Starting phenix.real_space_refine on Wed Aug 5 00:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ffy_29070/08_2026/8ffy_29070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffy_29070/08_2026/8ffy_29070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2026/8ffy_29070.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2026/8ffy_29070.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2026/8ffy_29070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2026/8ffy_29070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2026/8ffy_29070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2026/8ffy_29070.map" } resolution = 3.6 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 34 5.16 5 C 4455 2.51 5 N 1333 2.21 5 O 1559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7442 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2493 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3590 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 424} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1301 Classifications: {'RNAv2': 61} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 25} Link IDs: {'rna2p': 6, 'rna3p': 54} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 1.60, per 1000 atoms: 0.21 Number of scatterers: 7442 At special positions: 0 Unit cell: (105.8, 80.5, 113.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 61 15.00 O 1559 8.00 N 1333 7.00 C 4455 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: 0.51 Conformation dependent library (CDL) restraints added in 378.0 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1422 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 40.9% alpha, 17.3% beta 20 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.510A pdb=" N LEU A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 299 through 307 removed outlier: 4.054A pdb=" N GLY A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 383 Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 59 through 65 removed outlier: 4.155A pdb=" N PHE B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.536A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 121 Processing helix chain 'B' and resid 132 through 168 Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'B' and resid 265 through 273 removed outlier: 3.800A pdb=" N PHE B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.780A pdb=" N GLY B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 383 Processing helix chain 'B' and resid 427 through 434 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 481 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192 removed outlier: 7.069A pdb=" N VAL A 388 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N MET A 191 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE A 386 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 402 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER A 423 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 404 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER A 421 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 406 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N VAL A 419 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS A 455 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER A 421 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 453 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 425 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 449 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 448 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 351 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA A 456 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 349 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 231 through 232 removed outlier: 3.618A pdb=" N LEU A 231 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 325 " --> pdb=" O MET B 258 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR B 349 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA B 456 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 351 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 357 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 448 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER B 421 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS B 455 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N VAL B 419 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE B 416 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET B 410 " --> pdb=" O PHE B 416 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU B 418 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA B 408 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 420 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 402 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS B 190 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP B 390 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 188 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265 Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 446 removed outlier: 5.642A pdb=" N HIS A 311 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN A 438 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 313 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.565A pdb=" N VAL A 475 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 438 Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 476 288 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.67 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: 2124 1.34 - 1.45: 1565 1.45 - 1.57: 3860 1.57 - 1.69: 128 1.69 - 1.81: 56 Bond restraints: 7733 Sorted by residual: bond pdb=" C6 SSA A 601 " pdb=" N6 SSA A 601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.13e+01 bond pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" O5' SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.581 1.735 -0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" O5' SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.581 1.733 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" O2S SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.435 1.586 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 7728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 10715 4.04 - 8.08: 42 8.08 - 12.11: 11 12.11 - 16.15: 0 16.15 - 20.19: 2 Bond angle restraints: 10770 Sorted by residual: angle pdb=" C3' U C 72 " pdb=" O3' U C 72 " pdb=" P G C 73 " ideal model delta sigma weight residual 119.70 109.80 9.90 1.20e+00 6.94e-01 6.80e+01 angle pdb=" C3' U C 71 " pdb=" O3' U C 71 " pdb=" P U C 72 " ideal model delta sigma weight residual 119.70 111.06 8.64 1.20e+00 6.94e-01 5.18e+01 angle pdb=" O1S SSA B 601 " pdb=" S1 SSA B 601 " pdb=" O2S SSA B 601 " ideal model delta sigma weight residual 121.34 101.15 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O1S SSA A 601 " pdb=" S1 SSA A 601 " pdb=" O2S SSA A 601 " ideal model delta sigma weight residual 121.34 101.15 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" C HIS A 226 " pdb=" N ARG A 227 " pdb=" CA ARG A 227 " ideal model delta sigma weight residual 122.93 113.99 8.94 1.51e+00 4.39e-01 3.51e+01 ... (remaining 10765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 4260 32.51 - 65.02: 212 65.02 - 97.54: 15 97.54 - 130.05: 0 130.05 - 162.56: 1 Dihedral angle restraints: 4488 sinusoidal: 2277 harmonic: 2211 Sorted by residual: dihedral pdb=" C4' U C 46 " pdb=" C3' U C 46 " pdb=" C2' U C 46 " pdb=" C1' U C 46 " ideal model delta sinusoidal sigma weight residual 36.35 -36.13 72.48 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' C C 30 " pdb=" C3' C C 30 " pdb=" C2' C C 30 " pdb=" C1' C C 30 " ideal model delta sinusoidal sigma weight residual 36.34 -35.61 71.95 1 3.10e+00 1.04e-01 6.89e+02 dihedral pdb=" C4' C C 74 " pdb=" C3' C C 74 " pdb=" C2' C C 74 " pdb=" C1' C C 74 " ideal model delta sinusoidal sigma weight residual 36.34 -35.40 71.74 1 3.10e+00 1.04e-01 6.86e+02 ... (remaining 4485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1155 0.142 - 0.283: 72 0.283 - 0.425: 2 0.425 - 0.566: 2 0.566 - 0.708: 4 Chirality restraints: 1235 Sorted by residual: chirality pdb=" P U C 71 " pdb=" OP1 U C 71 " pdb=" OP2 U C 71 " pdb=" O5' U C 71 " both_signs ideal model delta sigma weight residual True 2.17 -2.88 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" P U C 72 " pdb=" OP1 U C 72 " pdb=" OP2 U C 72 " pdb=" O5' U C 72 " both_signs ideal model delta sigma weight residual True 2.17 -2.83 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P U C 9 " pdb=" OP1 U C 9 " pdb=" OP2 U C 9 " pdb=" O5' U C 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.81 -0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 1232 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 226 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C HIS A 226 " -0.038 2.00e-02 2.50e+03 pdb=" O HIS A 226 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 227 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 71 " -0.012 2.00e-02 2.50e+03 1.25e-02 3.50e+00 pdb=" N1 U C 71 " 0.018 2.00e-02 2.50e+03 pdb=" C2 U C 71 " 0.020 2.00e-02 2.50e+03 pdb=" O2 U C 71 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U C 71 " -0.011 2.00e-02 2.50e+03 pdb=" C4 U C 71 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U C 71 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U C 71 " 0.012 2.00e-02 2.50e+03 pdb=" C6 U C 71 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 457 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO B 458 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.020 5.00e-02 4.00e+02 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 207 2.68 - 3.24: 6870 3.24 - 3.79: 12206 3.79 - 4.35: 15896 4.35 - 4.90: 25105 Nonbonded interactions: 60284 Sorted by model distance: nonbonded pdb=" OG1 THR A 333 " pdb=" OP2 G C 1 " model vdw 2.125 3.040 nonbonded pdb=" OE2 GLU A 352 " pdb=" OG SSA A 601 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU B 352 " pdb=" OG SSA B 601 " model vdw 2.144 3.040 nonbonded pdb=" OE2 GLU A 352 " pdb=" N10 SSA A 601 " model vdw 2.243 3.120 nonbonded pdb=" O GLU B 418 " pdb=" NH1 ARG B 459 " model vdw 2.246 3.120 ... (remaining 60279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.470 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: 8.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 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 : 0.008 0.191 7733 Z= 0.391 Angle : 0.810 20.191 10770 Z= 0.382 Chirality : 0.082 0.708 1235 Planarity : 0.003 0.036 1178 Dihedral : 17.000 162.558 3066 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.29), residues: 760 helix: 1.87 (0.30), residues: 285 sheet: -1.42 (0.46), residues: 105 loop : -2.11 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 227 TYR 0.006 0.000 TYR B 230 PHE 0.007 0.000 PHE A 348 TRP 0.001 0.000 TRP B 409 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.39 ( 7733) covalent geometry : angle 0.80957 / 0.38 (10770) hydrogen bonds : bond 0.11885 / 7.54 ( 338) hydrogen bonds : angle 6.40850 / 4.51 ( 926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7346 (mtt180) cc_final: 0.7135 (mtm-85) REVERT: A 218 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7629 (mmmt) REVERT: A 244 ASN cc_start: 0.7760 (m-40) cc_final: 0.7385 (m110) REVERT: A 366 GLN cc_start: 0.7154 (pt0) cc_final: 0.6864 (tm-30) REVERT: A 438 GLN cc_start: 0.8244 (tt0) cc_final: 0.8043 (tt0) REVERT: A 451 ASN cc_start: 0.7540 (p0) cc_final: 0.6953 (p0) REVERT: A 460 LEU cc_start: 0.7512 (mm) cc_final: 0.7277 (mm) REVERT: A 466 GLU cc_start: 0.6244 (mt-10) cc_final: 0.6031 (mt-10) REVERT: B 143 ARG cc_start: 0.6815 (mmm-85) cc_final: 0.5986 (ttm170) REVERT: B 203 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7094 (mtm-85) REVERT: B 313 VAL cc_start: 0.8292 (t) cc_final: 0.8066 (m) REVERT: B 332 GLU cc_start: 0.7442 (tp30) cc_final: 0.7221 (mm-30) REVERT: B 451 ASN cc_start: 0.8028 (p0) cc_final: 0.7425 (p0) REVERT: B 499 GLN cc_start: 0.7939 (tp40) cc_final: 0.7269 (tt0) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1052 time to fit residues: 27.9043 Evaluate side-chains 113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 226 HIS ** A 469 GLN ** 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 = 0.4212 r_free = 0.4212 target = 0.189245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156143 restraints weight = 9072.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159367 restraints weight = 4951.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.161410 restraints weight = 3307.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162534 restraints weight = 2572.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162543 restraints weight = 2228.387| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7733 Z= 0.140 Angle : 0.782 15.210 10770 Z= 0.323 Chirality : 0.063 0.760 1235 Planarity : 0.004 0.040 1178 Dihedral : 12.856 156.069 1579 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.39 % Allowed : 18.03 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.30), residues: 760 helix: 2.45 (0.31), residues: 284 sheet: -0.52 (0.49), residues: 105 loop : -1.60 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 216 TYR 0.009 0.001 TYR A 343 PHE 0.010 0.001 PHE A 371 TRP 0.006 0.001 TRP B 409 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7733) covalent geometry : angle 0.78189 / 0.32 (10770) hydrogen bonds : bond 0.04807 / 3.54 ( 338) hydrogen bonds : angle 4.59428 / 3.30 ( 926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.7475 (mpp) cc_final: 0.7137 (mtt) REVERT: B 143 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.6937 (ttm170) REVERT: B 451 ASN cc_start: 0.8326 (p0) cc_final: 0.8053 (p0) REVERT: B 466 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6686 (mt-10) outliers start: 22 outliers final: 13 residues processed: 130 average time/residue: 0.0981 time to fit residues: 16.3490 Evaluate side-chains 98 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 217 GLN A 346 HIS ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS B 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.173981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139216 restraints weight = 9018.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142203 restraints weight = 4997.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144165 restraints weight = 3420.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144880 restraints weight = 2699.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145751 restraints weight = 2421.819| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7733 Z= 0.221 Angle : 0.793 11.532 10770 Z= 0.355 Chirality : 0.059 0.585 1235 Planarity : 0.005 0.032 1178 Dihedral : 12.985 159.899 1579 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.08 % Allowed : 18.34 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.29), residues: 760 helix: 1.63 (0.30), residues: 301 sheet: -0.30 (0.47), residues: 99 loop : -1.74 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 459 TYR 0.018 0.002 TYR B 45 PHE 0.017 0.002 PHE A 354 TRP 0.005 0.002 TRP A 409 HIS 0.006 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 7733) covalent geometry : angle 0.79334 / 0.35 (10770) hydrogen bonds : bond 0.05004 / 3.72 ( 338) hydrogen bonds : angle 4.73689 / 3.39 ( 926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.256 Fit side-chains REVERT: A 244 ASN cc_start: 0.8410 (m-40) cc_final: 0.7911 (m110) REVERT: A 322 MET cc_start: 0.7558 (mpp) cc_final: 0.7190 (mtt) REVERT: B 143 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7059 (ttm170) REVERT: B 309 MET cc_start: 0.8782 (ttt) cc_final: 0.8566 (ttt) REVERT: B 398 LEU cc_start: 0.8953 (mm) cc_final: 0.8739 (mt) outliers start: 33 outliers final: 25 residues processed: 119 average time/residue: 0.0975 time to fit residues: 15.2965 Evaluate side-chains 106 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 0.0270 chunk 46 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.175406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141047 restraints weight = 9196.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144103 restraints weight = 5024.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146047 restraints weight = 3385.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147178 restraints weight = 2659.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147965 restraints weight = 2312.368| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7733 Z= 0.143 Angle : 0.694 10.358 10770 Z= 0.305 Chirality : 0.056 0.636 1235 Planarity : 0.004 0.029 1178 Dihedral : 12.760 161.325 1579 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.31 % Allowed : 20.96 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.29), residues: 760 helix: 1.95 (0.30), residues: 297 sheet: -0.21 (0.48), residues: 100 loop : -1.65 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 252 TYR 0.014 0.001 TYR B 45 PHE 0.027 0.002 PHE B 308 TRP 0.005 0.001 TRP A 409 HIS 0.003 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7733) covalent geometry : angle 0.69384 / 0.31 (10770) hydrogen bonds : bond 0.04081 / 2.97 ( 338) hydrogen bonds : angle 4.51123 / 3.24 ( 926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8213 (m-40) cc_final: 0.7675 (m110) REVERT: A 307 TYR cc_start: 0.9018 (t80) cc_final: 0.8775 (t80) REVERT: A 338 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7690 (pp20) REVERT: B 143 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.6985 (ttm170) outliers start: 28 outliers final: 19 residues processed: 100 average time/residue: 0.0903 time to fit residues: 12.1523 Evaluate side-chains 94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 61 optimal weight: 0.0770 chunk 56 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141679 restraints weight = 9164.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144690 restraints weight = 5015.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146618 restraints weight = 3393.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147618 restraints weight = 2669.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148417 restraints weight = 2343.889| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7733 Z= 0.133 Angle : 0.673 8.844 10770 Z= 0.295 Chirality : 0.055 0.664 1235 Planarity : 0.004 0.029 1178 Dihedral : 12.584 162.070 1579 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 6.01 % Allowed : 19.88 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.30), residues: 760 helix: 2.15 (0.31), residues: 290 sheet: -0.07 (0.48), residues: 100 loop : -1.40 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 203 TYR 0.013 0.001 TYR B 45 PHE 0.015 0.001 PHE A 371 TRP 0.005 0.001 TRP A 409 HIS 0.002 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7733) covalent geometry : angle 0.67314 / 0.29 (10770) hydrogen bonds : bond 0.03794 / 2.78 ( 338) hydrogen bonds : angle 4.39600 / 3.13 ( 926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8085 (m-40) cc_final: 0.7591 (m110) REVERT: A 338 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: B 143 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.6983 (ttm170) outliers start: 39 outliers final: 26 residues processed: 108 average time/residue: 0.1023 time to fit residues: 14.6423 Evaluate side-chains 99 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 54 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139607 restraints weight = 9169.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142535 restraints weight = 5111.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144465 restraints weight = 3509.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145471 restraints weight = 2768.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146264 restraints weight = 2433.371| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7733 Z= 0.173 Angle : 0.710 9.289 10770 Z= 0.315 Chirality : 0.056 0.679 1235 Planarity : 0.004 0.029 1178 Dihedral : 12.561 162.085 1579 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.55 % Allowed : 20.65 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.29), residues: 760 helix: 2.14 (0.31), residues: 289 sheet: -0.02 (0.48), residues: 100 loop : -1.63 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 203 TYR 0.017 0.002 TYR B 45 PHE 0.016 0.002 PHE A 371 TRP 0.006 0.001 TRP A 409 HIS 0.004 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 7733) covalent geometry : angle 0.70983 / 0.31 (10770) hydrogen bonds : bond 0.04193 / 3.04 ( 338) hydrogen bonds : angle 4.48494 / 3.20 ( 926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.232 Fit side-chains REVERT: A 244 ASN cc_start: 0.8108 (m-40) cc_final: 0.7521 (m110) REVERT: A 307 TYR cc_start: 0.8943 (t80) cc_final: 0.8717 (t80) REVERT: A 322 MET cc_start: 0.7663 (mmt) cc_final: 0.7205 (mtt) REVERT: A 338 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: B 143 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.6962 (ttm170) REVERT: B 203 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7416 (mtm110) outliers start: 36 outliers final: 26 residues processed: 106 average time/residue: 0.0917 time to fit residues: 13.0239 Evaluate side-chains 101 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.177417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143166 restraints weight = 9090.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146166 restraints weight = 4980.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148063 restraints weight = 3379.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149117 restraints weight = 2664.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149769 restraints weight = 2330.387| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7733 Z= 0.107 Angle : 0.643 8.259 10770 Z= 0.283 Chirality : 0.052 0.561 1235 Planarity : 0.004 0.031 1178 Dihedral : 12.404 162.638 1579 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.31 % Allowed : 22.34 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.30), residues: 760 helix: 2.56 (0.31), residues: 285 sheet: 0.27 (0.49), residues: 102 loop : -1.33 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 203 TYR 0.010 0.001 TYR B 45 PHE 0.012 0.001 PHE A 371 TRP 0.006 0.001 TRP B 409 HIS 0.002 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7733) covalent geometry : angle 0.64322 / 0.28 (10770) hydrogen bonds : bond 0.03444 / 2.55 ( 338) hydrogen bonds : angle 4.24094 / 3.03 ( 926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASN cc_start: 0.7809 (m-40) cc_final: 0.7336 (m110) REVERT: A 338 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: B 64 CYS cc_start: 0.6134 (t) cc_final: 0.5860 (t) REVERT: B 143 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.6967 (ttm170) REVERT: B 203 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7408 (mtm-85) outliers start: 28 outliers final: 18 residues processed: 102 average time/residue: 0.0827 time to fit residues: 11.2384 Evaluate side-chains 96 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 0.0070 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 overall best weight: 2.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.171985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137428 restraints weight = 9196.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140292 restraints weight = 5063.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142137 restraints weight = 3454.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143252 restraints weight = 2726.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143845 restraints weight = 2376.724| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7733 Z= 0.216 Angle : 0.752 9.339 10770 Z= 0.338 Chirality : 0.056 0.624 1235 Planarity : 0.004 0.033 1178 Dihedral : 12.557 162.064 1579 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.08 % Allowed : 20.80 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.30), residues: 760 helix: 1.92 (0.30), residues: 298 sheet: 0.16 (0.49), residues: 102 loop : -1.53 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.018 0.002 TYR B 45 PHE 0.017 0.002 PHE A 371 TRP 0.007 0.002 TRP A 409 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 7733) covalent geometry : angle 0.75224 / 0.34 (10770) hydrogen bonds : bond 0.04377 / 3.13 ( 338) hydrogen bonds : angle 4.59436 / 3.28 ( 926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8131 (m-40) cc_final: 0.7575 (m110) REVERT: A 322 MET cc_start: 0.7794 (mmt) cc_final: 0.7318 (mtt) REVERT: A 338 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: B 64 CYS cc_start: 0.5990 (t) cc_final: 0.5766 (t) REVERT: B 143 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7056 (ttm170) REVERT: B 203 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7520 (mtm-85) outliers start: 33 outliers final: 27 residues processed: 101 average time/residue: 0.0810 time to fit residues: 10.9738 Evaluate side-chains 100 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142201 restraints weight = 9021.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.145152 restraints weight = 4981.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147027 restraints weight = 3407.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148168 restraints weight = 2696.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.148689 restraints weight = 2348.962| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7733 Z= 0.122 Angle : 0.675 8.216 10770 Z= 0.302 Chirality : 0.053 0.540 1235 Planarity : 0.004 0.030 1178 Dihedral : 12.438 162.160 1579 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.47 % Allowed : 21.73 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.30), residues: 760 helix: 2.37 (0.30), residues: 292 sheet: 0.27 (0.49), residues: 100 loop : -1.48 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 432 TYR 0.019 0.001 TYR B 153 PHE 0.011 0.001 PHE A 371 TRP 0.006 0.001 TRP A 409 HIS 0.002 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7733) covalent geometry : angle 0.67529 / 0.30 (10770) hydrogen bonds : bond 0.03661 / 2.65 ( 338) hydrogen bonds : angle 4.33836 / 3.11 ( 926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASN cc_start: 0.7882 (m-40) cc_final: 0.7404 (m110) REVERT: A 338 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: B 64 CYS cc_start: 0.6083 (t) cc_final: 0.5846 (t) REVERT: B 143 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.6970 (ttm170) REVERT: B 203 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: B 322 MET cc_start: 0.7564 (mtt) cc_final: 0.7161 (mtm) outliers start: 29 outliers final: 23 residues processed: 95 average time/residue: 0.0980 time to fit residues: 12.4453 Evaluate side-chains 94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 78 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143380 restraints weight = 9035.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146340 restraints weight = 4908.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148109 restraints weight = 3303.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149341 restraints weight = 2604.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149873 restraints weight = 2253.347| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7733 Z= 0.120 Angle : 0.668 8.024 10770 Z= 0.301 Chirality : 0.052 0.502 1235 Planarity : 0.004 0.030 1178 Dihedral : 12.380 162.388 1579 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.85 % Allowed : 22.03 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.30), residues: 760 helix: 2.48 (0.30), residues: 292 sheet: 0.31 (0.50), residues: 100 loop : -1.43 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 432 TYR 0.011 0.001 TYR B 45 PHE 0.011 0.001 PHE A 371 TRP 0.006 0.001 TRP A 409 HIS 0.002 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7733) covalent geometry : angle 0.66840 / 0.30 (10770) hydrogen bonds : bond 0.03597 / 2.57 ( 338) hydrogen bonds : angle 4.36670 / 3.11 ( 926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 244 ASN cc_start: 0.7868 (m-40) cc_final: 0.7390 (m110) REVERT: A 338 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7840 (pp20) REVERT: B 64 CYS cc_start: 0.6090 (t) cc_final: 0.5826 (t) REVERT: B 143 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7016 (ttm170) REVERT: B 203 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7418 (mtm-85) REVERT: B 432 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7303 (mtp180) outliers start: 25 outliers final: 22 residues processed: 92 average time/residue: 0.0939 time to fit residues: 11.4986 Evaluate side-chains 92 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.176014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141794 restraints weight = 9054.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144754 restraints weight = 5000.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146600 restraints weight = 3393.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147583 restraints weight = 2683.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.148329 restraints weight = 2360.120| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7733 Z= 0.135 Angle : 0.681 8.009 10770 Z= 0.308 Chirality : 0.052 0.481 1235 Planarity : 0.004 0.041 1178 Dihedral : 12.369 162.412 1579 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.54 % Allowed : 22.65 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.30), residues: 760 helix: 2.45 (0.30), residues: 292 sheet: 0.34 (0.49), residues: 100 loop : -1.43 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 252 TYR 0.037 0.002 TYR B 153 PHE 0.013 0.001 PHE A 371 TRP 0.006 0.001 TRP A 409 HIS 0.003 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7733) covalent geometry : angle 0.68104 / 0.31 (10770) hydrogen bonds : bond 0.03685 / 2.62 ( 338) hydrogen bonds : angle 4.40345 / 3.16 ( 926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.40 seconds wall clock time: 22 minutes 3.21 seconds (1323.21 seconds total)