Starting phenix.real_space_refine on Thu Jul 2 08:44:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9g_36095/07_2026/8j9g_36095.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9g_36095/07_2026/8j9g_36095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9g_36095/07_2026/8j9g_36095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9g_36095/07_2026/8j9g_36095.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9g_36095/07_2026/8j9g_36095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9g_36095/07_2026/8j9g_36095.cif" } resolution = 3.5 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= 0.014 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 24 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 5006 2.51 5 N 1318 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s 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: 7868 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "B" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3759 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "E" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 244 Classifications: {'DNA': 9, 'RNA': 3} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 246 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} 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: 1.42, per 1000 atoms: 0.18 Number of scatterers: 7868 At special positions: 0 Unit cell: (91.35, 92.4, 131.25, 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 22 16.00 P 24 15.00 Mg 1 11.99 O 1497 8.00 N 1318 7.00 C 5006 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: 0.50 Conformation dependent library (CDL) restraints added in 252.5 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 33.4% alpha, 13.4% beta 6 base pairs and 11 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 30 Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.592A pdb=" N ASP A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 109 through 132 removed outlier: 4.305A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.883A pdb=" N GLU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.501A pdb=" N ALA A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.679A pdb=" N ALA A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.792A pdb=" N LYS A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.953A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 29 removed outlier: 4.188A pdb=" N TRP B 20 " --> pdb=" O ASP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 4.517A pdb=" N ILE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 123 through 138 removed outlier: 4.049A pdb=" N GLY B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 158 removed outlier: 3.539A pdb=" N PHE B 158 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.922A pdb=" N GLU B 237 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.738A pdb=" N LEU B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 247' Processing helix chain 'B' and resid 257 through 272 removed outlier: 3.630A pdb=" N CYS B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.820A pdb=" N ARG B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.827A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.720A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 4.132A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 450 removed outlier: 4.240A pdb=" N GLU B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.912A pdb=" N LYS A 2 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N LYS B 413 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 169 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET B 414 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS B 167 " --> pdb=" O MET B 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 7.007A pdb=" N GLY A 385 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.668A pdb=" N GLN A 18 " --> pdb=" O PHE A 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.694A pdb=" N PHE A 140 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 142 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.523A pdb=" N VAL A 284 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 300 " --> pdb=" O VAL A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 297 removed outlier: 3.717A pdb=" N GLY A 318 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.188A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.500A pdb=" N ALA B 292 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.500A pdb=" N ALA B 292 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 328 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 179 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 187 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.597A pdb=" N ILE B 208 " --> pdb=" O CYS B 215 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2266 1.34 - 1.45: 1396 1.45 - 1.57: 4365 1.57 - 1.69: 46 1.69 - 1.81: 34 Bond restraints: 8107 Sorted by residual: bond pdb=" C3' DC F 22 " pdb=" C2' DC F 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.55e+00 bond pdb=" C3' DG F 17 " pdb=" C2' DG F 17 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.80e+00 bond pdb=" C1' DC F 22 " pdb=" N1 DC F 22 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.18e+00 bond pdb=" C1' C E 7 " pdb=" N1 C E 7 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 3.91e+00 bond pdb=" C4' C E 4 " pdb=" C3' C E 4 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.00e-02 1.00e+04 3.62e+00 ... (remaining 8102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 10803 1.61 - 3.22: 221 3.22 - 4.83: 26 4.83 - 6.44: 3 6.44 - 8.05: 2 Bond angle restraints: 11055 Sorted by residual: angle pdb=" O4' U E 1 " pdb=" C1' U E 1 " pdb=" N1 U E 1 " ideal model delta sigma weight residual 108.50 113.01 -4.51 7.00e-01 2.04e+00 4.16e+01 angle pdb=" O5' U E 10 " pdb=" C5' U E 10 " pdb=" C4' U E 10 " ideal model delta sigma weight residual 109.40 112.99 -3.59 8.00e-01 1.56e+00 2.01e+01 angle pdb=" N TYR A 505 " pdb=" CA TYR A 505 " pdb=" C TYR A 505 " ideal model delta sigma weight residual 113.15 107.99 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" N3 DT F 21 " pdb=" C4 DT F 21 " pdb=" O4 DT F 21 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT F 13 " pdb=" C4 DT F 13 " pdb=" O4 DT F 13 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 11050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.74: 4383 27.74 - 55.48: 395 55.48 - 83.22: 36 83.22 - 110.96: 4 110.96 - 138.70: 2 Dihedral angle restraints: 4820 sinusoidal: 2180 harmonic: 2640 Sorted by residual: dihedral pdb=" CA ARG A 225 " pdb=" C ARG A 225 " pdb=" N GLU A 226 " pdb=" CA GLU A 226 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA PRO A 499 " pdb=" C PRO A 499 " pdb=" N PRO A 500 " pdb=" CA PRO A 500 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+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 81.30 138.70 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 4817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 944 0.049 - 0.098: 200 0.098 - 0.147: 48 0.147 - 0.196: 0 0.196 - 0.245: 2 Chirality restraints: 1194 Sorted by residual: 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 2.23 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" P U E 1 " pdb=" OP1 U E 1 " pdb=" OP2 U E 1 " pdb=" O5' U E 1 " both_signs ideal model delta sigma weight residual True 2.17 2.37 -0.20 2.00e-01 2.50e+01 9.79e-01 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 2.51 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1191 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 499 " 0.058 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 500 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 498 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 499 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 112 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C ILE B 112 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE B 112 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL B 113 " -0.008 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 108 2.58 - 3.16: 6585 3.16 - 3.74: 13629 3.74 - 4.32: 17402 4.32 - 4.90: 27712 Nonbonded interactions: 65436 Sorted by model distance: nonbonded pdb=" OP1 A E 3 " pdb="MG MG A 601 " model vdw 1.995 2.170 nonbonded pdb=" OD1 ASN A 468 " pdb="MG MG A 601 " model vdw 2.025 2.170 nonbonded pdb=" ND2 ASN A 468 " pdb="MG MG A 601 " model vdw 2.121 2.250 nonbonded pdb=" O ASN A 34 " pdb=" OH TYR A 261 " model vdw 2.153 3.040 nonbonded pdb=" OG SER B 385 " pdb=" O ASP B 387 " model vdw 2.183 3.040 ... (remaining 65431 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=0.68 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.240 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8107 Z= 0.187 Angle : 0.544 8.050 11055 Z= 0.350 Chirality : 0.043 0.245 1194 Planarity : 0.004 0.088 1322 Dihedral : 19.064 138.697 3112 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.25 % Allowed : 29.98 % Favored : 69.78 % 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: -1.46 (0.28), residues: 892 helix: 0.55 (0.34), residues: 239 sheet: -0.98 (0.43), residues: 154 loop : -1.78 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 407 TYR 0.021 0.001 TYR B 416 PHE 0.013 0.001 PHE A 93 TRP 0.006 0.001 TRP A 231 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.19 ( 8107) covalent geometry : angle 0.54450 / 0.35 (11055) hydrogen bonds : bond 0.27583 / 18.20 ( 254) hydrogen bonds : angle 9.20427 / 6.60 ( 728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 321 TYR cc_start: 0.6264 (t80) cc_final: 0.5769 (t80) REVERT: A 435 MET cc_start: 0.8705 (mmm) cc_final: 0.8035 (mmt) REVERT: A 474 ASP cc_start: 0.5790 (t0) cc_final: 0.5276 (t0) REVERT: B 1 MET cc_start: 0.6309 (pmm) cc_final: 0.6010 (ptm) REVERT: B 14 ASP cc_start: 0.8357 (p0) cc_final: 0.8134 (p0) REVERT: B 88 LEU cc_start: 0.8882 (tp) cc_final: 0.8657 (tp) REVERT: B 92 MET cc_start: 0.8537 (mmp) cc_final: 0.8274 (mmp) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.0789 time to fit residues: 12.2427 Evaluate side-chains 92 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 74 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.113733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.095565 restraints weight = 25495.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.098307 restraints weight = 13620.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.100171 restraints weight = 8957.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.101407 restraints weight = 6696.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.102246 restraints weight = 5471.146| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8107 Z= 0.162 Angle : 0.667 9.917 11055 Z= 0.358 Chirality : 0.046 0.177 1194 Planarity : 0.005 0.089 1322 Dihedral : 15.650 148.894 1243 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.99 % Allowed : 31.84 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.27), residues: 892 helix: 0.17 (0.30), residues: 260 sheet: -0.98 (0.42), residues: 147 loop : -2.03 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 209 TYR 0.033 0.002 TYR A 328 PHE 0.027 0.002 PHE A 93 TRP 0.010 0.001 TRP A 231 HIS 0.008 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 8107) covalent geometry : angle 0.66680 / 0.36 (11055) hydrogen bonds : bond 0.07113 / 4.61 ( 254) hydrogen bonds : angle 6.34886 / 4.64 ( 728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLN cc_start: 0.6926 (tt0) cc_final: 0.6579 (mt0) REVERT: A 321 TYR cc_start: 0.6039 (t80) cc_final: 0.5543 (t80) REVERT: A 435 MET cc_start: 0.8579 (mmm) cc_final: 0.7942 (mmt) REVERT: A 507 ILE cc_start: 0.7764 (tt) cc_final: 0.7490 (tt) REVERT: B 14 ASP cc_start: 0.8240 (p0) cc_final: 0.7999 (p0) REVERT: B 88 LEU cc_start: 0.8928 (tp) cc_final: 0.8647 (tt) REVERT: B 92 MET cc_start: 0.8506 (mmp) cc_final: 0.8258 (mmp) REVERT: B 139 ASN cc_start: 0.8747 (t0) cc_final: 0.8542 (t0) REVERT: B 366 LYS cc_start: 0.9115 (ptpt) cc_final: 0.8899 (ptmt) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.0830 time to fit residues: 13.3400 Evaluate side-chains 109 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 0.0370 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.112914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.094558 restraints weight = 25538.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.097227 restraints weight = 13545.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.099113 restraints weight = 8904.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100367 restraints weight = 6667.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.101120 restraints weight = 5453.408| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8107 Z= 0.157 Angle : 0.629 9.816 11055 Z= 0.337 Chirality : 0.046 0.185 1194 Planarity : 0.005 0.089 1322 Dihedral : 15.720 147.707 1243 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.73 % Allowed : 30.35 % Favored : 65.92 % 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: -1.73 (0.27), residues: 892 helix: 0.33 (0.31), residues: 260 sheet: -0.98 (0.42), residues: 145 loop : -2.11 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.020 0.002 TYR A 328 PHE 0.023 0.002 PHE A 93 TRP 0.013 0.001 TRP B 373 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 8107) covalent geometry : angle 0.62929 / 0.34 (11055) hydrogen bonds : bond 0.05587 / 3.71 ( 254) hydrogen bonds : angle 5.82787 / 4.28 ( 728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7769 (mmmm) REVERT: A 302 GLN cc_start: 0.7088 (tt0) cc_final: 0.6604 (mt0) REVERT: A 321 TYR cc_start: 0.5975 (t80) cc_final: 0.5443 (t80) REVERT: A 435 MET cc_start: 0.8544 (mmm) cc_final: 0.7800 (mmt) REVERT: A 466 ASN cc_start: 0.8171 (t0) cc_final: 0.7888 (t0) REVERT: A 481 ARG cc_start: 0.7311 (ttm-80) cc_final: 0.7063 (ttm170) REVERT: B 14 ASP cc_start: 0.8326 (p0) cc_final: 0.8060 (p0) REVERT: B 55 GLU cc_start: 0.5796 (tm-30) cc_final: 0.4947 (tm-30) REVERT: B 88 LEU cc_start: 0.8927 (tp) cc_final: 0.8659 (tt) REVERT: B 92 MET cc_start: 0.8584 (mmp) cc_final: 0.8314 (mmp) REVERT: B 139 ASN cc_start: 0.8765 (t0) cc_final: 0.8539 (t0) REVERT: B 285 TYR cc_start: 0.7933 (t80) cc_final: 0.7704 (t80) outliers start: 30 outliers final: 17 residues processed: 135 average time/residue: 0.0723 time to fit residues: 13.1504 Evaluate side-chains 115 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** 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 = 0.4157 r_free = 0.4157 target = 0.113219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.094877 restraints weight = 26135.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.097553 restraints weight = 14076.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.099397 restraints weight = 9339.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.100595 restraints weight = 7006.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.101305 restraints weight = 5774.600| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8107 Z= 0.156 Angle : 0.641 9.967 11055 Z= 0.337 Chirality : 0.046 0.194 1194 Planarity : 0.005 0.090 1322 Dihedral : 15.756 149.342 1243 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.48 % Allowed : 31.34 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.28), residues: 892 helix: 0.42 (0.31), residues: 260 sheet: -0.96 (0.43), residues: 145 loop : -2.15 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.014 0.001 TYR B 416 PHE 0.029 0.002 PHE A 78 TRP 0.011 0.001 TRP B 373 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 8107) covalent geometry : angle 0.64091 / 0.34 (11055) hydrogen bonds : bond 0.04887 / 3.15 ( 254) hydrogen bonds : angle 5.61090 / 4.13 ( 728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8546 (pp30) cc_final: 0.8324 (pp30) REVERT: A 106 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6905 (t80) REVERT: A 287 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7690 (mmmm) REVERT: A 302 GLN cc_start: 0.7145 (tt0) cc_final: 0.6673 (mt0) REVERT: A 321 TYR cc_start: 0.5999 (t80) cc_final: 0.5503 (t80) REVERT: A 406 MET cc_start: 0.7834 (pmm) cc_final: 0.7420 (pmm) REVERT: A 435 MET cc_start: 0.8557 (mmm) cc_final: 0.7866 (mmt) REVERT: A 466 ASN cc_start: 0.8190 (t0) cc_final: 0.7867 (t0) REVERT: A 481 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7247 (ttm170) REVERT: B 1 MET cc_start: 0.6660 (ptm) cc_final: 0.6205 (ptm) REVERT: B 14 ASP cc_start: 0.8303 (p0) cc_final: 0.8037 (p0) REVERT: B 55 GLU cc_start: 0.5867 (tm-30) cc_final: 0.4956 (tm-30) REVERT: B 88 LEU cc_start: 0.8928 (tp) cc_final: 0.8695 (tt) REVERT: B 92 MET cc_start: 0.8551 (mmp) cc_final: 0.8299 (mmp) REVERT: B 139 ASN cc_start: 0.8699 (t0) cc_final: 0.8478 (t0) REVERT: B 285 TYR cc_start: 0.7897 (t80) cc_final: 0.7674 (t80) outliers start: 28 outliers final: 16 residues processed: 130 average time/residue: 0.0811 time to fit residues: 14.1882 Evaluate side-chains 118 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 70 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.113816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095327 restraints weight = 25791.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.098002 restraints weight = 13959.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099841 restraints weight = 9260.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.101077 restraints weight = 6968.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.101857 restraints weight = 5747.355| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8107 Z= 0.147 Angle : 0.631 9.969 11055 Z= 0.333 Chirality : 0.046 0.190 1194 Planarity : 0.005 0.090 1322 Dihedral : 15.735 150.101 1243 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.48 % Allowed : 30.47 % Favored : 65.05 % 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: -1.63 (0.28), residues: 892 helix: 0.55 (0.32), residues: 260 sheet: -0.91 (0.43), residues: 145 loop : -2.14 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.014 0.001 TYR B 416 PHE 0.024 0.002 PHE B 343 TRP 0.010 0.001 TRP B 373 HIS 0.003 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 8107) covalent geometry : angle 0.63114 / 0.33 (11055) hydrogen bonds : bond 0.04479 / 2.86 ( 254) hydrogen bonds : angle 5.42248 / 3.98 ( 728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.6860 (t80) REVERT: A 287 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7472 (mmmm) REVERT: A 302 GLN cc_start: 0.7232 (tt0) cc_final: 0.6909 (mt0) REVERT: A 321 TYR cc_start: 0.5923 (t80) cc_final: 0.5496 (t80) REVERT: A 356 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6176 (tp30) REVERT: A 435 MET cc_start: 0.8552 (mmm) cc_final: 0.7866 (mmt) REVERT: A 466 ASN cc_start: 0.8196 (t0) cc_final: 0.7853 (t0) REVERT: A 481 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7182 (ttm170) REVERT: B 1 MET cc_start: 0.6697 (ptm) cc_final: 0.6331 (ptm) REVERT: B 14 ASP cc_start: 0.8292 (p0) cc_final: 0.8026 (p0) REVERT: B 55 GLU cc_start: 0.5826 (tm-30) cc_final: 0.4944 (tm-30) REVERT: B 88 LEU cc_start: 0.8930 (tp) cc_final: 0.8698 (tt) REVERT: B 92 MET cc_start: 0.8602 (mmp) cc_final: 0.8354 (mmp) REVERT: B 139 ASN cc_start: 0.8693 (t0) cc_final: 0.8461 (t0) REVERT: B 285 TYR cc_start: 0.7904 (t80) cc_final: 0.7703 (t80) outliers start: 36 outliers final: 20 residues processed: 139 average time/residue: 0.0726 time to fit residues: 13.7298 Evaluate side-chains 121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 87 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** 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 = 0.4062 r_free = 0.4062 target = 0.108098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.089541 restraints weight = 26618.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.092066 restraints weight = 14658.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.093821 restraints weight = 9866.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.094958 restraints weight = 7506.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.095750 restraints weight = 6238.361| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 8107 Z= 0.296 Angle : 0.740 9.653 11055 Z= 0.393 Chirality : 0.049 0.258 1194 Planarity : 0.006 0.094 1322 Dihedral : 15.972 151.233 1243 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 5.22 % Allowed : 30.35 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.27), residues: 892 helix: 0.31 (0.32), residues: 254 sheet: -1.10 (0.43), residues: 142 loop : -2.20 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 243 TYR 0.015 0.002 TYR A 328 PHE 0.027 0.002 PHE A 93 TRP 0.017 0.002 TRP B 373 HIS 0.006 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 ( 8107) covalent geometry : angle 0.73951 / 0.39 (11055) hydrogen bonds : bond 0.05373 / 3.43 ( 254) hydrogen bonds : angle 5.59742 / 4.07 ( 728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 TYR cc_start: 0.6145 (t80) cc_final: 0.5714 (t80) REVERT: A 466 ASN cc_start: 0.8244 (t0) cc_final: 0.8002 (t0) REVERT: A 481 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.7281 (ttm170) REVERT: B 1 MET cc_start: 0.6634 (ptm) cc_final: 0.6232 (ptm) REVERT: B 14 ASP cc_start: 0.8275 (p0) cc_final: 0.8016 (p0) REVERT: B 55 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.4962 (tm-30) REVERT: B 92 MET cc_start: 0.8560 (mmp) cc_final: 0.8319 (mmp) REVERT: B 269 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5751 (tt) REVERT: B 389 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.6769 (m-40) outliers start: 42 outliers final: 33 residues processed: 139 average time/residue: 0.0716 time to fit residues: 13.6705 Evaluate side-chains 138 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.111825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.093286 restraints weight = 25858.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.095937 restraints weight = 14044.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.097659 restraints weight = 9327.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.098906 restraints weight = 7115.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.099653 restraints weight = 5860.407| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8107 Z= 0.144 Angle : 0.666 9.804 11055 Z= 0.347 Chirality : 0.047 0.202 1194 Planarity : 0.005 0.093 1322 Dihedral : 15.890 151.024 1243 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.73 % Allowed : 32.34 % Favored : 63.93 % 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 (0.28), residues: 892 helix: 0.49 (0.32), residues: 268 sheet: -0.86 (0.43), residues: 145 loop : -2.23 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 243 TYR 0.028 0.002 TYR B 416 PHE 0.024 0.002 PHE B 343 TRP 0.014 0.001 TRP B 373 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8107) covalent geometry : angle 0.66648 / 0.35 (11055) hydrogen bonds : bond 0.04193 / 2.69 ( 254) hydrogen bonds : angle 5.37497 / 3.93 ( 728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.7997 (pt0) cc_final: 0.7707 (pm20) REVERT: A 287 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8187 (mmmt) REVERT: A 302 GLN cc_start: 0.7191 (mt0) cc_final: 0.6831 (mt0) REVERT: A 321 TYR cc_start: 0.6015 (t80) cc_final: 0.5582 (t80) REVERT: A 406 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6746 (pmm) REVERT: A 435 MET cc_start: 0.8531 (mmm) cc_final: 0.7920 (mmt) REVERT: A 466 ASN cc_start: 0.8258 (t0) cc_final: 0.7953 (t0) REVERT: B 1 MET cc_start: 0.6664 (ptm) cc_final: 0.6301 (ptm) REVERT: B 14 ASP cc_start: 0.8289 (p0) cc_final: 0.8009 (p0) REVERT: B 55 GLU cc_start: 0.5776 (OUTLIER) cc_final: 0.4871 (tm-30) REVERT: B 92 MET cc_start: 0.8614 (mmp) cc_final: 0.8352 (mmp) outliers start: 30 outliers final: 24 residues processed: 134 average time/residue: 0.0886 time to fit residues: 15.7511 Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 30 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 67 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.112935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.094313 restraints weight = 26038.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.096966 restraints weight = 14125.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.098799 restraints weight = 9392.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.099865 restraints weight = 7098.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.100811 restraints weight = 5940.786| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3933 r_free = 0.3933 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3933 r_free = 0.3933 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8107 Z= 0.138 Angle : 0.657 10.272 11055 Z= 0.341 Chirality : 0.047 0.318 1194 Planarity : 0.005 0.089 1322 Dihedral : 15.867 152.096 1243 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.86 % Allowed : 33.21 % Favored : 62.94 % 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: -1.61 (0.28), residues: 892 helix: 0.56 (0.32), residues: 268 sheet: -0.82 (0.43), residues: 145 loop : -2.20 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 481 TYR 0.028 0.001 TYR B 416 PHE 0.023 0.002 PHE B 343 TRP 0.019 0.001 TRP B 373 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 8107) covalent geometry : angle 0.65676 / 0.34 (11055) hydrogen bonds : bond 0.04013 / 2.56 ( 254) hydrogen bonds : angle 5.28530 / 3.89 ( 728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8254 (pp30) REVERT: A 287 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8208 (mmmt) REVERT: A 302 GLN cc_start: 0.7251 (mt0) cc_final: 0.6931 (mt0) REVERT: A 321 TYR cc_start: 0.6028 (t80) cc_final: 0.5611 (t80) REVERT: A 406 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.6735 (pmm) REVERT: A 435 MET cc_start: 0.8509 (mmm) cc_final: 0.7888 (mmt) REVERT: A 466 ASN cc_start: 0.8192 (t0) cc_final: 0.7913 (t0) REVERT: A 481 ARG cc_start: 0.6785 (ttm170) cc_final: 0.6409 (mtp180) REVERT: B 1 MET cc_start: 0.6793 (ptm) cc_final: 0.6434 (ptm) REVERT: B 14 ASP cc_start: 0.8273 (p0) cc_final: 0.7997 (p0) REVERT: B 55 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.4867 (tm-30) REVERT: B 92 MET cc_start: 0.8635 (mmp) cc_final: 0.8395 (mmp) outliers start: 31 outliers final: 24 residues processed: 129 average time/residue: 0.0974 time to fit residues: 16.6604 Evaluate side-chains 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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 = 0.4122 r_free = 0.4122 target = 0.111143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.092655 restraints weight = 26078.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.095262 restraints weight = 14225.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.097072 restraints weight = 9486.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.098271 restraints weight = 7172.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.098986 restraints weight = 5922.512| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8107 Z= 0.202 Angle : 0.694 10.261 11055 Z= 0.360 Chirality : 0.048 0.434 1194 Planarity : 0.005 0.092 1322 Dihedral : 15.934 152.566 1243 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.73 % Allowed : 32.34 % Favored : 62.94 % 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 (0.28), residues: 892 helix: 0.38 (0.31), residues: 269 sheet: -0.80 (0.43), residues: 145 loop : -2.25 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 481 TYR 0.028 0.002 TYR B 416 PHE 0.025 0.002 PHE A 93 TRP 0.018 0.002 TRP B 373 HIS 0.005 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 8107) covalent geometry : angle 0.69399 / 0.36 (11055) hydrogen bonds : bond 0.04274 / 2.75 ( 254) hydrogen bonds : angle 5.36636 / 3.93 ( 728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLN cc_start: 0.7268 (mt0) cc_final: 0.6948 (mt0) REVERT: A 321 TYR cc_start: 0.6058 (t80) cc_final: 0.5662 (t80) REVERT: A 406 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.6863 (pmm) REVERT: A 435 MET cc_start: 0.8507 (mmm) cc_final: 0.7918 (mmt) REVERT: B 1 MET cc_start: 0.6802 (ptm) cc_final: 0.6425 (ptm) REVERT: B 14 ASP cc_start: 0.8292 (p0) cc_final: 0.8018 (p0) REVERT: B 55 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.4865 (tm-30) REVERT: B 92 MET cc_start: 0.8659 (mmp) cc_final: 0.8417 (mmp) outliers start: 38 outliers final: 33 residues processed: 136 average time/residue: 0.0913 time to fit residues: 16.5298 Evaluate side-chains 139 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 GLN ** 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 = 0.4148 r_free = 0.4148 target = 0.112513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.094059 restraints weight = 25663.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.096693 restraints weight = 14007.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.098482 restraints weight = 9308.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.099583 restraints weight = 7051.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.100467 restraints weight = 5889.044| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3928 r_free = 0.3928 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3928 r_free = 0.3928 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8107 Z= 0.146 Angle : 0.693 12.388 11055 Z= 0.355 Chirality : 0.047 0.252 1194 Planarity : 0.006 0.107 1322 Dihedral : 15.910 152.615 1243 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.98 % Allowed : 32.59 % Favored : 63.43 % 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 (0.28), residues: 892 helix: 0.42 (0.32), residues: 269 sheet: -0.75 (0.43), residues: 145 loop : -2.20 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 481 TYR 0.028 0.001 TYR B 416 PHE 0.022 0.002 PHE A 93 TRP 0.019 0.002 TRP B 373 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8107) covalent geometry : angle 0.69270 / 0.36 (11055) hydrogen bonds : bond 0.04019 / 2.61 ( 254) hydrogen bonds : angle 5.31588 / 3.90 ( 728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLN cc_start: 0.7264 (mt0) cc_final: 0.6983 (mt0) REVERT: A 321 TYR cc_start: 0.5991 (t80) cc_final: 0.5610 (t80) REVERT: A 406 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.6779 (pmm) REVERT: A 435 MET cc_start: 0.8497 (mmm) cc_final: 0.7921 (mmt) REVERT: B 1 MET cc_start: 0.6801 (ptm) cc_final: 0.6430 (ptm) REVERT: B 14 ASP cc_start: 0.8262 (p0) cc_final: 0.7981 (p0) REVERT: B 55 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.4824 (tm-30) REVERT: B 92 MET cc_start: 0.8673 (mmp) cc_final: 0.8429 (mmp) outliers start: 32 outliers final: 29 residues processed: 129 average time/residue: 0.0809 time to fit residues: 14.1467 Evaluate side-chains 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 47 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** 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 = 0.4114 r_free = 0.4114 target = 0.110141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.091599 restraints weight = 26405.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.094193 restraints weight = 14579.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.095932 restraints weight = 9795.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.096775 restraints weight = 7483.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.097759 restraints weight = 6405.015| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8107 Z= 0.228 Angle : 0.754 11.206 11055 Z= 0.394 Chirality : 0.048 0.223 1194 Planarity : 0.005 0.092 1322 Dihedral : 16.032 153.387 1243 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.60 % Allowed : 32.71 % Favored : 62.69 % 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 (0.28), residues: 892 helix: 0.24 (0.32), residues: 263 sheet: -0.78 (0.43), residues: 149 loop : -2.21 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 243 TYR 0.028 0.002 TYR B 416 PHE 0.025 0.002 PHE A 93 TRP 0.023 0.002 TRP B 373 HIS 0.008 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 ( 8107) covalent geometry : angle 0.75441 / 0.39 (11055) hydrogen bonds : bond 0.04520 / 2.91 ( 254) hydrogen bonds : angle 5.51190 / 4.03 ( 728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1555.16 seconds wall clock time: 27 minutes 28.13 seconds (1648.13 seconds total)