Starting phenix.real_space_refine on Sat Apr 4 22:44:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t3s_55518/04_2026/9t3s_55518.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t3s_55518/04_2026/9t3s_55518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t3s_55518/04_2026/9t3s_55518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t3s_55518/04_2026/9t3s_55518.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t3s_55518/04_2026/9t3s_55518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t3s_55518/04_2026/9t3s_55518.map" } resolution = 3.0 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= 0.001 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3179 2.51 5 N 890 2.21 5 O 974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5080 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 906 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain breaks: 1 Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3388 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.23 Number of scatterers: 5080 At special positions: 0 Unit cell: (77.274, 78.732, 114.453, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 974 8.00 N 890 7.00 C 3179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 204 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 252 " distance=2.02 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 367 " distance=2.03 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: 0.26 Conformation dependent library (CDL) restraints added in 337.9 milliseconds 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1214 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 15 sheets defined 10.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.509A pdb=" N LEU A 46 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.534A pdb=" N LEU A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 75 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 76 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.594A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 4.007A pdb=" N SER A 202 " --> pdb=" O CYS A 199 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 203 " --> pdb=" O LYS A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 203' Processing helix chain 'A' and resid 208 through 212 removed outlier: 4.062A pdb=" N CYS A 212 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.669A pdb=" N ALA A 365 " --> pdb=" O GLN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.677A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 398 " --> pdb=" O PRO A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 398' Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 481 through 486 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.813A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.430A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.430A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.377A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA L 86 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.377A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA L 86 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'A' and resid 60 through 63 removed outlier: 7.314A pdb=" N LEU A 154 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 115 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN A 156 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 117 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 258 through 260 removed outlier: 3.656A pdb=" N ILE A 263 " --> pdb=" O HIS A 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 272 through 274 Processing sheet with id=AB3, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AB4, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AB5, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AB6, first strand: chain 'A' and resid 374 through 376 removed outlier: 6.299A pdb=" N LEU A 374 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 410 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLN A 446 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 412 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR A 441 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU A 467 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 443 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N HIS A 469 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 445 " --> pdb=" O HIS A 469 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.73 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1689 1.34 - 1.46: 1079 1.46 - 1.58: 2376 1.58 - 1.70: 0 1.70 - 1.81: 45 Bond restraints: 5189 Sorted by residual: bond pdb=" CA THR A 278 " pdb=" CB THR A 278 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.69e-02 3.50e+03 2.58e+00 bond pdb=" CA ASN A 302 " pdb=" CB ASN A 302 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.54e-02 4.22e+03 9.72e-01 bond pdb=" N THR A 278 " pdb=" CA THR A 278 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.41e-01 bond pdb=" CA ASN A 388 " pdb=" CB ASN A 388 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.95e-01 bond pdb=" N GLY A 262 " pdb=" CA GLY A 262 " ideal model delta sigma weight residual 1.449 1.462 -0.013 1.45e-02 4.76e+03 7.71e-01 ... (remaining 5184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 6841 1.41 - 2.82: 178 2.82 - 4.23: 27 4.23 - 5.64: 5 5.64 - 7.05: 1 Bond angle restraints: 7052 Sorted by residual: angle pdb=" C ASP A 277 " pdb=" N THR A 278 " pdb=" CA THR A 278 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" C TYR A 301 " pdb=" N ASN A 302 " pdb=" CA ASN A 302 " ideal model delta sigma weight residual 122.08 126.77 -4.69 1.47e+00 4.63e-01 1.02e+01 angle pdb=" C SER A 387 " pdb=" N ASN A 388 " pdb=" CA ASN A 388 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 angle pdb=" CA GLN H 43 " pdb=" CB GLN H 43 " pdb=" CG GLN H 43 " ideal model delta sigma weight residual 114.10 119.12 -5.02 2.00e+00 2.50e-01 6.31e+00 angle pdb=" CA THR A 278 " pdb=" CB THR A 278 " pdb=" CG2 THR A 278 " ideal model delta sigma weight residual 110.50 114.59 -4.09 1.70e+00 3.46e-01 5.79e+00 ... (remaining 7047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 2637 17.43 - 34.87: 341 34.87 - 52.30: 106 52.30 - 69.74: 23 69.74 - 87.17: 8 Dihedral angle restraints: 3115 sinusoidal: 1218 harmonic: 1897 Sorted by residual: dihedral pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " pdb=" SG CYS A 244 " pdb=" CB CYS A 244 " ideal model delta sinusoidal sigma weight residual 93.00 176.94 -83.94 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS A 224 " pdb=" SG CYS A 224 " pdb=" SG CYS A 235 " pdb=" CB CYS A 235 " ideal model delta sinusoidal sigma weight residual -86.00 -139.79 53.79 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CA CYS A 255 " pdb=" C CYS A 255 " pdb=" N LEU A 256 " pdb=" CA LEU A 256 " ideal model delta harmonic sigma weight residual 180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 3112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 471 0.031 - 0.061: 219 0.061 - 0.092: 54 0.092 - 0.122: 42 0.122 - 0.153: 10 Chirality restraints: 796 Sorted by residual: chirality pdb=" CA ASN A 302 " pdb=" N ASN A 302 " pdb=" C ASN A 302 " pdb=" CB ASN A 302 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA THR A 278 " pdb=" N THR A 278 " pdb=" C THR A 278 " pdb=" CB THR A 278 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 793 not shown) Planarity restraints: 912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " 0.015 2.00e-02 2.50e+03 1.44e-02 5.15e+00 pdb=" CG TRP H 36 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 73 " 0.006 2.00e-02 2.50e+03 1.06e-02 1.98e+00 pdb=" CG PHE A 73 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 73 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 73 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 73 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 73 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 73 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 146 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C THR A 146 " -0.020 2.00e-02 2.50e+03 pdb=" O THR A 146 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU A 147 " 0.007 2.00e-02 2.50e+03 ... (remaining 909 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 2390 2.96 - 3.45: 4803 3.45 - 3.93: 8306 3.93 - 4.42: 9976 4.42 - 4.90: 16347 Nonbonded interactions: 41822 Sorted by model distance: nonbonded pdb=" O THR A 278 " pdb=" OG1 THR A 278 " model vdw 2.476 3.040 nonbonded pdb=" O TYR A 301 " pdb=" OD1 ASN A 302 " model vdw 2.491 3.040 nonbonded pdb=" O SER A 387 " pdb=" OD1 ASN A 388 " model vdw 2.526 3.040 nonbonded pdb=" C THR H 91 " pdb=" OG1 THR H 91 " model vdw 2.590 2.616 nonbonded pdb=" N ASN L 62 " pdb=" OD1 ASN L 62 " model vdw 2.597 3.120 ... (remaining 41817 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: 3.700 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.003 0.027 5203 Z= 0.131 Angle : 0.570 7.053 7080 Z= 0.313 Chirality : 0.044 0.153 796 Planarity : 0.004 0.026 912 Dihedral : 17.526 87.173 1859 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.37 % Allowed : 26.82 % Favored : 69.80 % 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: -1.20 (0.33), residues: 651 helix: -3.34 (1.17), residues: 15 sheet: -0.33 (0.45), residues: 145 loop : -0.90 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.015 0.001 TYR A 274 PHE 0.023 0.002 PHE A 73 TRP 0.038 0.002 TRP H 36 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5189) covalent geometry : angle 0.56871 ( 7052) SS BOND : bond 0.00346 ( 14) SS BOND : angle 0.91105 ( 28) hydrogen bonds : bond 0.16103 ( 96) hydrogen bonds : angle 7.97309 ( 228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: H 17 SER cc_start: 0.7380 (OUTLIER) cc_final: 0.6603 (m) REVERT: H 114 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: H 119 THR cc_start: 0.8495 (p) cc_final: 0.8202 (t) REVERT: A 32 LYS cc_start: 0.8395 (mptp) cc_final: 0.8088 (mppt) REVERT: A 161 LEU cc_start: 0.7104 (tp) cc_final: 0.6795 (tt) REVERT: A 198 MET cc_start: 0.7838 (ppp) cc_final: 0.7594 (tmm) REVERT: A 301 TYR cc_start: 0.6470 (t80) cc_final: 0.6085 (t80) REVERT: A 368 LYS cc_start: 0.8060 (tppt) cc_final: 0.7810 (mmtp) outliers start: 19 outliers final: 14 residues processed: 71 average time/residue: 0.4251 time to fit residues: 31.9172 Evaluate side-chains 71 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 499 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0030 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 68 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 177 ASN A 237 HIS A 249 HIS A 275 ASN A 302 ASN A 427 ASN A 498 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.140453 restraints weight = 6818.957| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.39 r_work: 0.3760 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5203 Z= 0.118 Angle : 0.536 8.653 7080 Z= 0.282 Chirality : 0.043 0.139 796 Planarity : 0.004 0.027 912 Dihedral : 6.137 45.452 736 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.15 % Allowed : 23.27 % Favored : 71.58 % 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: -1.13 (0.34), residues: 651 helix: -3.32 (1.00), residues: 21 sheet: -0.27 (0.45), residues: 145 loop : -0.81 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.014 0.001 TYR A 274 PHE 0.010 0.001 PHE A 279 TRP 0.017 0.002 TRP H 36 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5189) covalent geometry : angle 0.53322 ( 7052) SS BOND : bond 0.00423 ( 14) SS BOND : angle 1.04338 ( 28) hydrogen bonds : bond 0.02761 ( 96) hydrogen bonds : angle 5.95447 ( 228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6945 (ttm170) REVERT: H 43 GLN cc_start: 0.7955 (mp10) cc_final: 0.7704 (mp10) REVERT: H 119 THR cc_start: 0.8508 (p) cc_final: 0.8220 (t) REVERT: A 32 LYS cc_start: 0.8326 (mptp) cc_final: 0.8033 (mppt) REVERT: A 301 TYR cc_start: 0.6561 (t80) cc_final: 0.6047 (t80) REVERT: A 399 VAL cc_start: 0.7613 (OUTLIER) cc_final: 0.7353 (m) outliers start: 29 outliers final: 13 residues processed: 79 average time/residue: 0.4244 time to fit residues: 35.3685 Evaluate side-chains 70 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 399 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN A 239 GLN A 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.156417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136637 restraints weight = 6881.061| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.48 r_work: 0.3704 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5203 Z= 0.165 Angle : 0.587 9.966 7080 Z= 0.305 Chirality : 0.045 0.193 796 Planarity : 0.004 0.035 912 Dihedral : 5.208 39.845 717 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 6.57 % Allowed : 23.09 % Favored : 70.34 % 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: -1.24 (0.33), residues: 651 helix: -3.55 (0.89), residues: 23 sheet: -0.57 (0.43), residues: 155 loop : -0.78 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 203 TYR 0.016 0.002 TYR A 274 PHE 0.016 0.002 PHE A 73 TRP 0.012 0.002 TRP H 36 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5189) covalent geometry : angle 0.58368 ( 7052) SS BOND : bond 0.00512 ( 14) SS BOND : angle 1.12523 ( 28) hydrogen bonds : bond 0.03140 ( 96) hydrogen bonds : angle 5.86654 ( 228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7044 (ttm170) REVERT: H 43 GLN cc_start: 0.7996 (mp10) cc_final: 0.7645 (mp10) REVERT: H 114 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: H 119 THR cc_start: 0.8525 (p) cc_final: 0.8261 (t) REVERT: A 32 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8029 (mppt) REVERT: A 301 TYR cc_start: 0.6476 (t80) cc_final: 0.6072 (t80) outliers start: 37 outliers final: 17 residues processed: 84 average time/residue: 0.3569 time to fit residues: 31.9249 Evaluate side-chains 71 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 302 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 43 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.160396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.141145 restraints weight = 6837.551| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.41 r_work: 0.3760 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5203 Z= 0.103 Angle : 0.531 9.814 7080 Z= 0.273 Chirality : 0.043 0.145 796 Planarity : 0.003 0.029 912 Dihedral : 4.707 39.599 715 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 6.39 % Allowed : 23.80 % Favored : 69.80 % 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: -1.08 (0.34), residues: 651 helix: -3.28 (0.97), residues: 23 sheet: -0.34 (0.45), residues: 144 loop : -0.72 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.015 0.001 TYR A 274 PHE 0.017 0.001 PHE A 73 TRP 0.011 0.001 TRP H 36 HIS 0.003 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 5189) covalent geometry : angle 0.53058 ( 7052) SS BOND : bond 0.00264 ( 14) SS BOND : angle 0.70887 ( 28) hydrogen bonds : bond 0.02483 ( 96) hydrogen bonds : angle 5.47276 ( 228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 54 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6988 (ttm170) REVERT: H 43 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: H 114 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: H 119 THR cc_start: 0.8524 (p) cc_final: 0.8239 (t) REVERT: A 32 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7982 (mppt) REVERT: A 301 TYR cc_start: 0.6438 (t80) cc_final: 0.6002 (t80) REVERT: A 368 LYS cc_start: 0.8080 (tppt) cc_final: 0.7839 (mmtp) outliers start: 36 outliers final: 14 residues processed: 78 average time/residue: 0.4294 time to fit residues: 35.3972 Evaluate side-chains 69 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 264 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN A 59 ASN ** A 158 ASN ** 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 = 0.4099 r_free = 0.4099 target = 0.159501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140020 restraints weight = 7031.538| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.46 r_work: 0.3744 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5203 Z= 0.115 Angle : 0.535 9.369 7080 Z= 0.276 Chirality : 0.043 0.141 796 Planarity : 0.004 0.031 912 Dihedral : 4.686 39.006 715 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.68 % Allowed : 24.87 % Favored : 69.45 % 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: -1.09 (0.33), residues: 651 helix: -3.46 (0.94), residues: 21 sheet: -0.32 (0.45), residues: 144 loop : -0.74 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.014 0.001 TYR A 274 PHE 0.015 0.001 PHE A 73 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5189) covalent geometry : angle 0.53344 ( 7052) SS BOND : bond 0.00336 ( 14) SS BOND : angle 0.78543 ( 28) hydrogen bonds : bond 0.02556 ( 96) hydrogen bonds : angle 5.41751 ( 228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6998 (ttm170) REVERT: H 43 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: H 119 THR cc_start: 0.8506 (p) cc_final: 0.8214 (t) REVERT: A 32 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7852 (mtmt) REVERT: A 198 MET cc_start: 0.7839 (ppp) cc_final: 0.7542 (tmm) REVERT: A 301 TYR cc_start: 0.6444 (t80) cc_final: 0.6072 (t80) REVERT: A 351 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5720 (tmt-80) REVERT: A 368 LYS cc_start: 0.8117 (tppt) cc_final: 0.7887 (mmtp) outliers start: 32 outliers final: 22 residues processed: 76 average time/residue: 0.4431 time to fit residues: 35.4139 Evaluate side-chains 77 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 351 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** A 158 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 = 0.4066 r_free = 0.4066 target = 0.156422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136955 restraints weight = 7012.151| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.44 r_work: 0.3704 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5203 Z= 0.160 Angle : 0.587 11.489 7080 Z= 0.304 Chirality : 0.044 0.153 796 Planarity : 0.004 0.039 912 Dihedral : 4.996 40.003 715 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 7.10 % Allowed : 24.16 % Favored : 68.74 % 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: -1.15 (0.33), residues: 651 helix: -3.57 (0.89), residues: 22 sheet: -0.34 (0.44), residues: 149 loop : -0.79 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 143 TYR 0.016 0.002 TYR A 274 PHE 0.010 0.002 PHE L 101 TRP 0.013 0.002 TRP H 47 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 5189) covalent geometry : angle 0.58517 ( 7052) SS BOND : bond 0.00433 ( 14) SS BOND : angle 0.97098 ( 28) hydrogen bonds : bond 0.02954 ( 96) hydrogen bonds : angle 5.63192 ( 228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 57 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: H 114 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: H 119 THR cc_start: 0.8534 (p) cc_final: 0.8250 (t) REVERT: A 32 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7893 (mtmt) REVERT: A 198 MET cc_start: 0.7846 (ppp) cc_final: 0.7620 (tmm) REVERT: A 235 CYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7087 (t) REVERT: A 301 TYR cc_start: 0.6512 (t80) cc_final: 0.6085 (t80) REVERT: A 351 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5727 (tmt-80) REVERT: A 368 LYS cc_start: 0.8142 (tppt) cc_final: 0.7930 (mmtp) REVERT: A 395 GLU cc_start: 0.7445 (pp20) cc_final: 0.7179 (mp0) outliers start: 40 outliers final: 20 residues processed: 85 average time/residue: 0.4552 time to fit residues: 40.7005 Evaluate side-chains 77 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 351 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN L 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.159116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140024 restraints weight = 6815.295| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.39 r_work: 0.3747 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5203 Z= 0.114 Angle : 0.546 12.186 7080 Z= 0.283 Chirality : 0.043 0.148 796 Planarity : 0.004 0.028 912 Dihedral : 4.735 39.359 715 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.04 % Allowed : 25.75 % Favored : 68.21 % 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: -1.19 (0.33), residues: 651 helix: -4.04 (0.68), residues: 27 sheet: -0.32 (0.44), residues: 149 loop : -0.76 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.015 0.001 TYR A 274 PHE 0.017 0.001 PHE A 73 TRP 0.048 0.002 TRP H 36 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5189) covalent geometry : angle 0.54496 ( 7052) SS BOND : bond 0.00338 ( 14) SS BOND : angle 0.83300 ( 28) hydrogen bonds : bond 0.02494 ( 96) hydrogen bonds : angle 5.51118 ( 228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: H 12 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6893 (mmmm) REVERT: H 28 THR cc_start: 0.6888 (OUTLIER) cc_final: 0.6542 (m) REVERT: H 43 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: H 114 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7267 (pt0) REVERT: H 119 THR cc_start: 0.8518 (p) cc_final: 0.8230 (t) REVERT: A 32 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7849 (mtmt) REVERT: A 235 CYS cc_start: 0.7253 (OUTLIER) cc_final: 0.7008 (t) REVERT: A 301 TYR cc_start: 0.6453 (t80) cc_final: 0.6060 (t80) REVERT: A 351 ARG cc_start: 0.6106 (OUTLIER) cc_final: 0.5558 (ttt180) REVERT: A 368 LYS cc_start: 0.8112 (tppt) cc_final: 0.7882 (mmtp) outliers start: 34 outliers final: 21 residues processed: 78 average time/residue: 0.3698 time to fit residues: 30.6652 Evaluate side-chains 80 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 351 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** A 158 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 = 0.4086 r_free = 0.4086 target = 0.158342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138976 restraints weight = 6851.018| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.41 r_work: 0.3731 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5203 Z= 0.130 Angle : 0.561 12.836 7080 Z= 0.290 Chirality : 0.044 0.150 796 Planarity : 0.004 0.030 912 Dihedral : 4.796 39.619 715 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.68 % Allowed : 25.75 % Favored : 68.56 % 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: -1.20 (0.33), residues: 651 helix: -3.83 (0.77), residues: 27 sheet: -0.32 (0.44), residues: 149 loop : -0.79 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.015 0.001 TYR A 274 PHE 0.011 0.001 PHE A 486 TRP 0.041 0.002 TRP H 36 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5189) covalent geometry : angle 0.55918 ( 7052) SS BOND : bond 0.00364 ( 14) SS BOND : angle 0.87015 ( 28) hydrogen bonds : bond 0.02625 ( 96) hydrogen bonds : angle 5.48844 ( 228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: H 12 LYS cc_start: 0.7105 (mmtt) cc_final: 0.6857 (mmmm) REVERT: H 28 THR cc_start: 0.6894 (OUTLIER) cc_final: 0.6539 (m) REVERT: H 43 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: H 119 THR cc_start: 0.8509 (p) cc_final: 0.8219 (t) REVERT: A 32 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7843 (mtmt) REVERT: A 235 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.7003 (t) REVERT: A 301 TYR cc_start: 0.6468 (t80) cc_final: 0.6079 (t80) REVERT: A 351 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5555 (ttt180) REVERT: A 368 LYS cc_start: 0.8135 (tppt) cc_final: 0.7916 (mmtp) outliers start: 32 outliers final: 21 residues processed: 74 average time/residue: 0.4240 time to fit residues: 33.1073 Evaluate side-chains 81 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 351 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.0040 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** A 158 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 = 0.4105 r_free = 0.4105 target = 0.159787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.140592 restraints weight = 6873.809| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.41 r_work: 0.3758 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5203 Z= 0.109 Angle : 0.547 13.124 7080 Z= 0.282 Chirality : 0.043 0.150 796 Planarity : 0.004 0.028 912 Dihedral : 4.624 39.232 715 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.97 % Allowed : 27.00 % Favored : 68.03 % 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: -1.13 (0.34), residues: 651 helix: -4.01 (0.69), residues: 27 sheet: -0.28 (0.45), residues: 144 loop : -0.71 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.014 0.001 TYR A 274 PHE 0.016 0.001 PHE A 73 TRP 0.042 0.002 TRP H 36 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 5189) covalent geometry : angle 0.54589 ( 7052) SS BOND : bond 0.00290 ( 14) SS BOND : angle 0.78295 ( 28) hydrogen bonds : bond 0.02383 ( 96) hydrogen bonds : angle 5.38031 ( 228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: H 12 LYS cc_start: 0.7103 (mmtt) cc_final: 0.6894 (mmmm) REVERT: H 28 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6478 (m) REVERT: H 43 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: H 114 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: H 119 THR cc_start: 0.8497 (p) cc_final: 0.8210 (t) REVERT: A 32 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7849 (mtmt) REVERT: A 198 MET cc_start: 0.7864 (ppp) cc_final: 0.7573 (tmm) REVERT: A 301 TYR cc_start: 0.6431 (t80) cc_final: 0.6069 (t80) REVERT: A 351 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5551 (ttt180) REVERT: A 368 LYS cc_start: 0.8105 (tppt) cc_final: 0.7882 (mmtp) REVERT: A 395 GLU cc_start: 0.7357 (pp20) cc_final: 0.7130 (mp0) outliers start: 28 outliers final: 21 residues processed: 71 average time/residue: 0.4084 time to fit residues: 30.5689 Evaluate side-chains 80 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 499 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134080 restraints weight = 7013.311| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.41 r_work: 0.3660 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5203 Z= 0.255 Angle : 0.700 13.670 7080 Z= 0.364 Chirality : 0.048 0.171 796 Planarity : 0.005 0.062 912 Dihedral : 5.552 41.604 715 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.44 % Allowed : 27.71 % Favored : 67.85 % 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: -1.37 (0.33), residues: 651 helix: -4.19 (0.67), residues: 28 sheet: -0.75 (0.41), residues: 167 loop : -0.74 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.019 0.002 TYR A 274 PHE 0.016 0.003 PHE A 486 TRP 0.053 0.004 TRP H 36 HIS 0.006 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 5189) covalent geometry : angle 0.69253 ( 7052) SS BOND : bond 0.00658 ( 14) SS BOND : angle 1.77060 ( 28) hydrogen bonds : bond 0.03740 ( 96) hydrogen bonds : angle 6.07871 ( 228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: H 12 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6921 (mmmt) REVERT: H 43 GLN cc_start: 0.7967 (mp10) cc_final: 0.7485 (mp10) REVERT: A 198 MET cc_start: 0.7757 (ppp) cc_final: 0.7546 (tmm) REVERT: A 301 TYR cc_start: 0.6577 (t80) cc_final: 0.6091 (t80) REVERT: A 351 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5609 (ttt180) REVERT: A 368 LYS cc_start: 0.8226 (tppt) cc_final: 0.8013 (mmtp) outliers start: 25 outliers final: 20 residues processed: 69 average time/residue: 0.4583 time to fit residues: 33.2568 Evaluate side-chains 74 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 499 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.0060 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.159079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.139677 restraints weight = 7010.936| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.44 r_work: 0.3735 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5203 Z= 0.114 Angle : 0.560 13.363 7080 Z= 0.290 Chirality : 0.043 0.152 796 Planarity : 0.004 0.032 912 Dihedral : 4.905 41.838 715 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.55 % Allowed : 28.60 % Favored : 67.85 % 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: -1.16 (0.33), residues: 651 helix: -3.81 (0.78), residues: 27 sheet: -0.39 (0.44), residues: 149 loop : -0.72 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.017 0.001 TYR A 274 PHE 0.024 0.002 PHE A 73 TRP 0.046 0.002 TRP H 36 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5189) covalent geometry : angle 0.55642 ( 7052) SS BOND : bond 0.00304 ( 14) SS BOND : angle 1.20898 ( 28) hydrogen bonds : bond 0.02502 ( 96) hydrogen bonds : angle 5.61401 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.19 seconds wall clock time: 28 minutes 46.80 seconds (1726.80 seconds total)