pdb=" OH TYR B 129 " pdb=" OG SER B 142 " model vdw 2.269 3.040 nonbonded pdb=" OP2 C C 131 " pdb=" NH2 ARG A 217 " model vdw 2.358 3.120 nonbonded pdb=" N2 G C 135 " pdb=" OG1 THR A 9 " model vdw 2.368 3.120 ... (remaining 74970 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: 1.840 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.210 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.005 0.091 9554 Z= 0.361 Angle : 0.881 10.780 13710 Z= 0.665 Chirality : 0.052 0.580 1615 Planarity : 0.007 0.090 1152 Dihedral : 22.424 169.554 4408 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.36 % Allowed : 13.69 % Favored : 85.95 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.29), residues: 686 helix: -0.08 (0.25), residues: 346 sheet: -0.16 (0.57), residues: 90 loop : -1.44 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 226 TYR 0.033 0.002 TYR B 80 PHE 0.025 0.003 PHE B 102 TRP 0.027 0.003 TRP B 36 HIS 0.009 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.36 ( 9554) covalent geometry : angle 0.88083 / 0.66 (13710) hydrogen bonds : bond 0.13940 / 9.53 ( 465) hydrogen bonds : angle 6.15538 / 4.36 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7468 (tpp-160) cc_final: 0.6842 (ttm110) REVERT: B 89 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8007 (tm-30) REVERT: B 91 ILE cc_start: 0.8823 (mm) cc_final: 0.8617 (mt) REVERT: B 213 PHE cc_start: 0.6979 (m-80) cc_final: 0.6774 (m-80) REVERT: A 66 ILE cc_start: 0.8589 (tp) cc_final: 0.8364 (mt) REVERT: A 111 THR cc_start: 0.8573 (m) cc_final: 0.8362 (m) REVERT: A 190 MET cc_start: 0.8036 (mmp) cc_final: 0.7281 (mtm) REVERT: A 216 ASP cc_start: 0.7565 (p0) cc_final: 0.7324 (p0) REVERT: A 225 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7693 (tp30) REVERT: A 226 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.7183 (mtt180) REVERT: A 229 SER cc_start: 0.8436 (m) cc_final: 0.8204 (p) REVERT: A 392 ARG cc_start: 0.7236 (tpm170) cc_final: 0.5526 (ttt-90) REVERT: A 416 TYR cc_start: 0.7434 (m-10) cc_final: 0.7118 (m-10) outliers start: 2 outliers final: 2 residues processed: 86 average time/residue: 0.0893 time to fit residues: 10.1353 Evaluate side-chains 75 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.219329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146409 restraints weight = 11345.380| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.90 r_work: 0.3474 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9554 Z= 0.156 Angle : 0.589 7.788 13710 Z= 0.348 Chirality : 0.042 0.264 1615 Planarity : 0.005 0.057 1152 Dihedral : 23.668 169.997 3136 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.06 % Allowed : 11.71 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.31), residues: 686 helix: 1.15 (0.26), residues: 341 sheet: -0.32 (0.55), residues: 90 loop : -1.30 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 226 TYR 0.019 0.002 TYR B 33 PHE 0.013 0.001 PHE A 56 TRP 0.012 0.002 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 9554) covalent geometry : angle 0.58920 / 0.35 (13710) hydrogen bonds : bond 0.06295 / 4.40 ( 465) hydrogen bonds : angle 4.48519 / 3.19 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7498 (tpp-160) cc_final: 0.6892 (ttm110) REVERT: B 89 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7847 (tm-30) REVERT: B 100 GLN cc_start: 0.8353 (tp-100) cc_final: 0.8089 (tp40) REVERT: A 66 ILE cc_start: 0.8646 (tp) cc_final: 0.8412 (mt) REVERT: A 90 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6477 (p0) REVERT: A 216 ASP cc_start: 0.7796 (p0) cc_final: 0.7520 (p0) REVERT: A 222 GLU cc_start: 0.7659 (tt0) cc_final: 0.7349 (tp30) REVERT: A 226 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7216 (mtt180) REVERT: A 392 ARG cc_start: 0.7204 (tpm170) cc_final: 0.5451 (ttt-90) REVERT: A 398 GLU cc_start: 0.7849 (tp30) cc_final: 0.7627 (tt0) outliers start: 17 outliers final: 9 residues processed: 78 average time/residue: 0.0922 time to fit residues: 9.8778 Evaluate side-chains 73 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 40.0000 chunk 54 optimal weight: 0.0020 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 ASN 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 = 0.218744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146225 restraints weight = 11315.418| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.68 r_work: 0.3492 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9554 Z= 0.138 Angle : 0.527 5.530 13710 Z= 0.316 Chirality : 0.040 0.279 1615 Planarity : 0.004 0.044 1152 Dihedral : 23.507 167.955 3134 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.52 % Allowed : 12.79 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.31), residues: 686 helix: 1.72 (0.27), residues: 343 sheet: -0.66 (0.52), residues: 96 loop : -1.15 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.019 0.002 TYR B 33 PHE 0.013 0.001 PHE A 56 TRP 0.008 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 9554) covalent geometry : angle 0.52739 / 0.32 (13710) hydrogen bonds : bond 0.05347 / 3.74 ( 465) hydrogen bonds : angle 4.10930 / 2.94 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7618 (tpp-160) cc_final: 0.7068 (ttm110) REVERT: B 72 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7155 (mt0) REVERT: A 66 ILE cc_start: 0.8806 (tp) cc_final: 0.8537 (mt) REVERT: A 160 SER cc_start: 0.8850 (t) cc_final: 0.8558 (p) REVERT: A 216 ASP cc_start: 0.7787 (p0) cc_final: 0.7509 (p0) REVERT: A 222 GLU cc_start: 0.7807 (tt0) cc_final: 0.7576 (tp30) REVERT: A 225 GLU cc_start: 0.8253 (tp30) cc_final: 0.7944 (tt0) REVERT: A 226 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7580 (mtt180) REVERT: A 392 ARG cc_start: 0.7269 (tpm170) cc_final: 0.5664 (ttt-90) REVERT: A 398 GLU cc_start: 0.8041 (tp30) cc_final: 0.7813 (tt0) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.0873 time to fit residues: 8.9484 Evaluate side-chains 74 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.0060 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.217889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.156772 restraints weight = 11180.753| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.83 r_work: 0.3371 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9554 Z= 0.123 Angle : 0.501 6.402 13710 Z= 0.300 Chirality : 0.039 0.278 1615 Planarity : 0.004 0.044 1152 Dihedral : 23.437 169.158 3134 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.70 % Allowed : 13.69 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.32), residues: 686 helix: 2.07 (0.27), residues: 343 sheet: -0.70 (0.51), residues: 101 loop : -1.05 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.013 0.001 TYR A 129 PHE 0.013 0.001 PHE A 56 TRP 0.006 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 9554) covalent geometry : angle 0.50080 / 0.30 (13710) hydrogen bonds : bond 0.05120 / 3.58 ( 465) hydrogen bonds : angle 3.90545 / 2.81 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7759 (tpp-160) cc_final: 0.7174 (ttm110) REVERT: B 72 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7083 (mt0) REVERT: B 89 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7953 (tm-30) REVERT: A 66 ILE cc_start: 0.8820 (tp) cc_final: 0.8540 (mt) REVERT: A 160 SER cc_start: 0.8841 (t) cc_final: 0.8541 (p) REVERT: A 216 ASP cc_start: 0.7695 (p0) cc_final: 0.7412 (p0) REVERT: A 222 GLU cc_start: 0.7861 (tt0) cc_final: 0.7605 (tp30) REVERT: A 226 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7612 (mtt180) REVERT: A 339 LYS cc_start: 0.8424 (ptpp) cc_final: 0.7948 (ptmm) REVERT: A 392 ARG cc_start: 0.7271 (tpm170) cc_final: 0.5556 (ttt-90) REVERT: A 398 GLU cc_start: 0.7987 (tp30) cc_final: 0.7775 (tt0) outliers start: 15 outliers final: 10 residues processed: 78 average time/residue: 0.1114 time to fit residues: 11.7696 Evaluate side-chains 76 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 405 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 HIS B 236 ASN A 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.217126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142441 restraints weight = 11383.293| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.84 r_work: 0.3405 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9554 Z= 0.148 Angle : 0.522 8.380 13710 Z= 0.308 Chirality : 0.039 0.282 1615 Planarity : 0.004 0.046 1152 Dihedral : 23.427 167.500 3134 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.70 % Allowed : 14.59 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.32), residues: 686 helix: 2.16 (0.27), residues: 344 sheet: -0.65 (0.51), residues: 101 loop : -1.02 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 83 TYR 0.015 0.002 TYR A 358 PHE 0.014 0.002 PHE A 56 TRP 0.008 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 9554) covalent geometry : angle 0.52167 / 0.31 (13710) hydrogen bonds : bond 0.05085 / 3.54 ( 465) hydrogen bonds : angle 3.91203 / 2.82 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7142 (ttm110) REVERT: B 72 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7005 (mt0) REVERT: B 150 GLN cc_start: 0.8144 (tt0) cc_final: 0.7581 (mm110) REVERT: A 8 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7946 (pt) REVERT: A 66 ILE cc_start: 0.8857 (tp) cc_final: 0.8574 (mt) REVERT: A 160 SER cc_start: 0.8792 (t) cc_final: 0.8476 (p) REVERT: A 216 ASP cc_start: 0.7800 (p0) cc_final: 0.7520 (p0) REVERT: A 226 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7403 (mtt180) REVERT: A 339 LYS cc_start: 0.8490 (ptpp) cc_final: 0.8108 (ptmm) REVERT: A 392 ARG cc_start: 0.7374 (tpm170) cc_final: 0.5602 (ttt-90) REVERT: A 398 GLU cc_start: 0.7889 (tp30) cc_final: 0.7639 (tt0) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.0970 time to fit residues: 9.5989 Evaluate side-chains 78 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 405 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.215147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140887 restraints weight = 11280.996| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.78 r_work: 0.3362 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9554 Z= 0.173 Angle : 0.538 6.405 13710 Z= 0.317 Chirality : 0.040 0.280 1615 Planarity : 0.004 0.047 1152 Dihedral : 23.441 166.978 3132 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.52 % Allowed : 14.95 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.32), residues: 686 helix: 2.19 (0.27), residues: 343 sheet: -0.70 (0.50), residues: 99 loop : -1.06 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.015 0.002 TYR A 129 PHE 0.014 0.002 PHE A 56 TRP 0.008 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 9554) covalent geometry : angle 0.53810 / 0.32 (13710) hydrogen bonds : bond 0.05298 / 3.67 ( 465) hydrogen bonds : angle 3.97296 / 2.88 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7162 (ttm110) REVERT: B 72 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7022 (mt0) REVERT: B 150 GLN cc_start: 0.8141 (tt0) cc_final: 0.7612 (mm110) REVERT: A 8 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8042 (pt) REVERT: A 66 ILE cc_start: 0.8848 (tp) cc_final: 0.8560 (mt) REVERT: A 160 SER cc_start: 0.8807 (t) cc_final: 0.8496 (p) REVERT: A 216 ASP cc_start: 0.7919 (p0) cc_final: 0.7621 (p0) REVERT: A 339 LYS cc_start: 0.8431 (ptpp) cc_final: 0.7908 (ptmm) REVERT: A 392 ARG cc_start: 0.7589 (tpm170) cc_final: 0.5789 (ttt-90) REVERT: A 398 GLU cc_start: 0.7932 (tp30) cc_final: 0.7662 (tt0) outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.1042 time to fit residues: 10.5163 Evaluate side-chains 75 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 405 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 69 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.215063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140675 restraints weight = 11200.456| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.79 r_work: 0.3380 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9554 Z= 0.143 Angle : 0.517 7.871 13710 Z= 0.305 Chirality : 0.039 0.282 1615 Planarity : 0.004 0.047 1152 Dihedral : 23.411 165.427 3132 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.88 % Allowed : 15.14 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.32), residues: 686 helix: 2.24 (0.27), residues: 344 sheet: -0.70 (0.50), residues: 99 loop : -1.05 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 226 TYR 0.014 0.001 TYR A 129 PHE 0.014 0.001 PHE A 56 TRP 0.006 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9554) covalent geometry : angle 0.51653 / 0.30 (13710) hydrogen bonds : bond 0.05050 / 3.52 ( 465) hydrogen bonds : angle 3.87856 / 2.81 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7146 (ttm110) REVERT: B 72 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7041 (mt0) REVERT: B 150 GLN cc_start: 0.8114 (tt0) cc_final: 0.7601 (mm110) REVERT: A 8 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8051 (pt) REVERT: A 66 ILE cc_start: 0.8806 (tp) cc_final: 0.8523 (mt) REVERT: A 160 SER cc_start: 0.8790 (t) cc_final: 0.8495 (p) REVERT: A 216 ASP cc_start: 0.7884 (p0) cc_final: 0.7570 (p0) REVERT: A 392 ARG cc_start: 0.7531 (tpm170) cc_final: 0.5745 (ttt-90) REVERT: A 398 GLU cc_start: 0.7925 (tp30) cc_final: 0.7649 (tt0) outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.1059 time to fit residues: 10.6694 Evaluate side-chains 71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 405 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 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 = 0.4379 r_free = 0.4379 target = 0.210066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132600 restraints weight = 11200.529| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.84 r_work: 0.3325 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 9554 Z= 0.307 Angle : 0.652 6.954 13710 Z= 0.372 Chirality : 0.045 0.277 1615 Planarity : 0.006 0.099 1152 Dihedral : 23.513 164.834 3132 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.52 % Allowed : 15.32 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.31), residues: 686 helix: 1.68 (0.26), residues: 345 sheet: -0.88 (0.48), residues: 104 loop : -1.16 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 226 TYR 0.023 0.002 TYR A 173 PHE 0.017 0.003 PHE A 56 TRP 0.009 0.002 TRP B 36 HIS 0.005 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.31 ( 9554) covalent geometry : angle 0.65213 / 0.37 (13710) hydrogen bonds : bond 0.06135 / 4.20 ( 465) hydrogen bonds : angle 4.18836 / 3.03 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7864 (tpp-160) cc_final: 0.7269 (ttm110) REVERT: B 72 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7202 (mt0) REVERT: B 150 GLN cc_start: 0.8316 (tt0) cc_final: 0.7696 (mm110) REVERT: B 242 SER cc_start: 0.7944 (t) cc_final: 0.7708 (m) REVERT: A 8 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8009 (pt) REVERT: A 66 ILE cc_start: 0.8852 (tp) cc_final: 0.8550 (mt) REVERT: A 190 MET cc_start: 0.8813 (mmp) cc_final: 0.7859 (mmm) REVERT: A 392 ARG cc_start: 0.7706 (tpm170) cc_final: 0.5816 (ttt-90) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.0981 time to fit residues: 9.2910 Evaluate side-chains 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 405 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 0.0570 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.215766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141452 restraints weight = 11077.124| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.57 r_work: 0.3432 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 9554 Z= 0.125 Angle : 0.520 7.171 13710 Z= 0.306 Chirality : 0.039 0.283 1615 Planarity : 0.004 0.048 1152 Dihedral : 23.441 162.582 3132 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.80 % Allowed : 16.40 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.31), residues: 686 helix: 2.11 (0.27), residues: 344 sheet: -0.73 (0.49), residues: 99 loop : -1.08 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 226 TYR 0.015 0.001 TYR A 358 PHE 0.015 0.001 PHE A 56 TRP 0.007 0.001 TRP A 343 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 9554) covalent geometry : angle 0.52013 / 0.31 (13710) hydrogen bonds : bond 0.05051 / 3.53 ( 465) hydrogen bonds : angle 3.89706 / 2.85 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7275 (ttm110) REVERT: B 72 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7334 (mt0) REVERT: B 242 SER cc_start: 0.8033 (t) cc_final: 0.7800 (m) REVERT: A 66 ILE cc_start: 0.8822 (tp) cc_final: 0.8568 (mt) REVERT: A 160 SER cc_start: 0.8907 (t) cc_final: 0.8649 (p) REVERT: A 190 MET cc_start: 0.8702 (mmp) cc_final: 0.7855 (mmm) REVERT: A 216 ASP cc_start: 0.8202 (p0) cc_final: 0.7852 (p0) REVERT: A 392 ARG cc_start: 0.7654 (tpm170) cc_final: 0.5809 (ttt-90) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.0897 time to fit residues: 8.2146 Evaluate side-chains 67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 405 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 69 optimal weight: 7.9990 chunk 31 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.216309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141973 restraints weight = 11114.714| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.57 r_work: 0.3412 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9554 Z= 0.131 Angle : 0.507 7.047 13710 Z= 0.300 Chirality : 0.038 0.280 1615 Planarity : 0.004 0.047 1152 Dihedral : 23.377 161.979 3132 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.26 % Allowed : 16.94 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.32), residues: 686 helix: 2.23 (0.27), residues: 344 sheet: -0.63 (0.47), residues: 105 loop : -1.08 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 226 TYR 0.015 0.001 TYR A 129 PHE 0.013 0.001 PHE A 56 TRP 0.005 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 9554) covalent geometry : angle 0.50720 / 0.30 (13710) hydrogen bonds : bond 0.05062 / 3.52 ( 465) hydrogen bonds : angle 3.76383 / 2.73 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7863 (tpp-160) cc_final: 0.7295 (ttm110) REVERT: B 72 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7353 (mt0) REVERT: B 242 SER cc_start: 0.8097 (t) cc_final: 0.7884 (m) REVERT: A 66 ILE cc_start: 0.8874 (tp) cc_final: 0.8597 (mt) REVERT: A 160 SER cc_start: 0.8843 (t) cc_final: 0.8596 (p) REVERT: A 190 MET cc_start: 0.8704 (mmp) cc_final: 0.7849 (mmm) REVERT: A 216 ASP cc_start: 0.8150 (p0) cc_final: 0.7810 (p0) REVERT: A 339 LYS cc_start: 0.8513 (ptpp) cc_final: 0.8004 (ptmm) REVERT: A 392 ARG cc_start: 0.7635 (tpm170) cc_final: 0.5793 (ttt-90) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.1210 time to fit residues: 10.6558 Evaluate side-chains 65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 405 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 30.0000 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.215215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.140963 restraints weight = 11007.868| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.51 r_work: 0.3393 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9554 Z= 0.153 Angle : 0.535 14.290 13710 Z= 0.308 Chirality : 0.039 0.277 1615 Planarity : 0.004 0.049 1152 Dihedral : 23.356 159.863 3132 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.26 % Allowed : 16.76 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.31), residues: 686 helix: 2.15 (0.26), residues: 345 sheet: -0.50 (0.49), residues: 102 loop : -1.07 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 70 TYR 0.014 0.002 TYR A 129 PHE 0.014 0.001 PHE A 56 TRP 0.006 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 9554) covalent geometry : angle 0.53532 / 0.31 (13710) hydrogen bonds : bond 0.05104 / 3.54 ( 465) hydrogen bonds : angle 3.75452 / 2.72 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2747.54 seconds wall clock time: 47 minutes 34.56 seconds (2854.56 seconds total)