Starting phenix.real_space_refine on Tue Feb 3 15:32:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kkb_62384/02_2026/9kkb_62384.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kkb_62384/02_2026/9kkb_62384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kkb_62384/02_2026/9kkb_62384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kkb_62384/02_2026/9kkb_62384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kkb_62384/02_2026/9kkb_62384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kkb_62384/02_2026/9kkb_62384.map" } resolution = 3.36 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= 0.010 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 3 5.49 5 S 10 5.16 5 C 2711 2.51 5 N 765 2.21 5 O 797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4286 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2969 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 18, 'TRANS': 354} Chain breaks: 2 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 143} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.13, per 1000 atoms: 0.26 Number of scatterers: 4286 At special positions: 0 Unit cell: (61.9378, 69.5609, 123.876, 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 10 16.00 P 3 15.00 O 797 8.00 N 765 7.00 C 2711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 101.2 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 45.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 Processing helix chain 'A' and resid 32 through 52 removed outlier: 3.556A pdb=" N GLU A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.955A pdb=" N LEU A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 95 removed outlier: 3.855A pdb=" N THR A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 95' Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.537A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.720A pdb=" N TYR A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.809A pdb=" N GLN A 219 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.715A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 261 removed outlier: 3.569A pdb=" N ILE A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 removed outlier: 4.110A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.560A pdb=" N ARG A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.768A pdb=" N PHE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.702A pdb=" N PHE A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.535A pdb=" N PHE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.246A pdb=" N VAL A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.525A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 removed outlier: 4.248A pdb=" N GLN B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 22 " --> pdb=" O GLN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 121 through 138 removed outlier: 4.487A pdb=" N THR B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Proline residue: B 128 - end of helix removed outlier: 3.589A pdb=" N GLU B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 66 removed outlier: 4.780A pdb=" N ASP A 86 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY A 142 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS A 89 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 157 removed outlier: 4.229A pdb=" N LEU A 155 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 167 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.689A pdb=" N LEU A 185 " --> pdb=" O TYR A 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 285 removed outlier: 3.962A pdb=" N VAL A 283 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 34 removed outlier: 7.215A pdb=" N TYR B 28 " --> pdb=" O TRP B 45 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N TRP B 45 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG B 30 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B 43 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 61 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY B 44 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 57 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS B 56 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N CYS B 69 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 98 " --> pdb=" O VAL B 71 " (cutoff:3.500A) 147 hydrogen bonds defined for protein. 423 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: 0.60 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1088 1.33 - 1.45: 873 1.45 - 1.57: 2415 1.57 - 1.69: 9 1.69 - 1.81: 14 Bond restraints: 4399 Sorted by residual: bond pdb=" CB TRP B 140 " pdb=" CG TRP B 140 " ideal model delta sigma weight residual 1.498 1.586 -0.088 3.10e-02 1.04e+03 8.00e+00 bond pdb=" N GLN A 286 " pdb=" CA GLN A 286 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.85e+00 bond pdb=" C GLN A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.25e-02 6.40e+03 5.15e+00 bond pdb=" C THR A 354 " pdb=" N PRO A 355 " ideal model delta sigma weight residual 1.337 1.360 -0.024 1.06e-02 8.90e+03 5.12e+00 bond pdb=" C ILE B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 1.336 1.362 -0.027 1.23e-02 6.61e+03 4.67e+00 ... (remaining 4394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 5819 3.60 - 7.21: 134 7.21 - 10.81: 35 10.81 - 14.41: 3 14.41 - 18.01: 2 Bond angle restraints: 5993 Sorted by residual: angle pdb=" CA ARG A 362 " pdb=" CB ARG A 362 " pdb=" CG ARG A 362 " ideal model delta sigma weight residual 114.10 125.87 -11.77 2.00e+00 2.50e-01 3.47e+01 angle pdb=" C ASP B 75 " pdb=" N LEU B 76 " pdb=" CA LEU B 76 " ideal model delta sigma weight residual 121.54 132.28 -10.74 1.91e+00 2.74e-01 3.16e+01 angle pdb=" C THR A 162 " pdb=" N ALA A 163 " pdb=" CA ALA A 163 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C LEU A 277 " pdb=" N MET A 278 " pdb=" CA MET A 278 " ideal model delta sigma weight residual 120.09 126.63 -6.54 1.25e+00 6.40e-01 2.74e+01 angle pdb=" CA GLU B 147 " pdb=" CB GLU B 147 " pdb=" CG GLU B 147 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+01 ... (remaining 5988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 2279 22.77 - 45.55: 282 45.55 - 68.32: 40 68.32 - 91.09: 10 91.09 - 113.87: 3 Dihedral angle restraints: 2614 sinusoidal: 1070 harmonic: 1544 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -9.27 113.87 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" O3A GTP A 501 " pdb=" O3B GTP A 501 " pdb=" PB GTP A 501 " pdb=" PG GTP A 501 " ideal model delta sinusoidal sigma weight residual -56.21 -159.92 103.71 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" CA MET A 364 " pdb=" C MET A 364 " pdb=" N GLU A 365 " pdb=" CA GLU A 365 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 2611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 519 0.083 - 0.165: 108 0.165 - 0.248: 15 0.248 - 0.330: 5 0.330 - 0.413: 4 Chirality restraints: 651 Sorted by residual: chirality pdb=" CB ILE A 386 " pdb=" CA ILE A 386 " pdb=" CG1 ILE A 386 " pdb=" CG2 ILE A 386 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB ILE B 33 " pdb=" CA ILE B 33 " pdb=" CG1 ILE B 33 " pdb=" CG2 ILE B 33 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CG LEU A 22 " pdb=" CB LEU A 22 " pdb=" CD1 LEU A 22 " pdb=" CD2 LEU A 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 648 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 313 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO A 314 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 314 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 314 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 89 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO B 90 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 123 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 124 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.041 5.00e-02 4.00e+02 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1599 2.96 - 3.44: 3992 3.44 - 3.93: 6720 3.93 - 4.41: 7362 4.41 - 4.90: 12224 Nonbonded interactions: 31897 Sorted by model distance: nonbonded pdb=" O2' GTP A 501 " pdb=" O3' GTP A 501 " model vdw 2.471 2.432 nonbonded pdb=" C SER A 68 " pdb=" OG SER A 68 " model vdw 2.561 2.616 nonbonded pdb=" N VAL A 338 " pdb=" O VAL A 338 " model vdw 2.619 2.496 nonbonded pdb=" N SER B 49 " pdb=" OG SER B 49 " model vdw 2.625 2.496 nonbonded pdb=" N THR B 65 " pdb=" O THR B 65 " model vdw 2.630 2.496 ... (remaining 31892 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: 3.100 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.650 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 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 : 0.007 0.088 4399 Z= 0.340 Angle : 1.395 18.013 5993 Z= 0.718 Chirality : 0.075 0.413 651 Planarity : 0.011 0.088 771 Dihedral : 19.600 113.867 1616 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.08 % Allowed : 30.99 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.24 (0.28), residues: 522 helix: -4.13 (0.17), residues: 220 sheet: -1.35 (0.72), residues: 44 loop : -1.72 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 32 TYR 0.035 0.004 TYR A 43 PHE 0.033 0.003 PHE A 176 TRP 0.023 0.004 TRP A 323 HIS 0.020 0.002 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00702 ( 4399) covalent geometry : angle 1.39482 ( 5993) hydrogen bonds : bond 0.26592 ( 147) hydrogen bonds : angle 9.21742 ( 423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.5030 (OUTLIER) cc_final: 0.4779 (ttpt) REVERT: A 59 GLN cc_start: 0.7171 (tt0) cc_final: 0.6766 (pt0) REVERT: A 164 TRP cc_start: 0.4280 (m100) cc_final: 0.3940 (m100) REVERT: A 188 ILE cc_start: 0.4114 (OUTLIER) cc_final: 0.3853 (tp) REVERT: A 265 ASP cc_start: 0.8019 (t70) cc_final: 0.7704 (t0) REVERT: A 316 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6591 (mtm-85) REVERT: A 361 GLN cc_start: 0.6658 (mt0) cc_final: 0.6290 (tp-100) REVERT: A 362 ARG cc_start: 0.5631 (tpt90) cc_final: 0.2923 (ttm110) REVERT: A 367 MET cc_start: 0.3375 (tpt) cc_final: 0.2410 (tpt) REVERT: B 18 GLN cc_start: 0.8378 (pm20) cc_final: 0.7210 (tp40) REVERT: B 138 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5473 (pm20) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.0715 time to fit residues: 5.4289 Evaluate side-chains 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 138 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.0670 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 145 HIS A 219 GLN A 255 ASN A 292 ASN A 300 ASN A 324 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5463 r_free = 0.5463 target = 0.287754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.247852 restraints weight = 4833.219| |-----------------------------------------------------------------------------| r_work (start): 0.5153 rms_B_bonded: 2.82 r_work: 0.5018 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.5018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4399 Z= 0.119 Angle : 0.685 9.078 5993 Z= 0.333 Chirality : 0.045 0.144 651 Planarity : 0.006 0.053 771 Dihedral : 11.297 118.487 621 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.05 % Allowed : 29.67 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.54 (0.32), residues: 522 helix: -2.05 (0.30), residues: 215 sheet: -0.18 (0.83), residues: 42 loop : -1.54 (0.33), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 32 TYR 0.023 0.002 TYR A 172 PHE 0.009 0.001 PHE A 320 TRP 0.008 0.001 TRP A 175 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4399) covalent geometry : angle 0.68538 ( 5993) hydrogen bonds : bond 0.04217 ( 147) hydrogen bonds : angle 5.26112 ( 423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 86 ASP cc_start: 0.6281 (OUTLIER) cc_final: 0.5548 (p0) REVERT: A 135 TYR cc_start: 0.6677 (p90) cc_final: 0.6422 (p90) REVERT: A 361 GLN cc_start: 0.6704 (mt0) cc_final: 0.6430 (tp40) REVERT: B 18 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7459 (tp40) REVERT: B 132 LEU cc_start: 0.4148 (OUTLIER) cc_final: 0.3932 (tt) outliers start: 23 outliers final: 13 residues processed: 75 average time/residue: 0.0639 time to fit residues: 6.3673 Evaluate side-chains 62 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.0030 chunk 39 optimal weight: 0.2980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5400 r_free = 0.5400 target = 0.279079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.237776 restraints weight = 4795.463| |-----------------------------------------------------------------------------| r_work (start): 0.5067 rms_B_bonded: 2.87 r_work: 0.4919 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4399 Z= 0.138 Angle : 0.673 8.504 5993 Z= 0.324 Chirality : 0.046 0.155 651 Planarity : 0.005 0.049 771 Dihedral : 10.452 117.257 605 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.37 % Allowed : 29.67 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.66 (0.34), residues: 522 helix: -1.09 (0.34), residues: 216 sheet: -0.11 (0.85), residues: 42 loop : -1.20 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 20 TYR 0.027 0.002 TYR A 43 PHE 0.010 0.001 PHE A 320 TRP 0.013 0.002 TRP B 45 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4399) covalent geometry : angle 0.67259 ( 5993) hydrogen bonds : bond 0.04032 ( 147) hydrogen bonds : angle 4.91241 ( 423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7634 (pt0) cc_final: 0.7295 (tt0) REVERT: A 86 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6365 (p0) REVERT: A 222 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7223 (mtmt) REVERT: A 278 MET cc_start: 0.6605 (tpp) cc_final: 0.6087 (mtt) REVERT: A 340 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: A 361 GLN cc_start: 0.6633 (mt0) cc_final: 0.6261 (tp40) REVERT: B 18 GLN cc_start: 0.8276 (pm20) cc_final: 0.7407 (tp-100) REVERT: B 132 LEU cc_start: 0.4244 (OUTLIER) cc_final: 0.3988 (tt) outliers start: 29 outliers final: 19 residues processed: 74 average time/residue: 0.0781 time to fit residues: 7.3592 Evaluate side-chains 71 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 HIS A 237 GLN A 295 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.273533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.228035 restraints weight = 4669.571| |-----------------------------------------------------------------------------| r_work (start): 0.4980 rms_B_bonded: 3.02 r_work: 0.4826 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4399 Z= 0.154 Angle : 0.680 9.266 5993 Z= 0.326 Chirality : 0.046 0.170 651 Planarity : 0.005 0.047 771 Dihedral : 10.265 118.098 605 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 8.57 % Allowed : 28.13 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.38 (0.35), residues: 522 helix: -0.70 (0.34), residues: 217 sheet: -1.09 (0.75), residues: 52 loop : -0.95 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 20 TYR 0.025 0.002 TYR A 172 PHE 0.011 0.002 PHE A 301 TRP 0.013 0.002 TRP B 45 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4399) covalent geometry : angle 0.67995 ( 5993) hydrogen bonds : bond 0.04101 ( 147) hydrogen bonds : angle 4.87190 ( 423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 52 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.5761 (OUTLIER) cc_final: 0.5521 (mt) REVERT: A 59 GLN cc_start: 0.7946 (pt0) cc_final: 0.7439 (tt0) REVERT: A 86 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6487 (p0) REVERT: A 145 HIS cc_start: 0.2546 (OUTLIER) cc_final: 0.1684 (t-90) REVERT: A 164 TRP cc_start: 0.4650 (m100) cc_final: 0.3904 (m100) REVERT: A 222 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7396 (mtmt) REVERT: A 278 MET cc_start: 0.6666 (tpp) cc_final: 0.6349 (mtt) REVERT: A 340 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6850 (mm-30) REVERT: A 361 GLN cc_start: 0.6220 (mt0) cc_final: 0.5915 (tp-100) REVERT: B 94 HIS cc_start: 0.4831 (OUTLIER) cc_final: 0.4526 (p90) REVERT: B 132 LEU cc_start: 0.4185 (OUTLIER) cc_final: 0.3980 (tt) outliers start: 39 outliers final: 18 residues processed: 86 average time/residue: 0.0747 time to fit residues: 8.2408 Evaluate side-chains 74 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5339 r_free = 0.5339 target = 0.273022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.228666 restraints weight = 4731.802| |-----------------------------------------------------------------------------| r_work (start): 0.4983 rms_B_bonded: 2.93 r_work: 0.4833 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4399 Z= 0.138 Angle : 0.668 7.678 5993 Z= 0.322 Chirality : 0.047 0.280 651 Planarity : 0.005 0.047 771 Dihedral : 10.175 116.580 604 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 7.25 % Allowed : 29.67 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.36), residues: 522 helix: -0.43 (0.35), residues: 217 sheet: -1.18 (0.73), residues: 52 loop : -0.83 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 20 TYR 0.025 0.002 TYR A 43 PHE 0.010 0.001 PHE A 301 TRP 0.012 0.002 TRP B 45 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4399) covalent geometry : angle 0.66817 ( 5993) hydrogen bonds : bond 0.03794 ( 147) hydrogen bonds : angle 4.79232 ( 423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.6237 (p0) REVERT: A 145 HIS cc_start: 0.2635 (OUTLIER) cc_final: 0.1799 (t-90) REVERT: A 164 TRP cc_start: 0.4628 (m100) cc_final: 0.3892 (m100) REVERT: A 222 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7450 (mtmt) REVERT: A 278 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6380 (mtt) REVERT: A 340 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6931 (mm-30) REVERT: A 361 GLN cc_start: 0.6311 (mt0) cc_final: 0.5986 (tp-100) REVERT: B 94 HIS cc_start: 0.4893 (OUTLIER) cc_final: 0.4544 (p90) REVERT: B 103 PHE cc_start: 0.4032 (OUTLIER) cc_final: 0.3725 (p90) REVERT: B 140 TRP cc_start: 0.7069 (t60) cc_final: 0.6795 (t60) outliers start: 33 outliers final: 20 residues processed: 78 average time/residue: 0.0653 time to fit residues: 6.6842 Evaluate side-chains 75 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.270261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.225546 restraints weight = 4903.979| |-----------------------------------------------------------------------------| r_work (start): 0.4949 rms_B_bonded: 3.00 r_work: 0.4800 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4399 Z= 0.153 Angle : 0.703 10.806 5993 Z= 0.334 Chirality : 0.046 0.197 651 Planarity : 0.005 0.048 771 Dihedral : 9.993 115.527 604 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 9.01 % Allowed : 28.13 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.10 (0.36), residues: 522 helix: -0.37 (0.35), residues: 216 sheet: -1.39 (0.71), residues: 52 loop : -0.78 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 20 TYR 0.025 0.002 TYR A 172 PHE 0.018 0.002 PHE B 135 TRP 0.014 0.002 TRP B 45 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4399) covalent geometry : angle 0.70255 ( 5993) hydrogen bonds : bond 0.04113 ( 147) hydrogen bonds : angle 4.80766 ( 423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 52 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.6071 (pt0) REVERT: A 31 LEU cc_start: 0.4724 (OUTLIER) cc_final: 0.4353 (tt) REVERT: A 59 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: A 86 ASP cc_start: 0.6691 (OUTLIER) cc_final: 0.6324 (p0) REVERT: A 222 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7455 (mtmt) REVERT: A 278 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6424 (mtt) REVERT: A 340 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: A 361 GLN cc_start: 0.6467 (mt0) cc_final: 0.6155 (tp-100) REVERT: B 94 HIS cc_start: 0.4709 (OUTLIER) cc_final: 0.4282 (p90) REVERT: B 103 PHE cc_start: 0.4321 (OUTLIER) cc_final: 0.4076 (p90) REVERT: B 146 TRP cc_start: 0.4606 (m100) cc_final: 0.3561 (m100) outliers start: 41 outliers final: 21 residues processed: 85 average time/residue: 0.0606 time to fit residues: 6.9069 Evaluate side-chains 80 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 332 ASN A 368 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5320 r_free = 0.5320 target = 0.270472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.225918 restraints weight = 4813.164| |-----------------------------------------------------------------------------| r_work (start): 0.4953 rms_B_bonded: 3.06 r_work: 0.4794 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4399 Z= 0.135 Angle : 0.695 9.564 5993 Z= 0.332 Chirality : 0.047 0.383 651 Planarity : 0.005 0.048 771 Dihedral : 9.784 114.722 601 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 7.25 % Allowed : 30.99 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.36), residues: 522 helix: -0.21 (0.35), residues: 216 sheet: -1.34 (0.72), residues: 52 loop : -0.68 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 20 TYR 0.021 0.001 TYR A 172 PHE 0.011 0.001 PHE B 135 TRP 0.025 0.002 TRP A 164 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4399) covalent geometry : angle 0.69518 ( 5993) hydrogen bonds : bond 0.03856 ( 147) hydrogen bonds : angle 4.76972 ( 423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.5969 (pt0) REVERT: A 31 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4289 (tt) REVERT: A 59 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: A 86 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6394 (p0) REVERT: A 222 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7201 (mtpt) REVERT: A 278 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6482 (mtt) REVERT: A 340 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6738 (mm-30) REVERT: A 361 GLN cc_start: 0.6205 (mt0) cc_final: 0.5851 (tp-100) REVERT: B 94 HIS cc_start: 0.4786 (OUTLIER) cc_final: 0.4292 (p90) REVERT: B 146 TRP cc_start: 0.4786 (m100) cc_final: 0.3854 (m100) outliers start: 33 outliers final: 22 residues processed: 78 average time/residue: 0.0604 time to fit residues: 6.3788 Evaluate side-chains 80 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.267600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.221994 restraints weight = 4863.735| |-----------------------------------------------------------------------------| r_work (start): 0.4913 rms_B_bonded: 3.15 r_work: 0.4753 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4399 Z= 0.166 Angle : 0.724 9.667 5993 Z= 0.347 Chirality : 0.049 0.377 651 Planarity : 0.005 0.048 771 Dihedral : 9.876 114.345 601 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 7.69 % Allowed : 30.55 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.02 (0.36), residues: 522 helix: -0.29 (0.35), residues: 220 sheet: -1.42 (0.71), residues: 52 loop : -0.74 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 20 TYR 0.025 0.002 TYR A 172 PHE 0.010 0.002 PHE A 351 TRP 0.024 0.002 TRP B 140 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4399) covalent geometry : angle 0.72397 ( 5993) hydrogen bonds : bond 0.04238 ( 147) hydrogen bonds : angle 4.88351 ( 423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 53 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.6050 (pt0) REVERT: A 86 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6343 (p0) REVERT: A 222 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7459 (mtmt) REVERT: A 278 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6335 (mtt) REVERT: A 340 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: A 361 GLN cc_start: 0.6293 (mt0) cc_final: 0.5744 (tp-100) REVERT: B 94 HIS cc_start: 0.4809 (OUTLIER) cc_final: 0.4272 (p90) outliers start: 35 outliers final: 25 residues processed: 82 average time/residue: 0.0471 time to fit residues: 5.2329 Evaluate side-chains 80 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5313 r_free = 0.5313 target = 0.269039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.224267 restraints weight = 4861.204| |-----------------------------------------------------------------------------| r_work (start): 0.4932 rms_B_bonded: 3.13 r_work: 0.4776 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4399 Z= 0.135 Angle : 0.698 9.813 5993 Z= 0.335 Chirality : 0.048 0.381 651 Planarity : 0.005 0.049 771 Dihedral : 9.729 113.454 601 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 7.03 % Allowed : 31.65 % Favored : 61.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.88 (0.36), residues: 522 helix: -0.15 (0.35), residues: 220 sheet: -1.42 (0.71), residues: 52 loop : -0.66 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 20 TYR 0.021 0.002 TYR A 172 PHE 0.008 0.001 PHE B 135 TRP 0.024 0.002 TRP B 140 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4399) covalent geometry : angle 0.69815 ( 5993) hydrogen bonds : bond 0.03900 ( 147) hydrogen bonds : angle 4.80722 ( 423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 51 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6246 (OUTLIER) cc_final: 0.5981 (pt0) REVERT: A 86 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6398 (p0) REVERT: A 222 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7201 (mtpt) REVERT: A 278 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6342 (mtt) REVERT: A 315 GLN cc_start: 0.6196 (mp10) cc_final: 0.5908 (mp10) REVERT: A 340 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6742 (mm-30) REVERT: A 361 GLN cc_start: 0.6254 (mt0) cc_final: 0.5750 (tp-100) REVERT: B 94 HIS cc_start: 0.4703 (OUTLIER) cc_final: 0.4098 (p90) outliers start: 32 outliers final: 22 residues processed: 78 average time/residue: 0.0613 time to fit residues: 6.4049 Evaluate side-chains 79 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 35 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.0050 chunk 22 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 chunk 39 optimal weight: 0.0170 overall best weight: 0.0506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS A 368 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5359 r_free = 0.5359 target = 0.274862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.231308 restraints weight = 4808.337| |-----------------------------------------------------------------------------| r_work (start): 0.5002 rms_B_bonded: 3.20 r_work: 0.4844 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4399 Z= 0.107 Angle : 0.647 10.308 5993 Z= 0.310 Chirality : 0.046 0.362 651 Planarity : 0.004 0.049 771 Dihedral : 9.172 109.642 601 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.05 % Allowed : 33.41 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.56 (0.37), residues: 522 helix: 0.19 (0.36), residues: 215 sheet: -1.18 (0.73), residues: 52 loop : -0.57 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 20 TYR 0.015 0.001 TYR A 43 PHE 0.009 0.001 PHE B 135 TRP 0.019 0.002 TRP A 164 HIS 0.005 0.000 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4399) covalent geometry : angle 0.64652 ( 5993) hydrogen bonds : bond 0.03099 ( 147) hydrogen bonds : angle 4.46085 ( 423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: A 86 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6308 (p0) REVERT: A 222 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7071 (mtpt) REVERT: A 315 GLN cc_start: 0.6135 (mp10) cc_final: 0.5861 (mp10) REVERT: A 361 GLN cc_start: 0.6084 (mt0) cc_final: 0.5632 (tp-100) REVERT: B 65 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8563 (p) outliers start: 23 outliers final: 17 residues processed: 70 average time/residue: 0.0627 time to fit residues: 5.8386 Evaluate side-chains 70 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.270750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.226190 restraints weight = 4750.075| |-----------------------------------------------------------------------------| r_work (start): 0.4959 rms_B_bonded: 3.18 r_work: 0.4798 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4399 Z= 0.128 Angle : 0.668 9.674 5993 Z= 0.318 Chirality : 0.047 0.370 651 Planarity : 0.005 0.049 771 Dihedral : 9.188 108.652 601 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.27 % Allowed : 32.75 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.57 (0.37), residues: 522 helix: 0.20 (0.36), residues: 214 sheet: -1.24 (0.73), residues: 52 loop : -0.58 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 20 TYR 0.018 0.001 TYR A 43 PHE 0.014 0.002 PHE B 135 TRP 0.021 0.002 TRP B 146 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4399) covalent geometry : angle 0.66817 ( 5993) hydrogen bonds : bond 0.03504 ( 147) hydrogen bonds : angle 4.48854 ( 423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.73 seconds wall clock time: 26 minutes 15.12 seconds (1575.12 seconds total)