Starting phenix.real_space_refine on Thu Jul 2 05:28:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8h_36070/07_2026/8j8h_36070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8h_36070/07_2026/8j8h_36070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8h_36070/07_2026/8j8h_36070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8h_36070/07_2026/8j8h_36070.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8h_36070/07_2026/8j8h_36070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8h_36070/07_2026/8j8h_36070.cif" } resolution = 3.4 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= 0.016 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: 6 Type Number sf(0) Gaussians P 39 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 4316 2.51 5 N 1167 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6868 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3651 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 25, 'TRANS': 426} Chain breaks: 1 Chain: "B" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2421 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain: "E" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 403 Classifications: {'DNA': 13, 'RNA': 7} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 392 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.71, per 1000 atoms: 0.25 Number of scatterers: 6868 At special positions: 0 Unit cell: (84, 79.8, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 39 15.00 Mg 1 11.99 O 1327 8.00 N 1167 7.00 C 4316 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: 0.43 Conformation dependent library (CDL) restraints added in 393.2 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 11 sheets defined 31.8% alpha, 15.6% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.747A pdb=" N ALA A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 61 removed outlier: 3.641A pdb=" N LYS A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.546A pdb=" N ILE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.050A pdb=" N TYR A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.496A pdb=" N ARG A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.188A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.591A pdb=" N VAL A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 4.211A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 removed outlier: 3.899A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.597A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.510A pdb=" N PHE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.510A pdb=" N GLY B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.562A pdb=" N PHE B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 282 removed outlier: 7.119A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE A 412 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU A 3 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS A 2 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.892A pdb=" N LYS A 270 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 5.827A pdb=" N SER A 41 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.684A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.532A pdb=" N VAL B 334 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 286 Processing sheet with id=AB1, first strand: chain 'B' and resid 283 through 286 Processing sheet with id=AB2, first strand: chain 'B' and resid 390 through 394 197 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.58 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: 1718 1.33 - 1.45: 1554 1.45 - 1.57: 3745 1.57 - 1.69: 77 1.69 - 1.81: 28 Bond restraints: 7122 Sorted by residual: bond pdb=" CB PRO B 419 " pdb=" CG PRO B 419 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.98e+00 bond pdb=" C3' DA F 16 " pdb=" C2' DA F 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.28e+00 bond pdb=" C3' DC F 22 " pdb=" C2' DC F 22 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.45e+00 bond pdb=" C1' DC F 22 " pdb=" N1 DC F 22 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.05e+00 bond pdb=" C2' DC F 22 " pdb=" C1' DC F 22 " ideal model delta sigma weight residual 1.518 1.540 -0.022 1.00e-02 1.00e+04 4.95e+00 ... (remaining 7117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 9694 2.91 - 5.82: 79 5.82 - 8.73: 9 8.73 - 11.64: 2 11.64 - 14.55: 3 Bond angle restraints: 9787 Sorted by residual: angle pdb=" CA PRO B 419 " pdb=" N PRO B 419 " pdb=" CD PRO B 419 " ideal model delta sigma weight residual 112.00 99.90 12.10 1.40e+00 5.10e-01 7.47e+01 angle pdb=" O4' U E 17 " pdb=" C1' U E 17 " pdb=" N1 U E 17 " ideal model delta sigma weight residual 108.50 114.04 -5.54 7.00e-01 2.04e+00 6.27e+01 angle pdb=" O4' U E 1 " pdb=" C1' U E 1 " pdb=" N1 U E 1 " ideal model delta sigma weight residual 108.50 113.60 -5.10 7.00e-01 2.04e+00 5.32e+01 angle pdb=" CA PRO A 241 " pdb=" N PRO A 241 " pdb=" CD PRO A 241 " ideal model delta sigma weight residual 112.00 105.55 6.45 1.40e+00 5.10e-01 2.12e+01 angle pdb=" O5' U E 8 " pdb=" C5' U E 8 " pdb=" C4' U E 8 " ideal model delta sigma weight residual 109.40 112.75 -3.35 8.00e-01 1.56e+00 1.75e+01 ... (remaining 9782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.87: 3797 28.87 - 57.75: 384 57.75 - 86.62: 29 86.62 - 115.49: 2 115.49 - 144.37: 3 Dihedral angle restraints: 4215 sinusoidal: 2047 harmonic: 2168 Sorted by residual: dihedral pdb=" C4' DA F 9 " pdb=" C3' DA F 9 " pdb=" O3' DA F 9 " pdb=" P A DG F 10 " ideal model delta sinusoidal sigma weight residual 220.00 75.63 144.37 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA LYS B 328 " pdb=" C LYS B 328 " pdb=" N LEU B 329 " pdb=" CA LEU B 329 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C4' DA F 16 " pdb=" C3' DA F 16 " pdb=" O3' DA F 16 " pdb=" P DG F 17 " ideal model delta sinusoidal sigma weight residual 220.00 82.66 137.34 1 3.50e+01 8.16e-04 1.36e+01 ... (remaining 4212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 828 0.054 - 0.108: 186 0.108 - 0.162: 31 0.162 - 0.215: 1 0.215 - 0.269: 4 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1' U E 17 " pdb=" O4' U E 17 " pdb=" C2' U E 17 " pdb=" N1 U E 17 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1' U E 1 " pdb=" O4' U E 1 " pdb=" C2' U E 1 " pdb=" N1 U E 1 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1047 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 418 " 0.056 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO B 419 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 419 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 419 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 240 " -0.040 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 241 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 320 " -0.014 2.00e-02 2.50e+03 1.33e-02 4.41e+00 pdb=" CG TRP A 320 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 320 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 320 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 320 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 320 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 320 " -0.001 2.00e-02 2.50e+03 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 81 2.51 - 3.11: 5082 3.11 - 3.71: 11814 3.71 - 4.30: 15642 4.30 - 4.90: 24702 Nonbonded interactions: 57321 Sorted by model distance: nonbonded pdb=" OP1 A E 3 " pdb="MG MG A 601 " model vdw 1.914 2.170 nonbonded pdb=" ND2 ASN A 468 " pdb="MG MG A 601 " model vdw 2.096 2.250 nonbonded pdb=" OG SER A 11 " pdb=" O CYS A 20 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASN A 468 " pdb="MG MG A 601 " model vdw 2.238 2.170 nonbonded pdb=" O TYR A 328 " pdb=" ND1 HIS A 329 " model vdw 2.254 3.120 ... (remaining 57316 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=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.660 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.004 0.158 7122 Z= 0.253 Angle : 0.730 14.547 9787 Z= 0.449 Chirality : 0.048 0.269 1050 Planarity : 0.005 0.079 1106 Dihedral : 20.214 144.365 2817 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.61 % Allowed : 33.69 % Favored : 65.71 % 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: -1.54 (0.31), residues: 732 helix: -0.66 (0.39), residues: 185 sheet: -0.98 (0.44), residues: 140 loop : -1.17 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.017 0.001 TYR B 416 PHE 0.017 0.001 PHE B 411 TRP 0.035 0.002 TRP A 320 HIS 0.003 0.000 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.25 ( 7122) covalent geometry : angle 0.73036 / 0.45 ( 9787) hydrogen bonds : bond 0.27968 / 18.43 ( 213) hydrogen bonds : angle 9.20553 / 6.27 ( 578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.255 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.0474 time to fit residues: 6.1690 Evaluate side-chains 83 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 349 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN B 349 ASN B 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.105407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084689 restraints weight = 19433.765| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 5.06 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 7122 Z= 0.170 Angle : 0.685 11.914 9787 Z= 0.355 Chirality : 0.047 0.190 1050 Planarity : 0.004 0.047 1106 Dihedral : 18.996 144.405 1280 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.55 % Allowed : 28.53 % Favored : 66.92 % 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: -1.79 (0.29), residues: 732 helix: -1.00 (0.32), residues: 210 sheet: -0.87 (0.44), residues: 142 loop : -1.36 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.017 0.001 TYR A 104 PHE 0.018 0.001 PHE B 411 TRP 0.019 0.002 TRP A 320 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 7122) covalent geometry : angle 0.68515 / 0.36 ( 9787) hydrogen bonds : bond 0.07158 / 4.63 ( 213) hydrogen bonds : angle 6.30180 / 4.32 ( 578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: A 436 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6609 (mm-30) REVERT: A 444 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 476 GLU cc_start: 0.8015 (pm20) cc_final: 0.7736 (pm20) REVERT: B 191 ASP cc_start: 0.8719 (t0) cc_final: 0.8461 (t0) REVERT: B 336 MET cc_start: 0.7697 (tpp) cc_final: 0.7472 (tpp) outliers start: 30 outliers final: 16 residues processed: 109 average time/residue: 0.0462 time to fit residues: 7.3875 Evaluate side-chains 98 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 328 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 0.0670 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.104766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084114 restraints weight = 19276.059| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 5.01 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7122 Z= 0.190 Angle : 0.672 12.413 9787 Z= 0.343 Chirality : 0.047 0.241 1050 Planarity : 0.004 0.046 1106 Dihedral : 18.860 143.344 1277 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.16 % Allowed : 27.47 % Favored : 67.37 % 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: -1.89 (0.29), residues: 732 helix: -0.99 (0.32), residues: 212 sheet: -1.07 (0.44), residues: 142 loop : -1.43 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.020 0.001 TYR A 104 PHE 0.017 0.001 PHE B 411 TRP 0.019 0.001 TRP A 320 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 7122) covalent geometry : angle 0.67198 / 0.34 ( 9787) hydrogen bonds : bond 0.05540 / 3.58 ( 213) hydrogen bonds : angle 5.83469 / 4.02 ( 578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 289 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: A 436 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6398 (mm-30) REVERT: A 444 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 476 GLU cc_start: 0.7991 (pm20) cc_final: 0.7648 (pm20) REVERT: B 307 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8659 (mmmt) outliers start: 34 outliers final: 21 residues processed: 104 average time/residue: 0.0481 time to fit residues: 7.3804 Evaluate side-chains 105 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.103694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082857 restraints weight = 19540.116| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 5.02 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7122 Z= 0.193 Angle : 0.667 11.395 9787 Z= 0.341 Chirality : 0.047 0.280 1050 Planarity : 0.004 0.044 1106 Dihedral : 18.819 143.281 1277 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.77 % Allowed : 26.86 % Favored : 67.37 % 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: -1.90 (0.29), residues: 732 helix: -0.94 (0.33), residues: 212 sheet: -1.14 (0.45), residues: 140 loop : -1.44 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 275 TYR 0.020 0.001 TYR A 104 PHE 0.021 0.001 PHE B 411 TRP 0.020 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 7122) covalent geometry : angle 0.66695 / 0.34 ( 9787) hydrogen bonds : bond 0.04896 / 3.18 ( 213) hydrogen bonds : angle 5.64794 / 3.89 ( 578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6710 (pmm) cc_final: 0.6466 (pmm) REVERT: A 95 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6811 (mm-30) REVERT: A 289 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: A 436 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6480 (mm-30) REVERT: A 444 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 476 GLU cc_start: 0.7998 (pm20) cc_final: 0.7608 (pm20) REVERT: B 191 ASP cc_start: 0.8783 (t0) cc_final: 0.8516 (t0) outliers start: 38 outliers final: 24 residues processed: 110 average time/residue: 0.0477 time to fit residues: 7.7541 Evaluate side-chains 104 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 74 optimal weight: 10.9990 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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 = 0.3821 r_free = 0.3821 target = 0.105175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084174 restraints weight = 19600.539| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 5.12 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7122 Z= 0.150 Angle : 0.656 14.019 9787 Z= 0.335 Chirality : 0.047 0.219 1050 Planarity : 0.004 0.043 1106 Dihedral : 18.729 142.863 1277 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.55 % Allowed : 27.92 % Favored : 67.53 % 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: -1.86 (0.30), residues: 732 helix: -0.89 (0.33), residues: 209 sheet: -1.20 (0.45), residues: 140 loop : -1.38 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 382 TYR 0.022 0.001 TYR B 416 PHE 0.020 0.001 PHE B 305 TRP 0.023 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 7122) covalent geometry : angle 0.65620 / 0.33 ( 9787) hydrogen bonds : bond 0.04547 / 2.97 ( 213) hydrogen bonds : angle 5.56505 / 3.85 ( 578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6617 (pmm) cc_final: 0.6386 (pmm) REVERT: A 86 TRP cc_start: 0.7777 (t60) cc_final: 0.7514 (t60) REVERT: A 289 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: A 436 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6291 (mm-30) REVERT: A 444 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 476 GLU cc_start: 0.8036 (pm20) cc_final: 0.7619 (pm20) REVERT: B 273 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: B 274 GLU cc_start: 0.8843 (mp0) cc_final: 0.8531 (mp0) outliers start: 30 outliers final: 22 residues processed: 103 average time/residue: 0.0525 time to fit residues: 7.8301 Evaluate side-chains 106 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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 = 0.3826 r_free = 0.3826 target = 0.105448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084502 restraints weight = 19350.415| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 5.04 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7122 Z= 0.147 Angle : 0.641 13.107 9787 Z= 0.328 Chirality : 0.046 0.210 1050 Planarity : 0.004 0.042 1106 Dihedral : 18.692 142.620 1277 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.01 % Allowed : 27.31 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.30), residues: 732 helix: -0.81 (0.34), residues: 209 sheet: -1.26 (0.45), residues: 140 loop : -1.37 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 250 TYR 0.020 0.001 TYR B 416 PHE 0.019 0.001 PHE B 305 TRP 0.025 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 7122) covalent geometry : angle 0.64098 / 0.33 ( 9787) hydrogen bonds : bond 0.04220 / 2.76 ( 213) hydrogen bonds : angle 5.43049 / 3.76 ( 578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6603 (pmm) cc_final: 0.6370 (pmm) REVERT: A 86 TRP cc_start: 0.7813 (t60) cc_final: 0.7483 (t60) REVERT: A 289 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: A 316 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6191 (tp30) REVERT: A 368 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8721 (pp20) REVERT: A 436 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6065 (mm-30) REVERT: A 444 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 476 GLU cc_start: 0.8024 (pm20) cc_final: 0.7584 (pm20) REVERT: B 191 ASP cc_start: 0.8814 (t0) cc_final: 0.8549 (t0) REVERT: B 273 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: B 274 GLU cc_start: 0.8845 (mp0) cc_final: 0.8613 (mp0) outliers start: 33 outliers final: 24 residues processed: 105 average time/residue: 0.0508 time to fit residues: 7.8769 Evaluate side-chains 104 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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 = 0.3833 r_free = 0.3833 target = 0.106078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085144 restraints weight = 19195.494| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.98 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7122 Z= 0.141 Angle : 0.641 13.696 9787 Z= 0.327 Chirality : 0.046 0.200 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.680 142.426 1277 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.16 % Allowed : 28.83 % Favored : 66.01 % 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: -1.79 (0.30), residues: 732 helix: -0.71 (0.34), residues: 209 sheet: -1.33 (0.45), residues: 140 loop : -1.34 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.021 0.001 TYR B 416 PHE 0.018 0.001 PHE B 305 TRP 0.028 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7122) covalent geometry : angle 0.64060 / 0.33 ( 9787) hydrogen bonds : bond 0.04013 / 2.63 ( 213) hydrogen bonds : angle 5.36025 / 3.71 ( 578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6612 (pmm) cc_final: 0.6367 (pmm) REVERT: A 86 TRP cc_start: 0.7806 (t60) cc_final: 0.7590 (t60) REVERT: A 289 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: A 316 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6047 (tp30) REVERT: A 436 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6165 (mm-30) REVERT: A 444 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 476 GLU cc_start: 0.8061 (pm20) cc_final: 0.7599 (pm20) REVERT: B 273 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: B 274 GLU cc_start: 0.8865 (mp0) cc_final: 0.8620 (mp0) REVERT: B 336 MET cc_start: 0.7610 (tpp) cc_final: 0.7164 (mmm) outliers start: 34 outliers final: 23 residues processed: 104 average time/residue: 0.0551 time to fit residues: 8.3817 Evaluate side-chains 106 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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 = 0.3844 r_free = 0.3844 target = 0.106310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085282 restraints weight = 19323.124| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 5.08 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7122 Z= 0.134 Angle : 0.644 13.992 9787 Z= 0.327 Chirality : 0.046 0.194 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.690 142.107 1277 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.70 % Allowed : 29.44 % Favored : 65.86 % 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: -1.72 (0.30), residues: 732 helix: -0.66 (0.34), residues: 208 sheet: -1.24 (0.45), residues: 138 loop : -1.32 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 250 TYR 0.018 0.001 TYR A 104 PHE 0.023 0.001 PHE B 411 TRP 0.030 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7122) covalent geometry : angle 0.64439 / 0.33 ( 9787) hydrogen bonds : bond 0.03901 / 2.56 ( 213) hydrogen bonds : angle 5.28855 / 3.65 ( 578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6588 (pmm) cc_final: 0.6347 (pmm) REVERT: A 86 TRP cc_start: 0.7838 (t60) cc_final: 0.7615 (t60) REVERT: A 289 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: A 316 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5875 (tp30) REVERT: A 436 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6083 (mm-30) REVERT: A 444 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 476 GLU cc_start: 0.8092 (pm20) cc_final: 0.7598 (pm20) REVERT: B 191 ASP cc_start: 0.8823 (t0) cc_final: 0.8555 (t0) REVERT: B 273 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: B 274 GLU cc_start: 0.8854 (mp0) cc_final: 0.8649 (mp0) REVERT: B 414 MET cc_start: 0.6517 (mmt) cc_final: 0.6244 (tpp) outliers start: 31 outliers final: 22 residues processed: 105 average time/residue: 0.0619 time to fit residues: 9.2821 Evaluate side-chains 105 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 398 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.108073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087348 restraints weight = 19357.857| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 5.03 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7122 Z= 0.131 Angle : 0.653 14.435 9787 Z= 0.331 Chirality : 0.046 0.185 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.689 141.636 1277 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.95 % Allowed : 30.80 % Favored : 65.25 % 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: -1.70 (0.30), residues: 732 helix: -0.68 (0.34), residues: 209 sheet: -1.19 (0.45), residues: 138 loop : -1.30 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.018 0.001 TYR B 416 PHE 0.016 0.001 PHE B 305 TRP 0.038 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7122) covalent geometry : angle 0.65308 / 0.33 ( 9787) hydrogen bonds : bond 0.03801 / 2.51 ( 213) hydrogen bonds : angle 5.24598 / 3.64 ( 578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6584 (pmm) cc_final: 0.6340 (pmm) REVERT: A 289 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: A 316 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5688 (tp30) REVERT: A 436 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6194 (mm-30) REVERT: A 444 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 476 GLU cc_start: 0.8124 (pm20) cc_final: 0.7706 (pm20) REVERT: B 273 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: B 274 GLU cc_start: 0.8801 (mp0) cc_final: 0.8591 (mp0) REVERT: B 345 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8486 (tmm) REVERT: B 346 ASP cc_start: 0.8862 (p0) cc_final: 0.8482 (p0) REVERT: B 414 MET cc_start: 0.6276 (mmt) cc_final: 0.5995 (tpp) outliers start: 26 outliers final: 18 residues processed: 98 average time/residue: 0.0557 time to fit residues: 7.9082 Evaluate side-chains 101 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 398 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 0.0030 chunk 2 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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 = 0.3888 r_free = 0.3888 target = 0.108591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087832 restraints weight = 19295.215| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 5.06 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7122 Z= 0.126 Angle : 0.658 14.592 9787 Z= 0.333 Chirality : 0.046 0.182 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.694 141.341 1277 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.64 % Allowed : 31.71 % Favored : 64.64 % 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: -1.65 (0.30), residues: 732 helix: -0.64 (0.34), residues: 209 sheet: -1.22 (0.45), residues: 133 loop : -1.25 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 250 TYR 0.017 0.001 TYR B 416 PHE 0.015 0.001 PHE B 305 TRP 0.030 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 7122) covalent geometry : angle 0.65796 / 0.33 ( 9787) hydrogen bonds : bond 0.03731 / 2.47 ( 213) hydrogen bonds : angle 5.20986 / 3.61 ( 578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6574 (pmm) cc_final: 0.6332 (pmm) REVERT: A 95 GLU cc_start: 0.7053 (tp30) cc_final: 0.6816 (mm-30) REVERT: A 289 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: A 436 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6213 (mm-30) REVERT: A 444 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 476 GLU cc_start: 0.8119 (pm20) cc_final: 0.7699 (pm20) REVERT: B 273 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: B 274 GLU cc_start: 0.8774 (mp0) cc_final: 0.8566 (mp0) REVERT: B 345 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8486 (tmm) REVERT: B 346 ASP cc_start: 0.8772 (p0) cc_final: 0.8422 (p0) REVERT: B 414 MET cc_start: 0.6336 (mmt) cc_final: 0.6078 (tpp) outliers start: 24 outliers final: 19 residues processed: 99 average time/residue: 0.0588 time to fit residues: 8.2831 Evaluate side-chains 101 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** 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 = 0.3884 r_free = 0.3884 target = 0.108089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087530 restraints weight = 19386.328| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 4.99 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7122 Z= 0.132 Angle : 0.654 14.714 9787 Z= 0.333 Chirality : 0.046 0.181 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.710 141.310 1277 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.49 % Allowed : 31.41 % Favored : 65.10 % 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: -1.60 (0.30), residues: 732 helix: -0.56 (0.34), residues: 209 sheet: -1.21 (0.45), residues: 133 loop : -1.23 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 250 TYR 0.018 0.001 TYR B 416 PHE 0.015 0.001 PHE B 305 TRP 0.035 0.002 TRP A 320 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7122) covalent geometry : angle 0.65416 / 0.33 ( 9787) hydrogen bonds : bond 0.03622 / 2.38 ( 213) hydrogen bonds : angle 5.17281 / 3.57 ( 578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1074.60 seconds wall clock time: 19 minutes 15.48 seconds (1155.48 seconds total)