Starting phenix.real_space_refine on Tue Aug 4 21:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8h_36070/08_2026/8j8h_36070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8h_36070/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j8h_36070/08_2026/8j8h_36070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8h_36070/08_2026/8j8h_36070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j8h_36070/08_2026/8j8h_36070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8h_36070/08_2026/8j8h_36070.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 1.29, per 1000 atoms: 0.19 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: 0.47 Conformation dependent library (CDL) restraints added in 256.1 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: 0.62 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: 0.73 Time building geometry restraints manager: 0.62 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: 1.560 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.060 ------------------------------------------------------------------------------- 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= 0.254 Angle : 0.731 14.547 9787 Z= 0.450 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 0.73112 / 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 : 0.187 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.0490 time to fit residues: 6.4124 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 : 0.144 ------------------------------------------------------------------------------- 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 = 0.105443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.084713 restraints weight = 19439.832| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 5.07 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 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 = 0.3437 r_free = 0.3437 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: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7122 Z= 0.170 Angle : 0.693 11.898 9787 Z= 0.358 Chirality : 0.048 0.215 1050 Planarity : 0.004 0.047 1106 Dihedral : 18.987 143.701 1280 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.31 % Allowed : 27.62 % Favored : 67.07 % 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 : -1.37 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 186 TYR 0.016 0.001 TYR A 104 PHE 0.018 0.001 PHE B 411 TRP 0.017 0.002 TRP A 320 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 7122) covalent geometry : angle 0.69275 / 0.36 ( 9787) hydrogen bonds : bond 0.06809 / 4.40 ( 213) hydrogen bonds : angle 6.26973 / 4.29 ( 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 126 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: A 436 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6618 (mm-30) REVERT: A 444 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 476 GLU cc_start: 0.8018 (pm20) cc_final: 0.7720 (pm20) REVERT: B 191 ASP cc_start: 0.8720 (t0) cc_final: 0.8461 (t0) REVERT: B 336 MET cc_start: 0.7703 (tpp) cc_final: 0.7475 (tpp) outliers start: 35 outliers final: 18 residues processed: 111 average time/residue: 0.0499 time to fit residues: 8.1885 Evaluate side-chains 102 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 248 ILE 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 Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.0060 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.105530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.084907 restraints weight = 19348.362| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 5.08 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 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 = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1295 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= 0.154 Angle : 0.658 12.522 9787 Z= 0.335 Chirality : 0.047 0.257 1050 Planarity : 0.004 0.045 1106 Dihedral : 18.800 142.327 1277 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.40 % Allowed : 28.38 % Favored : 67.22 % 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: -1.87 (0.29), residues: 732 helix: -0.98 (0.32), residues: 212 sheet: -1.02 (0.42), residues: 150 loop : -1.42 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.019 0.001 TYR A 104 PHE 0.021 0.001 PHE B 411 TRP 0.019 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 7122) covalent geometry : angle 0.65781 / 0.34 ( 9787) hydrogen bonds : bond 0.05555 / 3.61 ( 213) hydrogen bonds : angle 5.84665 / 4.01 ( 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 112 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6549 (pmm) cc_final: 0.6272 (pmm) REVERT: A 95 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6982 (mm-30) REVERT: A 289 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: A 436 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6574 (mm-30) REVERT: A 444 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 476 GLU cc_start: 0.7980 (pm20) cc_final: 0.7640 (pm20) REVERT: B 307 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (mmmt) REVERT: B 336 MET cc_start: 0.7659 (tpp) cc_final: 0.7381 (tpp) outliers start: 29 outliers final: 17 residues processed: 100 average time/residue: 0.0571 time to fit residues: 8.4848 Evaluate side-chains 99 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 470 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 328 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: 7.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.0020 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 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 = 0.3803 r_free = 0.3803 target = 0.104222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083206 restraints weight = 19835.495| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 5.14 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 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 = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7122 Z= 0.185 Angle : 0.655 12.599 9787 Z= 0.335 Chirality : 0.047 0.293 1050 Planarity : 0.004 0.044 1106 Dihedral : 18.782 142.333 1277 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.31 % Allowed : 27.16 % 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: -1.82 (0.29), residues: 732 helix: -0.94 (0.33), residues: 212 sheet: -0.98 (0.44), residues: 145 loop : -1.40 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.019 0.001 TYR A 104 PHE 0.021 0.001 PHE B 305 TRP 0.019 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 7122) covalent geometry : angle 0.65470 / 0.34 ( 9787) hydrogen bonds : bond 0.04867 / 3.17 ( 213) hydrogen bonds : angle 5.63860 / 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 120 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6659 (pmm) cc_final: 0.6410 (pmm) REVERT: A 95 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6985 (mm-30) REVERT: A 289 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: A 436 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6401 (mm-30) REVERT: A 444 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 476 GLU cc_start: 0.8001 (pm20) cc_final: 0.7642 (pm20) REVERT: B 191 ASP cc_start: 0.8744 (t0) cc_final: 0.8469 (t0) outliers start: 35 outliers final: 22 residues processed: 107 average time/residue: 0.0526 time to fit residues: 8.2638 Evaluate side-chains 101 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 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 328 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 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 = 0.3831 r_free = 0.3831 target = 0.106141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085093 restraints weight = 19869.663| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 5.15 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 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: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1655 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= 0.139 Angle : 0.649 12.798 9787 Z= 0.330 Chirality : 0.047 0.228 1050 Planarity : 0.004 0.043 1106 Dihedral : 18.696 141.926 1277 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.86 % Allowed : 28.07 % Favored : 67.07 % 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: -1.81 (0.29), residues: 732 helix: -0.84 (0.33), residues: 212 sheet: -1.12 (0.44), residues: 140 loop : -1.38 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.019 0.001 TYR B 416 PHE 0.014 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 0.00299 / 0.14 ( 7122) covalent geometry : angle 0.64900 / 0.33 ( 9787) hydrogen bonds : bond 0.04536 / 2.97 ( 213) hydrogen bonds : angle 5.49730 / 3.79 ( 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 113 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6638 (pmm) cc_final: 0.6396 (pmm) REVERT: A 289 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: A 436 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6307 (mm-30) REVERT: A 444 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 476 GLU cc_start: 0.8055 (pm20) cc_final: 0.7655 (pm20) REVERT: B 274 GLU cc_start: 0.8873 (mp0) cc_final: 0.8620 (mp0) outliers start: 32 outliers final: 21 residues processed: 104 average time/residue: 0.0494 time to fit residues: 7.5243 Evaluate side-chains 100 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 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 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 328 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 0.0770 chunk 51 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.107258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086115 restraints weight = 19608.444| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 5.22 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1836 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= 0.125 Angle : 0.637 13.309 9787 Z= 0.325 Chirality : 0.047 0.216 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.619 141.265 1277 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.31 % Allowed : 27.77 % 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: -1.78 (0.30), residues: 732 helix: -0.81 (0.33), residues: 209 sheet: -1.23 (0.44), residues: 135 loop : -1.31 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 250 TYR 0.021 0.001 TYR B 416 PHE 0.015 0.001 PHE B 305 TRP 0.030 0.001 TRP A 320 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 7122) covalent geometry : angle 0.63702 / 0.32 ( 9787) hydrogen bonds : bond 0.04201 / 2.77 ( 213) hydrogen bonds : angle 5.38533 / 3.73 ( 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 121 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6602 (pmm) cc_final: 0.6343 (pmm) REVERT: A 289 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: A 316 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5948 (tp30) REVERT: A 436 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6020 (mm-30) REVERT: A 444 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7295 (tm-30) REVERT: A 476 GLU cc_start: 0.8061 (pm20) cc_final: 0.7624 (pm20) REVERT: B 191 ASP cc_start: 0.8872 (t0) cc_final: 0.8598 (t0) REVERT: B 274 GLU cc_start: 0.8839 (mp0) cc_final: 0.8609 (mp0) outliers start: 35 outliers final: 20 residues processed: 110 average time/residue: 0.0500 time to fit residues: 8.1951 Evaluate side-chains 102 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 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 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 277 MET Chi-restraints excluded: chain B residue 329 LEU 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: 2.9990 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3829 r_free = 0.3829 target = 0.105319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.084601 restraints weight = 19409.940| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 5.00 r_work (final): 0.3440 ------------------------------------------------------------------------------- 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 = 0.55 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 = 0.54 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: 0.7757 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7122 Z= 0.198 Angle : 0.669 13.378 9787 Z= 0.341 Chirality : 0.046 0.206 1050 Planarity : 0.004 0.042 1106 Dihedral : 18.692 142.147 1277 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.16 % Allowed : 28.68 % Favored : 66.16 % 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: -1.76 (0.30), residues: 732 helix: -0.72 (0.34), residues: 209 sheet: -1.21 (0.44), residues: 145 loop : -1.35 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 275 TYR 0.022 0.001 TYR B 416 PHE 0.018 0.001 PHE B 411 TRP 0.023 0.002 TRP A 320 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 ( 7122) covalent geometry : angle 0.66900 / 0.34 ( 9787) hydrogen bonds : bond 0.04233 / 2.75 ( 213) hydrogen bonds : angle 5.39101 / 3.74 ( 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 : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6638 (pmm) cc_final: 0.6392 (pmm) REVERT: A 289 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: A 316 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5876 (tp30) REVERT: A 334 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: A 436 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6379 (mm-30) REVERT: A 444 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 476 GLU cc_start: 0.8049 (pm20) cc_final: 0.7600 (pm20) REVERT: B 274 GLU cc_start: 0.8891 (mp0) cc_final: 0.8627 (mp0) outliers start: 34 outliers final: 26 residues processed: 101 average time/residue: 0.0558 time to fit residues: 8.0720 Evaluate side-chains 109 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 316 GLU Chi-restraints excluded: chain A residue 334 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 A residue 507 ILE 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 Chi-restraints excluded: chain B residue 398 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3854 r_free = 0.3854 target = 0.106971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085820 restraints weight = 19626.122| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 5.17 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7122 Z= 0.127 Angle : 0.660 13.991 9787 Z= 0.334 Chirality : 0.046 0.209 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.624 141.188 1277 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.61 % Allowed : 28.83 % Favored : 65.55 % 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: -1.69 (0.30), residues: 732 helix: -0.61 (0.34), residues: 208 sheet: -1.20 (0.45), residues: 140 loop : -1.32 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.018 0.001 TYR B 416 PHE 0.023 0.001 PHE B 411 TRP 0.033 0.002 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 7122) covalent geometry : angle 0.65998 / 0.33 ( 9787) hydrogen bonds : bond 0.03906 / 2.59 ( 213) hydrogen bonds : angle 5.23634 / 3.61 ( 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 125 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.147 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: 0.6345 (pmm) REVERT: A 289 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: A 316 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5727 (tp30) REVERT: A 436 GLU cc_start: 0.6660 (mm-30) cc_final: 0.5973 (mm-30) REVERT: A 444 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 476 GLU cc_start: 0.8141 (pm20) cc_final: 0.7752 (pm20) REVERT: B 191 ASP cc_start: 0.8772 (t0) cc_final: 0.8502 (t0) REVERT: B 274 GLU cc_start: 0.8791 (mp0) cc_final: 0.8476 (mp0) REVERT: B 336 MET cc_start: 0.7506 (tpp) cc_final: 0.6995 (mmm) outliers start: 37 outliers final: 21 residues processed: 115 average time/residue: 0.0557 time to fit residues: 9.1996 Evaluate side-chains 109 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR 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 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 277 MET Chi-restraints excluded: chain B residue 320 HIS 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 398 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3878 r_free = 0.3878 target = 0.107838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.086405 restraints weight = 19705.956| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 5.31 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 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: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2181 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= 0.139 Angle : 0.660 14.323 9787 Z= 0.335 Chirality : 0.046 0.197 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.643 141.148 1277 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.64 % Allowed : 30.96 % Favored : 65.40 % 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: -1.68 (0.30), residues: 732 helix: -0.64 (0.34), residues: 208 sheet: -1.25 (0.44), residues: 142 loop : -1.27 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 283 TYR 0.017 0.001 TYR A 104 PHE 0.016 0.001 PHE B 411 TRP 0.029 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7122) covalent geometry : angle 0.65955 / 0.33 ( 9787) hydrogen bonds : bond 0.03831 / 2.54 ( 213) hydrogen bonds : angle 5.19542 / 3.58 ( 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: 24 poor density : 82 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6569 (pmm) cc_final: 0.6327 (pmm) REVERT: A 289 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 316 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5809 (tp30) REVERT: A 436 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6026 (mm-30) REVERT: A 444 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 476 GLU cc_start: 0.8134 (pm20) cc_final: 0.7710 (pm20) REVERT: B 274 GLU cc_start: 0.8846 (mp0) cc_final: 0.8619 (mp0) REVERT: B 336 MET cc_start: 0.7440 (tpp) cc_final: 0.6938 (mmm) outliers start: 24 outliers final: 19 residues processed: 97 average time/residue: 0.0560 time to fit residues: 7.8034 Evaluate side-chains 100 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR 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 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 329 LEU 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: 1.9990 chunk 45 optimal weight: 0.0470 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3856 r_free = 0.3856 target = 0.107366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085921 restraints weight = 19615.347| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 5.24 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2238 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= 0.140 Angle : 0.668 14.550 9787 Z= 0.339 Chirality : 0.046 0.199 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.662 141.040 1277 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.03 % Allowed : 31.87 % 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: -1.67 (0.30), residues: 732 helix: -0.68 (0.34), residues: 208 sheet: -1.15 (0.45), residues: 140 loop : -1.27 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 283 TYR 0.020 0.001 TYR B 416 PHE 0.014 0.001 PHE B 411 TRP 0.033 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 7122) covalent geometry : angle 0.66777 / 0.34 ( 9787) hydrogen bonds : bond 0.03800 / 2.51 ( 213) hydrogen bonds : angle 5.22006 / 3.62 ( 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 98 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6581 (pmm) cc_final: 0.6340 (pmm) REVERT: A 289 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 436 GLU cc_start: 0.6709 (mm-30) cc_final: 0.5985 (mm-30) REVERT: A 444 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 476 GLU cc_start: 0.8152 (pm20) cc_final: 0.7726 (pm20) REVERT: B 191 ASP cc_start: 0.8929 (t0) cc_final: 0.8672 (t0) REVERT: B 274 GLU cc_start: 0.8824 (mp0) cc_final: 0.8602 (mp0) REVERT: B 416 TYR cc_start: 0.7938 (p90) cc_final: 0.7703 (p90) outliers start: 20 outliers final: 18 residues processed: 92 average time/residue: 0.0537 time to fit residues: 7.2651 Evaluate side-chains 96 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 121 PHE 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 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 277 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 335 LEU 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 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3885 r_free = 0.3885 target = 0.108710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.087235 restraints weight = 19556.950| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 5.34 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2331 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= 0.134 Angle : 0.652 14.615 9787 Z= 0.332 Chirality : 0.046 0.198 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.662 140.851 1277 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.19 % Allowed : 31.56 % 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: -1.64 (0.30), residues: 732 helix: -0.65 (0.34), residues: 208 sheet: -1.12 (0.45), residues: 140 loop : -1.27 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.017 0.001 TYR B 416 PHE 0.014 0.001 PHE B 411 TRP 0.033 0.002 TRP A 320 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7122) covalent geometry : angle 0.65226 / 0.33 ( 9787) hydrogen bonds : bond 0.03647 / 2.41 ( 213) hydrogen bonds : angle 5.15576 / 3.56 ( 578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1112.72 seconds wall clock time: 19 minutes 52.58 seconds (1192.58 seconds total)