Starting phenix.real_space_refine on Sat May 2 23:22:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzo_49954/05_2026/9nzo_49954.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzo_49954/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nzo_49954/05_2026/9nzo_49954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzo_49954/05_2026/9nzo_49954.map" model { file = "/net/cci-nas-00/data/ceres_data/9nzo_49954/05_2026/9nzo_49954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzo_49954/05_2026/9nzo_49954.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 2.26, per 1000 atoms: 0.25 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: 1.11 Conformation dependent library (CDL) restraints added in 240.3 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: 1.40 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: 1.89 Time building geometry restraints manager: 1.41 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=" CG1 ILE A 292 " pdb=" CD1 ILE A 292 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.42e+00 bond pdb=" C3' DT D 1 " pdb=" O3' DT D 1 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.81e+00 bond pdb=" CB ASP B 210 " pdb=" CG ASP B 210 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.72e+00 bond pdb=" CG1 ILE A 8 " pdb=" CD1 ILE A 8 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.05e+00 bond pdb=" P DC D 16 " pdb=" OP2 DC D 16 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 9549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 13284 2.16 - 4.31: 353 4.31 - 6.47: 53 6.47 - 8.62: 15 8.62 - 10.78: 5 Bond angle restraints: 13710 Sorted by residual: 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=" CA ARG A 341 " pdb=" CB ARG A 341 " pdb=" CG ARG A 341 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" O3' G C 136 " pdb=" C3' G C 136 " pdb=" C2' G C 136 " ideal model delta sigma weight residual 113.70 119.76 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C3' U C 39 " pdb=" O3' U C 39 " pdb=" P U C 40 " ideal model delta sigma weight residual 120.20 126.13 -5.93 1.50e+00 4.44e-01 1.56e+01 angle pdb=" C ASP A 216 " pdb=" CA ASP A 216 " pdb=" CB ASP A 216 " ideal model delta sigma weight residual 111.05 117.62 -6.57 1.69e+00 3.50e-01 1.51e+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 - 0.114: 1562 0.114 - 0.228: 47 0.228 - 0.342: 4 0.342 - 0.455: 0 0.455 - 0.569: 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 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.10e+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 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.31e+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: 3.110 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.390 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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= 0.211 Angle : 0.849 10.780 13710 Z= 0.456 Chirality : 0.050 0.569 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 covalent geometry : bond 0.00478 ( 9554) covalent geometry : angle 0.84873 (13710) hydrogen bonds : bond 0.13940 ( 465) hydrogen bonds : angle 6.15538 ( 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 : 0.242 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: 0.1097 time to fit residues: 12.5070 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 : 0.239 ------------------------------------------------------------------------------- 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: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: B 15 HIS ** B 42 ASN ** 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 = 0.4443 r_free = 0.4443 target = 0.216655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.155734 restraints weight = 11094.498| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.76 r_work: 0.3367 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9554 Z= 0.156 Angle : 0.587 8.403 13710 Z= 0.321 Chirality : 0.038 0.231 1615 Planarity : 0.005 0.060 1152 Dihedral : 23.438 167.897 3136 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.52 % Allowed : 12.07 % Favored : 85.41 % 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: 0.28 (0.31), residues: 686 helix: 1.33 (0.26), residues: 343 sheet: -0.50 (0.52), residues: 96 loop : -1.12 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 221 TYR 0.024 0.002 TYR B 33 PHE 0.014 0.002 PHE A 56 TRP 0.014 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9554) covalent geometry : angle 0.58697 (13710) hydrogen bonds : bond 0.04980 ( 465) hydrogen bonds : angle 4.16776 ( 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 81 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7612 (tpp-160) cc_final: 0.7072 (ttm110) REVERT: B 72 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7089 (mt0) REVERT: B 150 GLN cc_start: 0.8175 (tt0) cc_final: 0.7632 (mm110) REVERT: A 66 ILE cc_start: 0.8834 (tp) cc_final: 0.8552 (mt) REVERT: A 216 ASP cc_start: 0.7728 (p0) cc_final: 0.7471 (p0) REVERT: A 222 GLU cc_start: 0.7821 (tt0) cc_final: 0.7520 (tp30) REVERT: A 226 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7506 (mtt180) REVERT: A 398 GLU cc_start: 0.7996 (tp30) cc_final: 0.7745 (tt0) outliers start: 14 outliers final: 6 residues processed: 74 average time/residue: 0.1203 time to fit residues: 11.7970 Evaluate side-chains 67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain A residue 78 LEU 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: 0.0270 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 30.0000 chunk 54 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 236 ASN A 17 HIS A 315 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.217717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146003 restraints weight = 11305.062| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.84 r_work: 0.3443 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9554 Z= 0.129 Angle : 0.541 7.366 13710 Z= 0.294 Chirality : 0.036 0.222 1615 Planarity : 0.004 0.051 1152 Dihedral : 23.371 167.168 3134 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.98 % Allowed : 13.33 % 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: 0.82 (0.32), residues: 686 helix: 1.97 (0.27), residues: 343 sheet: -0.55 (0.52), residues: 98 loop : -1.04 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.012 0.001 TYR B 156 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 covalent geometry : bond 0.00282 ( 9554) covalent geometry : angle 0.54086 (13710) hydrogen bonds : bond 0.04739 ( 465) hydrogen bonds : angle 3.93913 ( 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 75 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7783 (tpp-160) cc_final: 0.7159 (ttm110) REVERT: B 72 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7028 (mt0) REVERT: B 89 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7945 (tm-30) REVERT: A 66 ILE cc_start: 0.8800 (tp) cc_final: 0.8533 (mt) REVERT: A 160 SER cc_start: 0.8801 (t) cc_final: 0.8507 (p) REVERT: A 216 ASP cc_start: 0.7688 (p0) cc_final: 0.7425 (p0) REVERT: A 226 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7431 (mtt180) REVERT: A 392 ARG cc_start: 0.7370 (tpm170) cc_final: 0.5647 (ttt-90) REVERT: A 398 GLU cc_start: 0.7934 (tp30) cc_final: 0.7639 (tt0) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.1135 time to fit residues: 10.3314 Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 405 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS A 347 GLN ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.216027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141724 restraints weight = 11217.106| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.57 r_work: 0.3408 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9554 Z= 0.162 Angle : 0.555 6.619 13710 Z= 0.303 Chirality : 0.036 0.227 1615 Planarity : 0.004 0.047 1152 Dihedral : 23.382 164.881 3132 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % 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 (0.32), residues: 686 helix: 2.13 (0.27), residues: 343 sheet: -0.58 (0.51), residues: 99 loop : -0.96 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 226 TYR 0.014 0.002 TYR B 156 PHE 0.016 0.002 PHE A 56 TRP 0.011 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9554) covalent geometry : angle 0.55518 (13710) hydrogen bonds : bond 0.04760 ( 465) hydrogen bonds : angle 3.87087 ( 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 82 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7282 (ttm110) REVERT: B 72 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7310 (mt0) REVERT: B 150 GLN cc_start: 0.8344 (tt0) cc_final: 0.7881 (mm110) REVERT: A 8 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8227 (pt) REVERT: A 66 ILE cc_start: 0.8885 (tp) cc_final: 0.8609 (mt) REVERT: A 160 SER cc_start: 0.8886 (t) cc_final: 0.8595 (p) REVERT: A 216 ASP cc_start: 0.8073 (p0) cc_final: 0.7722 (p0) REVERT: A 392 ARG cc_start: 0.7634 (tpm170) cc_final: 0.5879 (ttt-90) REVERT: A 398 GLU cc_start: 0.8130 (tp30) cc_final: 0.7834 (tt0) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.1157 time to fit residues: 11.4236 Evaluate side-chains 72 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 401 THR 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: 0.3980 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 72 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.217343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143976 restraints weight = 11259.441| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.55 r_work: 0.3434 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9554 Z= 0.138 Angle : 0.519 6.059 13710 Z= 0.285 Chirality : 0.035 0.224 1615 Planarity : 0.004 0.047 1152 Dihedral : 23.280 163.303 3132 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.52 % Allowed : 13.33 % Favored : 84.14 % 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: 1.04 (0.32), residues: 686 helix: 2.21 (0.27), residues: 344 sheet: -0.71 (0.48), residues: 107 loop : -0.91 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 226 TYR 0.015 0.001 TYR A 358 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 covalent geometry : bond 0.00310 ( 9554) covalent geometry : angle 0.51901 (13710) hydrogen bonds : bond 0.04739 ( 465) hydrogen bonds : angle 3.74337 ( 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 77 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7895 (tpp-160) cc_final: 0.7317 (ttm110) REVERT: B 72 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7342 (mt0) REVERT: A 66 ILE cc_start: 0.8891 (tp) cc_final: 0.8609 (mt) REVERT: A 160 SER cc_start: 0.8848 (t) cc_final: 0.8596 (p) REVERT: A 164 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: A 216 ASP cc_start: 0.7992 (p0) cc_final: 0.7654 (p0) REVERT: A 363 ASN cc_start: 0.8763 (t0) cc_final: 0.8283 (t0) REVERT: A 392 ARG cc_start: 0.7619 (tpm170) cc_final: 0.5868 (ttt-90) REVERT: A 416 TYR cc_start: 0.7745 (m-10) cc_final: 0.7539 (m-10) outliers start: 14 outliers final: 6 residues processed: 70 average time/residue: 0.1151 time to fit residues: 10.9776 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 : 0.247 ------------------------------------------------------------------------------- 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 104 ASP Chi-restraints excluded: chain A residue 164 GLU 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: 4.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN A 362 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.214115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139124 restraints weight = 11125.152| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.53 r_work: 0.3374 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9554 Z= 0.196 Angle : 0.560 6.360 13710 Z= 0.306 Chirality : 0.037 0.234 1615 Planarity : 0.004 0.049 1152 Dihedral : 23.336 159.093 3132 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.16 % Allowed : 14.41 % Favored : 83.42 % 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: 2.07 (0.27), residues: 345 sheet: -0.64 (0.49), residues: 101 loop : -0.88 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 226 TYR 0.014 0.002 TYR A 129 PHE 0.016 0.002 PHE A 56 TRP 0.005 0.001 TRP B 36 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9554) covalent geometry : angle 0.55980 (13710) hydrogen bonds : bond 0.04988 ( 465) hydrogen bonds : angle 3.85813 ( 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 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.7285 (ttp-110) REVERT: B 72 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7362 (mt0) REVERT: B 150 GLN cc_start: 0.8361 (tt0) cc_final: 0.7875 (mm110) REVERT: A 66 ILE cc_start: 0.8849 (tp) cc_final: 0.8553 (mt) REVERT: A 392 ARG cc_start: 0.7735 (tpm170) cc_final: 0.5950 (ttt-90) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.1179 time to fit residues: 10.1830 Evaluate side-chains 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 255 ILE 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: 20.0000 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.212132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137815 restraints weight = 11075.441| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.46 r_work: 0.3355 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9554 Z= 0.226 Angle : 0.587 6.384 13710 Z= 0.320 Chirality : 0.038 0.237 1615 Planarity : 0.005 0.056 1152 Dihedral : 23.404 149.775 3132 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.98 % Allowed : 14.59 % Favored : 83.42 % 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: 0.87 (0.31), residues: 686 helix: 1.96 (0.27), residues: 344 sheet: -0.37 (0.52), residues: 87 loop : -1.02 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 226 TYR 0.015 0.002 TYR A 129 PHE 0.016 0.002 PHE A 56 TRP 0.006 0.001 TRP B 36 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9554) covalent geometry : angle 0.58738 (13710) hydrogen bonds : bond 0.05164 ( 465) hydrogen bonds : angle 3.91236 ( 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 71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7282 (ttp-110) REVERT: B 72 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7560 (mt0) REVERT: B 150 GLN cc_start: 0.8458 (tt0) cc_final: 0.8032 (mm110) REVERT: B 242 SER cc_start: 0.8149 (t) cc_final: 0.7924 (m) REVERT: A 66 ILE cc_start: 0.8867 (tp) cc_final: 0.8567 (mt) REVERT: A 363 ASN cc_start: 0.8694 (t0) cc_final: 0.8268 (t0) REVERT: A 392 ARG cc_start: 0.7887 (tpm170) cc_final: 0.6082 (ttt-90) outliers start: 11 outliers final: 10 residues processed: 67 average time/residue: 0.1109 time to fit residues: 10.1554 Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 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 111 THR 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: 3.9990 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 63 optimal weight: 0.1980 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.210960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128092 restraints weight = 11199.072| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.95 r_work: 0.3326 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9554 Z= 0.203 Angle : 0.564 6.850 13710 Z= 0.308 Chirality : 0.037 0.233 1615 Planarity : 0.004 0.050 1152 Dihedral : 23.302 142.955 3132 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.98 % Allowed : 15.14 % Favored : 82.88 % 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: 0.92 (0.31), residues: 686 helix: 2.02 (0.27), residues: 344 sheet: -0.32 (0.53), residues: 87 loop : -1.04 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 226 TYR 0.014 0.002 TYR A 129 PHE 0.016 0.002 PHE A 56 TRP 0.005 0.001 TRP A 343 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9554) covalent geometry : angle 0.56426 (13710) hydrogen bonds : bond 0.05049 ( 465) hydrogen bonds : angle 3.79935 ( 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 70 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7176 (ttp-110) REVERT: B 72 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7212 (mt0) REVERT: B 150 GLN cc_start: 0.8270 (tt0) cc_final: 0.7644 (mm110) REVERT: A 66 ILE cc_start: 0.8807 (tp) cc_final: 0.8490 (mt) REVERT: A 301 MET cc_start: 0.5378 (tpt) cc_final: 0.5068 (tpt) REVERT: A 363 ASN cc_start: 0.8364 (t0) cc_final: 0.7949 (t0) REVERT: A 392 ARG cc_start: 0.7754 (tpm170) cc_final: 0.5901 (ttt-90) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.1247 time to fit residues: 11.0346 Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 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 111 THR 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: 7.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.215456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134702 restraints weight = 11186.386| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.89 r_work: 0.3396 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9554 Z= 0.130 Angle : 0.521 7.814 13710 Z= 0.282 Chirality : 0.035 0.221 1615 Planarity : 0.004 0.049 1152 Dihedral : 23.155 142.398 3132 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.44 % Allowed : 15.68 % Favored : 82.88 % 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: 1.14 (0.32), residues: 686 helix: 2.29 (0.27), residues: 344 sheet: -0.21 (0.50), residues: 100 loop : -1.11 (0.38), residues: 242 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 209 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9554) covalent geometry : angle 0.52138 (13710) hydrogen bonds : bond 0.04669 ( 465) hydrogen bonds : angle 3.64155 ( 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 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7303 (ttm110) REVERT: B 72 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7059 (mt0) REVERT: A 66 ILE cc_start: 0.8839 (tp) cc_final: 0.8512 (mt) REVERT: A 190 MET cc_start: 0.8592 (mmp) cc_final: 0.7735 (mmm) REVERT: A 216 ASP cc_start: 0.8058 (p0) cc_final: 0.7721 (p0) REVERT: A 301 MET cc_start: 0.5552 (tpt) cc_final: 0.5214 (tpt) REVERT: A 363 ASN cc_start: 0.8232 (t0) cc_final: 0.7782 (t0) REVERT: A 392 ARG cc_start: 0.7654 (tpm170) cc_final: 0.5867 (ttt-90) outliers start: 8 outliers final: 8 residues processed: 61 average time/residue: 0.1244 time to fit residues: 10.0784 Evaluate side-chains 61 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 42 ASN 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 111 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 69 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 34 optimal weight: 9.9990 chunk 52 optimal weight: 0.0270 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.215637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135079 restraints weight = 11155.860| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.89 r_work: 0.3414 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9554 Z= 0.123 Angle : 0.510 7.249 13710 Z= 0.277 Chirality : 0.034 0.220 1615 Planarity : 0.004 0.049 1152 Dihedral : 23.004 141.900 3132 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.26 % Allowed : 15.86 % Favored : 82.88 % 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: 1.34 (0.32), residues: 686 helix: 2.46 (0.27), residues: 345 sheet: -0.07 (0.51), residues: 100 loop : -1.07 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 226 TYR 0.018 0.001 TYR A 358 PHE 0.012 0.001 PHE A 56 TRP 0.006 0.001 TRP B 209 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9554) covalent geometry : angle 0.51005 (13710) hydrogen bonds : bond 0.04631 ( 465) hydrogen bonds : angle 3.54198 ( 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 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.248 Fit side-chains REVERT: B 34 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.7286 (ttm110) REVERT: B 72 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7018 (mt0) REVERT: A 66 ILE cc_start: 0.8832 (tp) cc_final: 0.8502 (mt) REVERT: A 111 THR cc_start: 0.8718 (m) cc_final: 0.8425 (m) REVERT: A 160 SER cc_start: 0.8854 (t) cc_final: 0.8578 (p) REVERT: A 190 MET cc_start: 0.8507 (mmp) cc_final: 0.7628 (mmm) REVERT: A 216 ASP cc_start: 0.7906 (p0) cc_final: 0.7625 (p0) REVERT: A 301 MET cc_start: 0.5531 (tpt) cc_final: 0.5138 (tpt) REVERT: A 363 ASN cc_start: 0.8223 (t0) cc_final: 0.7726 (t0) REVERT: A 392 ARG cc_start: 0.7653 (tpm170) cc_final: 0.5829 (ttt-90) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.1138 time to fit residues: 9.3930 Evaluate side-chains 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 391 LEU Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.212880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132784 restraints weight = 11110.855| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.83 r_work: 0.3406 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9554 Z= 0.152 Angle : 0.526 7.002 13710 Z= 0.286 Chirality : 0.035 0.226 1615 Planarity : 0.004 0.049 1152 Dihedral : 23.068 142.449 3132 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.08 % Allowed : 16.22 % 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: 1.30 (0.32), residues: 686 helix: 2.41 (0.27), residues: 345 sheet: -0.08 (0.52), residues: 94 loop : -1.05 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 70 TYR 0.013 0.001 TYR A 129 PHE 0.014 0.001 PHE A 56 TRP 0.005 0.001 TRP B 209 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9554) covalent geometry : angle 0.52643 (13710) hydrogen bonds : bond 0.04770 ( 465) hydrogen bonds : angle 3.61364 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3227.48 seconds wall clock time: 55 minutes 41.23 seconds (3341.23 seconds total)