Starting phenix.real_space_refine on Sun Apr 5 02:12:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mct_63805/04_2026/9mct_63805_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mct_63805/04_2026/9mct_63805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mct_63805/04_2026/9mct_63805_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mct_63805/04_2026/9mct_63805_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mct_63805/04_2026/9mct_63805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mct_63805/04_2026/9mct_63805.map" } resolution = 2.94 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= -0.002 sd= 0.090 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 28 5.16 5 C 4794 2.51 5 N 1102 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 7130 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3554 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 447} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'AKG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B Time building chain proxies: 2.41, per 1000 atoms: 0.34 Number of scatterers: 7130 At special positions: 0 Unit cell: (86.676, 109.044, 77.356, 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 28 16.00 O 1206 8.00 N 1102 7.00 C 4794 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: 0.80 Conformation dependent library (CDL) restraints added in 287.2 milliseconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 81.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.622A pdb=" N PHE A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 135 Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 163 through 166 removed outlier: 4.049A pdb=" N GLY A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.583A pdb=" N TRP A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 183 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.622A pdb=" N GLN A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.768A pdb=" N LEU A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.793A pdb=" N ILE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.773A pdb=" N LEU A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.601A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 298 through 325 removed outlier: 4.966A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Proline residue: A 318 - end of helix Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.774A pdb=" N GLN A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 367 Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.780A pdb=" N TRP A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.584A pdb=" N GLY A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 467 through 484 removed outlier: 6.528A pdb=" N THR A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.740A pdb=" N ASN A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.455A pdb=" N ILE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 544 Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'B' and resid 91 through 107 removed outlier: 3.622A pdb=" N PHE B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 135 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 163 through 166 removed outlier: 4.049A pdb=" N GLY B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 167 through 187 removed outlier: 3.583A pdb=" N TRP B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 183 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.623A pdb=" N GLN B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.768A pdb=" N LEU B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.794A pdb=" N ILE B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.773A pdb=" N LEU B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 removed outlier: 3.601A pdb=" N LEU B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 298 through 325 removed outlier: 4.966A pdb=" N VAL B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Proline residue: B 309 - end of helix Proline residue: B 318 - end of helix Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.774A pdb=" N GLN B 340 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 367 Processing helix chain 'B' and resid 376 through 391 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.780A pdb=" N TRP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.584A pdb=" N GLY B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 467 through 484 removed outlier: 6.528A pdb=" N THR B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.739A pdb=" N ASN B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 512 through 519 removed outlier: 4.455A pdb=" N ILE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 544 Processing helix chain 'B' and resid 545 through 554 484 hydrogen bonds defined for protein. 1440 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: 1.16 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1061 1.29 - 1.42: 2041 1.42 - 1.55: 4186 1.55 - 1.68: 6 1.68 - 1.81: 48 Bond restraints: 7342 Sorted by residual: bond pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 1.527 1.393 0.133 1.21e-02 6.83e+03 1.22e+02 bond pdb=" CA ARG B 255 " pdb=" C ARG B 255 " ideal model delta sigma weight residual 1.527 1.393 0.133 1.21e-02 6.83e+03 1.21e+02 bond pdb=" CA GLU B 253 " pdb=" C GLU B 253 " ideal model delta sigma weight residual 1.524 1.394 0.130 1.48e-02 4.57e+03 7.73e+01 bond pdb=" CA GLU A 253 " pdb=" C GLU A 253 " ideal model delta sigma weight residual 1.524 1.395 0.129 1.48e-02 4.57e+03 7.65e+01 bond pdb=" N ARG A 255 " pdb=" CA ARG A 255 " ideal model delta sigma weight residual 1.460 1.363 0.096 1.22e-02 6.72e+03 6.26e+01 ... (remaining 7337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 9780 3.26 - 6.52: 212 6.52 - 9.77: 40 9.77 - 13.03: 10 13.03 - 16.29: 2 Bond angle restraints: 10044 Sorted by residual: angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 111.56 95.27 16.29 1.53e+00 4.27e-01 1.13e+02 angle pdb=" N ARG B 255 " pdb=" CA ARG B 255 " pdb=" C ARG B 255 " ideal model delta sigma weight residual 111.56 95.28 16.28 1.53e+00 4.27e-01 1.13e+02 angle pdb=" N GLU A 253 " pdb=" CA GLU A 253 " pdb=" C GLU A 253 " ideal model delta sigma weight residual 112.72 101.48 11.24 1.14e+00 7.69e-01 9.72e+01 angle pdb=" N GLU B 253 " pdb=" CA GLU B 253 " pdb=" C GLU B 253 " ideal model delta sigma weight residual 112.72 101.52 11.20 1.14e+00 7.69e-01 9.65e+01 angle pdb=" N THR A 252 " pdb=" CA THR A 252 " pdb=" C THR A 252 " ideal model delta sigma weight residual 111.90 123.46 -11.56 1.32e+00 5.74e-01 7.66e+01 ... (remaining 10039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3783 17.57 - 35.14: 265 35.14 - 52.71: 50 52.71 - 70.28: 10 70.28 - 87.85: 6 Dihedral angle restraints: 4114 sinusoidal: 1460 harmonic: 2654 Sorted by residual: dihedral pdb=" C ARG B 255 " pdb=" N ARG B 255 " pdb=" CA ARG B 255 " pdb=" CB ARG B 255 " ideal model delta harmonic sigma weight residual -122.60 -109.85 -12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ARG A 255 " pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" CB ARG A 255 " ideal model delta harmonic sigma weight residual -122.60 -109.87 -12.73 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N ARG B 255 " pdb=" C ARG B 255 " pdb=" CA ARG B 255 " pdb=" CB ARG B 255 " ideal model delta harmonic sigma weight residual 122.80 111.83 10.97 0 2.50e+00 1.60e-01 1.93e+01 ... (remaining 4111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1001 0.079 - 0.158: 152 0.158 - 0.237: 11 0.237 - 0.316: 10 0.316 - 0.395: 4 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CA PRO A 489 " pdb=" N PRO A 489 " pdb=" C PRO A 489 " pdb=" CB PRO A 489 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PRO B 489 " pdb=" N PRO B 489 " pdb=" C PRO B 489 " pdb=" CB PRO B 489 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA THR B 252 " pdb=" N THR B 252 " pdb=" C THR B 252 " pdb=" CB THR B 252 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 1175 not shown) Planarity restraints: 1210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 465 " -0.023 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C ALA A 465 " 0.082 2.00e-02 2.50e+03 pdb=" O ALA A 465 " -0.031 2.00e-02 2.50e+03 pdb=" N SER A 466 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 465 " 0.023 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C ALA B 465 " -0.082 2.00e-02 2.50e+03 pdb=" O ALA B 465 " 0.030 2.00e-02 2.50e+03 pdb=" N SER B 466 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 223 " 0.024 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C PRO B 223 " -0.081 2.00e-02 2.50e+03 pdb=" O PRO B 223 " 0.029 2.00e-02 2.50e+03 pdb=" N SER B 224 " 0.028 2.00e-02 2.50e+03 ... (remaining 1207 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2330 2.83 - 3.35: 6624 3.35 - 3.86: 12722 3.86 - 4.38: 15124 4.38 - 4.90: 25468 Nonbonded interactions: 62268 Sorted by model distance: nonbonded pdb=" N GLU A 253 " pdb=" N HIS A 254 " model vdw 2.311 2.560 nonbonded pdb=" N GLU B 253 " pdb=" N HIS B 254 " model vdw 2.312 2.560 nonbonded pdb=" O TRP A 259 " pdb=" OG1 THR A 263 " model vdw 2.343 3.040 nonbonded pdb=" O TRP B 259 " pdb=" OG1 THR B 263 " model vdw 2.344 3.040 nonbonded pdb=" NH2 ARG A 228 " pdb=" O ALA A 278 " model vdw 2.349 3.120 ... (remaining 62263 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.410 Find NCS groups from input model: 0.060 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.011 0.133 7342 Z= 0.707 Angle : 1.201 16.289 10044 Z= 0.730 Chirality : 0.064 0.395 1178 Planarity : 0.008 0.058 1210 Dihedral : 13.099 87.853 2426 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.28 % Allowed : 4.41 % Favored : 95.32 % Cbeta Deviations : 0.47 % 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: -3.92 (0.20), residues: 936 helix: -2.56 (0.13), residues: 752 sheet: None (None), residues: 0 loop : -1.54 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 116 TYR 0.033 0.003 TYR B 325 PHE 0.027 0.002 PHE A 265 TRP 0.019 0.002 TRP A 411 HIS 0.005 0.002 HIS B 508 Details of bonding type rmsd covalent geometry : bond 0.01068 ( 7342) covalent geometry : angle 1.20071 (10044) hydrogen bonds : bond 0.16462 ( 484) hydrogen bonds : angle 7.84057 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.249 Fit side-chains REVERT: A 145 MET cc_start: 0.8218 (mtt) cc_final: 0.7868 (mtp) REVERT: A 169 ILE cc_start: 0.8485 (mt) cc_final: 0.8138 (mm) REVERT: A 261 MET cc_start: 0.8709 (mmm) cc_final: 0.8467 (mmt) REVERT: A 452 ILE cc_start: 0.8183 (mt) cc_final: 0.7658 (mm) REVERT: A 503 MET cc_start: 0.7940 (ptt) cc_final: 0.7641 (ptp) REVERT: A 552 LYS cc_start: 0.7848 (tppt) cc_final: 0.7218 (tttt) REVERT: B 169 ILE cc_start: 0.8411 (mt) cc_final: 0.8106 (mm) REVERT: B 261 MET cc_start: 0.8787 (mmm) cc_final: 0.8554 (mmt) REVERT: B 344 ASP cc_start: 0.7239 (m-30) cc_final: 0.6957 (m-30) REVERT: B 452 ILE cc_start: 0.8165 (mt) cc_final: 0.7684 (mm) REVERT: B 503 MET cc_start: 0.7926 (ptt) cc_final: 0.7662 (ptp) REVERT: B 552 LYS cc_start: 0.8030 (tppt) cc_final: 0.7480 (tttt) outliers start: 2 outliers final: 0 residues processed: 152 average time/residue: 0.4991 time to fit residues: 80.4415 Evaluate side-chains 87 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130106 restraints weight = 9236.583| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.41 r_work: 0.3427 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7342 Z= 0.133 Angle : 0.603 8.124 10044 Z= 0.304 Chirality : 0.040 0.215 1178 Planarity : 0.005 0.052 1210 Dihedral : 6.197 75.205 988 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.72 % Allowed : 11.16 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.26), residues: 936 helix: -0.29 (0.18), residues: 748 sheet: None (None), residues: 0 loop : -0.98 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 191 TYR 0.013 0.001 TYR B 421 PHE 0.021 0.001 PHE B 553 TRP 0.016 0.001 TRP A 411 HIS 0.002 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7342) covalent geometry : angle 0.60257 (10044) hydrogen bonds : bond 0.03675 ( 484) hydrogen bonds : angle 4.84160 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.8403 (mtt) cc_final: 0.8168 (mtp) REVERT: A 214 SER cc_start: 0.8860 (t) cc_final: 0.8038 (p) REVERT: A 261 MET cc_start: 0.8893 (mmm) cc_final: 0.8685 (mmt) REVERT: A 362 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7012 (tp) REVERT: A 503 MET cc_start: 0.8184 (ptt) cc_final: 0.7925 (ptp) REVERT: B 104 ILE cc_start: 0.8316 (mt) cc_final: 0.8088 (mp) REVERT: B 214 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8137 (p) REVERT: B 442 LEU cc_start: 0.6752 (tp) cc_final: 0.6424 (mt) REVERT: B 503 MET cc_start: 0.8099 (ptt) cc_final: 0.7883 (ptp) outliers start: 27 outliers final: 8 residues processed: 124 average time/residue: 0.3776 time to fit residues: 50.5133 Evaluate side-chains 105 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 556 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 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 423 ASN B 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122486 restraints weight = 9227.771| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.55 r_work: 0.3284 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7342 Z= 0.131 Angle : 0.576 7.776 10044 Z= 0.287 Chirality : 0.040 0.194 1178 Planarity : 0.004 0.038 1210 Dihedral : 5.547 66.577 988 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.44 % Allowed : 13.50 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 936 helix: 0.78 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -0.84 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 191 TYR 0.013 0.002 TYR A 421 PHE 0.024 0.001 PHE A 553 TRP 0.016 0.001 TRP A 411 HIS 0.002 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7342) covalent geometry : angle 0.57589 (10044) hydrogen bonds : bond 0.03496 ( 484) hydrogen bonds : angle 4.49233 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.8460 (mtt) cc_final: 0.8201 (mtp) REVERT: A 272 SER cc_start: 0.7372 (p) cc_final: 0.7102 (m) REVERT: A 503 MET cc_start: 0.8286 (ptt) cc_final: 0.8015 (ptp) REVERT: B 214 SER cc_start: 0.8710 (t) cc_final: 0.7946 (p) REVERT: B 442 LEU cc_start: 0.6721 (tp) cc_final: 0.6393 (mt) REVERT: B 503 MET cc_start: 0.8327 (ptt) cc_final: 0.8079 (ptp) outliers start: 25 outliers final: 13 residues processed: 108 average time/residue: 0.4051 time to fit residues: 47.0890 Evaluate side-chains 102 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 476 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119532 restraints weight = 9400.861| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.56 r_work: 0.3212 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7342 Z= 0.140 Angle : 0.578 7.309 10044 Z= 0.287 Chirality : 0.041 0.209 1178 Planarity : 0.004 0.034 1210 Dihedral : 5.468 63.042 988 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.44 % Allowed : 14.33 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.29), residues: 936 helix: 1.07 (0.20), residues: 750 sheet: None (None), residues: 0 loop : -0.55 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 191 TYR 0.012 0.001 TYR A 421 PHE 0.027 0.002 PHE B 553 TRP 0.015 0.001 TRP B 411 HIS 0.001 0.000 HIS B 508 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7342) covalent geometry : angle 0.57834 (10044) hydrogen bonds : bond 0.03436 ( 484) hydrogen bonds : angle 4.41996 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.8468 (mtt) cc_final: 0.8243 (mtp) REVERT: A 272 SER cc_start: 0.7513 (p) cc_final: 0.7296 (m) REVERT: A 307 ILE cc_start: 0.7923 (tp) cc_final: 0.7689 (mm) REVERT: A 503 MET cc_start: 0.8408 (ptt) cc_final: 0.8085 (ptp) REVERT: B 214 SER cc_start: 0.8653 (t) cc_final: 0.7855 (p) REVERT: B 272 SER cc_start: 0.7588 (p) cc_final: 0.7371 (m) REVERT: B 503 MET cc_start: 0.8386 (ptt) cc_final: 0.8083 (ptp) outliers start: 25 outliers final: 11 residues processed: 102 average time/residue: 0.4279 time to fit residues: 46.9744 Evaluate side-chains 100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 485 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 0.0070 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121550 restraints weight = 9364.619| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.57 r_work: 0.3243 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7342 Z= 0.109 Angle : 0.542 7.395 10044 Z= 0.267 Chirality : 0.039 0.163 1178 Planarity : 0.003 0.031 1210 Dihedral : 5.161 55.538 988 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.99 % Allowed : 15.15 % Favored : 80.85 % 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: 1.51 (0.29), residues: 936 helix: 1.38 (0.20), residues: 750 sheet: None (None), residues: 0 loop : -0.33 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 191 TYR 0.012 0.001 TYR A 421 PHE 0.025 0.001 PHE A 553 TRP 0.016 0.001 TRP A 411 HIS 0.002 0.000 HIS B 508 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7342) covalent geometry : angle 0.54242 (10044) hydrogen bonds : bond 0.03160 ( 484) hydrogen bonds : angle 4.25044 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7901 (tp) cc_final: 0.7626 (mm) REVERT: A 362 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6845 (tp) REVERT: A 503 MET cc_start: 0.8368 (ptt) cc_final: 0.8068 (ptp) REVERT: B 214 SER cc_start: 0.8606 (t) cc_final: 0.7813 (p) REVERT: B 272 SER cc_start: 0.7575 (p) cc_final: 0.7323 (m) REVERT: B 503 MET cc_start: 0.8377 (ptt) cc_final: 0.8088 (ptp) outliers start: 29 outliers final: 15 residues processed: 111 average time/residue: 0.4048 time to fit residues: 48.4804 Evaluate side-chains 108 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 329 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120770 restraints weight = 9251.834| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.55 r_work: 0.3259 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7342 Z= 0.129 Angle : 0.561 7.269 10044 Z= 0.277 Chirality : 0.041 0.177 1178 Planarity : 0.003 0.029 1210 Dihedral : 5.165 53.993 988 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.13 % Allowed : 15.70 % Favored : 80.17 % 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: 1.64 (0.29), residues: 936 helix: 1.45 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -0.16 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 228 TYR 0.012 0.001 TYR A 421 PHE 0.023 0.001 PHE B 553 TRP 0.014 0.001 TRP A 411 HIS 0.002 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7342) covalent geometry : angle 0.56081 (10044) hydrogen bonds : bond 0.03285 ( 484) hydrogen bonds : angle 4.25065 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7962 (tp) cc_final: 0.7734 (mm) REVERT: A 362 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6941 (tp) REVERT: A 442 LEU cc_start: 0.6849 (tp) cc_final: 0.6223 (mt) REVERT: A 503 MET cc_start: 0.8411 (ptt) cc_final: 0.8113 (ptp) REVERT: B 214 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 272 SER cc_start: 0.7722 (p) cc_final: 0.7478 (m) REVERT: B 362 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6904 (tp) REVERT: B 503 MET cc_start: 0.8404 (ptt) cc_final: 0.8115 (ptp) outliers start: 30 outliers final: 15 residues processed: 110 average time/residue: 0.4279 time to fit residues: 50.5565 Evaluate side-chains 107 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 44 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120642 restraints weight = 9287.857| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.56 r_work: 0.3252 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7342 Z= 0.124 Angle : 0.555 6.690 10044 Z= 0.274 Chirality : 0.040 0.175 1178 Planarity : 0.003 0.028 1210 Dihedral : 5.079 50.552 988 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.86 % Allowed : 15.70 % Favored : 80.44 % 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: 1.75 (0.29), residues: 936 helix: 1.52 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -0.10 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 228 TYR 0.012 0.001 TYR A 421 PHE 0.024 0.001 PHE A 553 TRP 0.015 0.001 TRP A 411 HIS 0.002 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7342) covalent geometry : angle 0.55490 (10044) hydrogen bonds : bond 0.03221 ( 484) hydrogen bonds : angle 4.23215 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7950 (tp) cc_final: 0.7723 (mm) REVERT: A 362 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6942 (tp) REVERT: A 442 LEU cc_start: 0.6900 (tp) cc_final: 0.6265 (mt) REVERT: A 503 MET cc_start: 0.8404 (ptt) cc_final: 0.8107 (ptp) REVERT: B 199 LEU cc_start: 0.7369 (mt) cc_final: 0.7150 (mt) REVERT: B 214 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.7857 (p) REVERT: B 272 SER cc_start: 0.7733 (p) cc_final: 0.7513 (m) REVERT: B 362 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6879 (tp) REVERT: B 503 MET cc_start: 0.8409 (ptt) cc_final: 0.8116 (ptp) outliers start: 28 outliers final: 17 residues processed: 114 average time/residue: 0.3833 time to fit residues: 47.2694 Evaluate side-chains 111 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 485 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118512 restraints weight = 9362.497| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.56 r_work: 0.3237 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7342 Z= 0.146 Angle : 0.579 6.913 10044 Z= 0.287 Chirality : 0.042 0.190 1178 Planarity : 0.003 0.028 1210 Dihedral : 5.137 48.962 988 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.86 % Allowed : 16.39 % Favored : 79.75 % 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: 1.73 (0.29), residues: 936 helix: 1.50 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -0.07 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.014 0.001 TYR B 322 PHE 0.023 0.001 PHE B 553 TRP 0.014 0.001 TRP A 411 HIS 0.002 0.001 HIS B 508 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7342) covalent geometry : angle 0.57878 (10044) hydrogen bonds : bond 0.03385 ( 484) hydrogen bonds : angle 4.29770 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7940 (tp) cc_final: 0.7695 (mm) REVERT: A 362 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6975 (tp) REVERT: A 503 MET cc_start: 0.8409 (ptt) cc_final: 0.8091 (ptp) REVERT: B 199 LEU cc_start: 0.7426 (mt) cc_final: 0.7205 (mt) REVERT: B 214 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.7876 (p) REVERT: B 362 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7001 (tp) REVERT: B 503 MET cc_start: 0.8406 (ptt) cc_final: 0.8100 (ptp) outliers start: 28 outliers final: 18 residues processed: 103 average time/residue: 0.4068 time to fit residues: 45.3128 Evaluate side-chains 105 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 485 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119590 restraints weight = 9281.521| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.56 r_work: 0.3246 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7342 Z= 0.138 Angle : 0.570 6.548 10044 Z= 0.283 Chirality : 0.041 0.187 1178 Planarity : 0.003 0.027 1210 Dihedral : 5.077 45.735 988 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.58 % Allowed : 17.22 % Favored : 79.20 % 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: 1.80 (0.29), residues: 936 helix: 1.54 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -0.01 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 228 TYR 0.013 0.001 TYR B 421 PHE 0.025 0.001 PHE A 553 TRP 0.017 0.001 TRP B 446 HIS 0.002 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7342) covalent geometry : angle 0.57033 (10044) hydrogen bonds : bond 0.03327 ( 484) hydrogen bonds : angle 4.28088 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7928 (tp) cc_final: 0.7680 (mm) REVERT: A 503 MET cc_start: 0.8388 (ptt) cc_final: 0.8071 (ptp) REVERT: B 199 LEU cc_start: 0.7481 (mt) cc_final: 0.7243 (mt) REVERT: B 214 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.7857 (p) REVERT: B 362 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6983 (tp) REVERT: B 503 MET cc_start: 0.8410 (ptt) cc_final: 0.8110 (ptp) outliers start: 26 outliers final: 16 residues processed: 103 average time/residue: 0.4015 time to fit residues: 44.6889 Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121105 restraints weight = 9260.507| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.43 r_work: 0.3264 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7342 Z= 0.139 Angle : 0.570 5.985 10044 Z= 0.284 Chirality : 0.041 0.184 1178 Planarity : 0.003 0.027 1210 Dihedral : 5.063 43.821 988 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.89 % Allowed : 18.04 % Favored : 79.06 % 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: 1.82 (0.29), residues: 936 helix: 1.55 (0.20), residues: 748 sheet: None (None), residues: 0 loop : 0.02 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 228 TYR 0.012 0.001 TYR B 421 PHE 0.018 0.001 PHE B 265 TRP 0.016 0.001 TRP B 446 HIS 0.002 0.000 HIS B 508 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7342) covalent geometry : angle 0.57021 (10044) hydrogen bonds : bond 0.03332 ( 484) hydrogen bonds : angle 4.28215 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7961 (tp) cc_final: 0.7715 (mm) REVERT: A 503 MET cc_start: 0.8425 (ptt) cc_final: 0.8116 (ptp) REVERT: B 199 LEU cc_start: 0.7552 (mt) cc_final: 0.7314 (mt) REVERT: B 214 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.7894 (p) REVERT: B 362 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7078 (tp) REVERT: B 503 MET cc_start: 0.8392 (ptt) cc_final: 0.8091 (ptp) outliers start: 21 outliers final: 19 residues processed: 98 average time/residue: 0.4272 time to fit residues: 45.0861 Evaluate side-chains 105 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.137660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122573 restraints weight = 9228.635| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.37 r_work: 0.3275 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7342 Z= 0.158 Angle : 0.591 6.622 10044 Z= 0.295 Chirality : 0.042 0.197 1178 Planarity : 0.003 0.027 1210 Dihedral : 5.143 43.109 988 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.17 % Allowed : 18.32 % Favored : 78.51 % 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: 1.71 (0.29), residues: 936 helix: 1.47 (0.20), residues: 748 sheet: None (None), residues: 0 loop : 0.00 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 228 TYR 0.013 0.002 TYR A 421 PHE 0.019 0.001 PHE B 265 TRP 0.017 0.001 TRP B 446 HIS 0.002 0.001 HIS B 508 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7342) covalent geometry : angle 0.59056 (10044) hydrogen bonds : bond 0.03466 ( 484) hydrogen bonds : angle 4.33742 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.82 seconds wall clock time: 38 minutes 21.67 seconds (2301.67 seconds total)