Starting phenix.real_space_refine on Thu Jul 2 08:18:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ffy_29070/07_2026/8ffy_29070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffy_29070/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ffy_29070/07_2026/8ffy_29070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffy_29070/07_2026/8ffy_29070.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ffy_29070/07_2026/8ffy_29070.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ffy_29070/07_2026/8ffy_29070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ffy_29070/07_2026/8ffy_29070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffy_29070/07_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-dev-6108/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: {'RNA': 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: 1.70, per 1000 atoms: 0.23 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: 0.68 Conformation dependent library (CDL) restraints added in 355.3 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: 0.91 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: 1.29 Time building geometry restraints manager: 0.90 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: 10717 4.04 - 8.08: 40 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 120.20 109.80 10.40 1.50e+00 4.44e-01 4.80e+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=" C3' U C 71 " pdb=" O3' U C 71 " pdb=" P U C 72 " ideal model delta sigma weight residual 120.20 111.06 9.14 1.50e+00 4.44e-01 3.71e+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: 4339 32.51 - 65.02: 137 65.02 - 97.54: 11 97.54 - 130.05: 0 130.05 - 162.56: 1 Dihedral angle restraints: 4488 sinusoidal: 2277 harmonic: 2211 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 232.00 162.24 69.76 1 1.70e+01 3.46e-03 2.17e+01 dihedral pdb=" C5' U C 9 " pdb=" C4' U C 9 " pdb=" C3' U C 9 " pdb=" O3' U C 9 " ideal model delta sinusoidal sigma weight residual 147.00 116.13 30.87 1 8.00e+00 1.56e-02 2.12e+01 dihedral pdb=" C3' U C 9 " pdb=" C4' U C 9 " pdb=" O4' U C 9 " pdb=" C1' U C 9 " ideal model delta sinusoidal sigma weight residual -2.00 24.84 -26.84 1 8.00e+00 1.56e-02 1.62e+01 ... (remaining 4485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1187 0.110 - 0.220: 40 0.220 - 0.329: 2 0.329 - 0.439: 3 0.439 - 0.549: 3 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CA SSA A 601 " pdb=" CB SSA A 601 " pdb=" C9 SSA A 601 " pdb=" N10 SSA A 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.02 0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CA SSA B 601 " pdb=" CB SSA B 601 " pdb=" C9 SSA B 601 " pdb=" N10 SSA B 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.01 0.55 2.00e-01 2.50e+01 7.43e+00 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 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.54e+00 ... (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: 0.500 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.030 ------------------------------------------------------------------------------- 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= 0.394 Angle : 0.732 20.191 10770 Z= 0.369 Chirality : 0.051 0.549 1235 Planarity : 0.003 0.036 1178 Dihedral : 14.706 162.558 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 0.00775 / 0.39 ( 7733) covalent geometry : angle 0.73188 / 0.37 (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 : 0.274 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: 0.1179 time to fit residues: 31.4415 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 : 0.260 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.186017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154694 restraints weight = 8756.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157691 restraints weight = 4809.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159606 restraints weight = 3232.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160627 restraints weight = 2521.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161417 restraints weight = 2192.577| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7733 Z= 0.127 Angle : 0.536 6.758 10770 Z= 0.262 Chirality : 0.038 0.208 1235 Planarity : 0.004 0.038 1178 Dihedral : 9.697 168.421 1579 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.08 % Allowed : 18.03 % Favored : 78.89 % 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: 2.43 (0.31), residues: 284 sheet: -0.56 (0.49), residues: 105 loop : -1.62 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 216 TYR 0.009 0.001 TYR A 343 PHE 0.010 0.001 PHE A 371 TRP 0.004 0.001 TRP B 409 HIS 0.006 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7733) covalent geometry : angle 0.53564 / 0.26 (10770) hydrogen bonds : bond 0.03798 / 2.76 ( 338) hydrogen bonds : angle 4.59521 / 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 141 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.7474 (mpp) cc_final: 0.7098 (mtt) REVERT: B 143 ARG cc_start: 0.7904 (mmm-85) cc_final: 0.7007 (ttm170) REVERT: B 451 ASN cc_start: 0.8330 (p0) cc_final: 0.8060 (p0) REVERT: B 466 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6604 (mt-10) outliers start: 20 outliers final: 12 residues processed: 131 average time/residue: 0.1127 time to fit residues: 18.8091 Evaluate side-chains 99 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.173547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140987 restraints weight = 8774.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143714 restraints weight = 5017.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145506 restraints weight = 3500.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146565 restraints weight = 2792.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147139 restraints weight = 2445.444| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7733 Z= 0.186 Angle : 0.604 6.732 10770 Z= 0.302 Chirality : 0.041 0.186 1235 Planarity : 0.005 0.039 1178 Dihedral : 9.819 167.988 1579 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.93 % Allowed : 18.34 % Favored : 76.73 % 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: 0.07 (0.30), residues: 760 helix: 1.89 (0.31), residues: 296 sheet: -0.33 (0.48), residues: 102 loop : -1.48 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 252 TYR 0.016 0.002 TYR B 401 PHE 0.016 0.002 PHE A 354 TRP 0.006 0.001 TRP A 409 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 7733) covalent geometry : angle 0.60376 / 0.30 (10770) hydrogen bonds : bond 0.04338 / 3.11 ( 338) hydrogen bonds : angle 4.56384 / 3.27 ( 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 126 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8436 (m-40) cc_final: 0.7997 (m110) REVERT: A 322 MET cc_start: 0.7502 (mpp) cc_final: 0.7266 (mtt) REVERT: B 143 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7126 (ttm170) REVERT: B 466 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7498 (mt-10) outliers start: 32 outliers final: 25 residues processed: 118 average time/residue: 0.1066 time to fit residues: 16.3913 Evaluate side-chains 104 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 420 THR 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: 0.2980 chunk 54 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.178222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146122 restraints weight = 8836.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148867 restraints weight = 4954.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150611 restraints weight = 3398.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151515 restraints weight = 2702.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152254 restraints weight = 2381.144| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7733 Z= 0.110 Angle : 0.503 6.563 10770 Z= 0.251 Chirality : 0.037 0.161 1235 Planarity : 0.004 0.028 1178 Dihedral : 9.691 167.840 1579 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.31 % Allowed : 19.88 % Favored : 75.81 % 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: 0.38 (0.30), residues: 760 helix: 2.42 (0.31), residues: 285 sheet: -0.16 (0.47), residues: 103 loop : -1.45 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 252 TYR 0.012 0.001 TYR B 45 PHE 0.014 0.001 PHE A 371 TRP 0.005 0.001 TRP A 409 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 7733) covalent geometry : angle 0.50336 / 0.25 (10770) hydrogen bonds : bond 0.03403 / 2.37 ( 338) hydrogen bonds : angle 4.29704 / 3.06 ( 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 114 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8024 (m-40) cc_final: 0.7608 (m110) REVERT: A 338 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7641 (pp20) REVERT: B 143 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7013 (ttm170) REVERT: B 466 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7242 (mt-10) outliers start: 28 outliers final: 17 residues processed: 103 average time/residue: 0.1125 time to fit residues: 15.0337 Evaluate side-chains 94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE 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 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 259 THR 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 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: 0.1980 chunk 33 optimal weight: 0.0040 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN B 448 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141231 restraints weight = 8810.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144000 restraints weight = 4921.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145792 restraints weight = 3377.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146856 restraints weight = 2677.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147382 restraints weight = 2341.955| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7733 Z= 0.129 Angle : 0.520 6.694 10770 Z= 0.258 Chirality : 0.037 0.160 1235 Planarity : 0.004 0.027 1178 Dihedral : 9.678 167.462 1579 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.78 % Allowed : 20.03 % Favored : 75.19 % 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: 2.44 (0.31), residues: 284 sheet: -0.02 (0.48), residues: 103 loop : -1.36 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 203 TYR 0.013 0.001 TYR B 45 PHE 0.016 0.001 PHE A 371 TRP 0.005 0.001 TRP A 409 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7733) covalent geometry : angle 0.51954 / 0.26 (10770) hydrogen bonds : bond 0.03514 / 2.42 ( 338) hydrogen bonds : angle 4.31790 / 3.07 ( 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 110 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8078 (m-40) cc_final: 0.7648 (m110) REVERT: A 338 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7630 (pp20) REVERT: B 143 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7033 (ttm170) REVERT: B 309 MET cc_start: 0.8542 (ttt) cc_final: 0.8143 (ttp) REVERT: B 432 ARG cc_start: 0.7391 (mtt90) cc_final: 0.6979 (mtt-85) outliers start: 31 outliers final: 25 residues processed: 100 average time/residue: 0.1055 time to fit residues: 13.8308 Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 323 VAL Chi-restraints excluded: chain A residue 328 CYS 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 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 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 Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.173444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140678 restraints weight = 8762.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143409 restraints weight = 4939.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145164 restraints weight = 3399.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146148 restraints weight = 2709.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146836 restraints weight = 2376.963| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7733 Z= 0.124 Angle : 0.513 6.708 10770 Z= 0.256 Chirality : 0.036 0.160 1235 Planarity : 0.004 0.028 1178 Dihedral : 9.664 167.005 1579 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.08 % Allowed : 19.88 % Favored : 75.04 % 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: 0.62 (0.30), residues: 760 helix: 2.50 (0.31), residues: 285 sheet: 0.26 (0.49), residues: 101 loop : -1.29 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 203 TYR 0.012 0.001 TYR B 45 PHE 0.014 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 0.00289 / 0.12 ( 7733) covalent geometry : angle 0.51344 / 0.26 (10770) hydrogen bonds : bond 0.03360 / 2.31 ( 338) hydrogen bonds : angle 4.26182 / 3.03 ( 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 108 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.272 Fit side-chains REVERT: A 206 LEU cc_start: 0.8122 (tp) cc_final: 0.7747 (mp) REVERT: A 244 ASN cc_start: 0.8024 (m-40) cc_final: 0.7572 (m110) REVERT: A 322 MET cc_start: 0.7587 (mmt) cc_final: 0.7064 (mtt) REVERT: A 338 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: B 64 CYS cc_start: 0.5988 (t) cc_final: 0.5738 (t) REVERT: B 143 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.6997 (ttm170) REVERT: B 168 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6795 (mp) REVERT: B 203 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7269 (mtm-85) REVERT: B 432 ARG cc_start: 0.7458 (mtt90) cc_final: 0.7081 (mtt-85) outliers start: 33 outliers final: 26 residues processed: 99 average time/residue: 0.0974 time to fit residues: 12.8409 Evaluate side-chains 98 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 CYS 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 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 168 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 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 Chi-restraints excluded: chain B residue 498 LEU 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: 6.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.170144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137090 restraints weight = 8800.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139826 restraints weight = 5024.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141454 restraints weight = 3485.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142583 restraints weight = 2794.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143138 restraints weight = 2445.186| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7733 Z= 0.163 Angle : 0.561 6.814 10770 Z= 0.281 Chirality : 0.038 0.166 1235 Planarity : 0.004 0.027 1178 Dihedral : 9.788 166.807 1579 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.70 % Allowed : 19.72 % Favored : 74.58 % 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: 0.37 (0.30), residues: 760 helix: 2.15 (0.30), residues: 295 sheet: 0.33 (0.49), residues: 100 loop : -1.48 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 203 TYR 0.016 0.002 TYR B 45 PHE 0.015 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 0.00383 / 0.16 ( 7733) covalent geometry : angle 0.56130 / 0.28 (10770) hydrogen bonds : bond 0.03825 / 2.64 ( 338) hydrogen bonds : angle 4.42268 / 3.15 ( 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 120 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.261 Fit side-chains REVERT: A 206 LEU cc_start: 0.8233 (tp) cc_final: 0.7853 (mp) REVERT: A 244 ASN cc_start: 0.8091 (m-40) cc_final: 0.7532 (m110) REVERT: A 322 MET cc_start: 0.7624 (mmt) cc_final: 0.7213 (mtt) REVERT: A 338 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7819 (pp20) REVERT: B 64 CYS cc_start: 0.6117 (t) cc_final: 0.5872 (t) REVERT: B 143 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7022 (ttm170) REVERT: B 168 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7004 (mp) REVERT: B 203 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: B 432 ARG cc_start: 0.7517 (mtt90) cc_final: 0.6862 (mtp85) REVERT: B 436 MET cc_start: 0.8346 (mmm) cc_final: 0.8104 (mmt) outliers start: 37 outliers final: 30 residues processed: 113 average time/residue: 0.0910 time to fit residues: 14.0713 Evaluate side-chains 105 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 323 VAL Chi-restraints excluded: chain A residue 328 CYS 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 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 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 168 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 320 VAL 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 Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.172176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139827 restraints weight = 8822.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142436 restraints weight = 5060.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144095 restraints weight = 3525.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145084 restraints weight = 2830.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.145610 restraints weight = 2488.156| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4824 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= 0.122 Angle : 0.530 7.603 10770 Z= 0.268 Chirality : 0.037 0.158 1235 Planarity : 0.004 0.029 1178 Dihedral : 9.734 166.507 1579 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.39 % Allowed : 20.34 % Favored : 74.27 % 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: 0.54 (0.30), residues: 760 helix: 2.25 (0.30), residues: 297 sheet: 0.31 (0.50), residues: 102 loop : -1.32 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 203 TYR 0.011 0.001 TYR B 45 PHE 0.014 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 0.00284 / 0.12 ( 7733) covalent geometry : angle 0.53034 / 0.27 (10770) hydrogen bonds : bond 0.03352 / 2.29 ( 338) hydrogen bonds : angle 4.27051 / 3.04 ( 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 110 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8150 (tp) cc_final: 0.7774 (mp) REVERT: A 244 ASN cc_start: 0.7937 (m-40) cc_final: 0.7485 (m110) REVERT: A 322 MET cc_start: 0.7845 (mmt) cc_final: 0.7298 (mtt) REVERT: A 338 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7791 (pp20) REVERT: B 64 CYS cc_start: 0.6099 (t) cc_final: 0.5848 (t) REVERT: B 143 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.6994 (ttm170) REVERT: B 168 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6885 (mp) REVERT: B 203 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: B 432 ARG cc_start: 0.7397 (mtt90) cc_final: 0.7099 (mtt-85) REVERT: B 436 MET cc_start: 0.8291 (mmm) cc_final: 0.8022 (mmt) outliers start: 35 outliers final: 26 residues processed: 99 average time/residue: 0.1023 time to fit residues: 13.4731 Evaluate side-chains 101 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 CYS 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 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 168 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 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 Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.169913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137391 restraints weight = 8670.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139909 restraints weight = 5023.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141540 restraints weight = 3542.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142363 restraints weight = 2848.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143053 restraints weight = 2534.907| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4972 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= 0.155 Angle : 0.561 7.276 10770 Z= 0.282 Chirality : 0.038 0.159 1235 Planarity : 0.004 0.028 1178 Dihedral : 9.803 166.234 1579 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.93 % Allowed : 20.96 % 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: 0.48 (0.30), residues: 760 helix: 2.16 (0.30), residues: 297 sheet: 0.48 (0.50), residues: 100 loop : -1.38 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 203 TYR 0.015 0.001 TYR B 45 PHE 0.014 0.001 PHE A 371 TRP 0.007 0.001 TRP A 409 HIS 0.004 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 7733) covalent geometry : angle 0.56091 / 0.28 (10770) hydrogen bonds : bond 0.03662 / 2.50 ( 338) hydrogen bonds : angle 4.36217 / 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: 32 poor density : 71 time to evaluate : 0.259 Fit side-chains REVERT: A 244 ASN cc_start: 0.8027 (m-40) cc_final: 0.7476 (m110) REVERT: A 338 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7843 (pp20) REVERT: B 64 CYS cc_start: 0.6083 (t) cc_final: 0.5853 (t) REVERT: B 143 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.6994 (ttm170) REVERT: B 168 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7060 (mp) REVERT: B 432 ARG cc_start: 0.7478 (mtt90) cc_final: 0.6876 (mtp85) REVERT: B 436 MET cc_start: 0.8324 (mmm) cc_final: 0.8050 (mmt) outliers start: 32 outliers final: 28 residues processed: 96 average time/residue: 0.0958 time to fit residues: 12.4171 Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 323 VAL Chi-restraints excluded: chain A residue 328 CYS 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 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 168 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 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 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: 0.3980 chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.175619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143120 restraints weight = 8803.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145736 restraints weight = 5094.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147389 restraints weight = 3566.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148418 restraints weight = 2866.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148877 restraints weight = 2520.663| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7733 Z= 0.108 Angle : 0.524 7.662 10770 Z= 0.265 Chirality : 0.036 0.158 1235 Planarity : 0.004 0.033 1178 Dihedral : 9.730 166.204 1579 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.70 % Allowed : 21.57 % 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: 0.69 (0.30), residues: 760 helix: 2.45 (0.30), residues: 292 sheet: 0.43 (0.50), residues: 103 loop : -1.28 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 252 TYR 0.020 0.001 TYR B 153 PHE 0.010 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 0.00247 / 0.11 ( 7733) covalent geometry : angle 0.52445 / 0.27 (10770) hydrogen bonds : bond 0.03139 / 2.15 ( 338) hydrogen bonds : angle 4.25852 / 3.04 ( 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 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8114 (tp) cc_final: 0.7785 (mp) REVERT: A 244 ASN cc_start: 0.7781 (m-40) cc_final: 0.7325 (m110) REVERT: A 338 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: B 64 CYS cc_start: 0.6082 (t) cc_final: 0.5834 (t) REVERT: B 143 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.6933 (ttm170) REVERT: B 203 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: B 432 ARG cc_start: 0.7335 (mtt90) cc_final: 0.7086 (mtt-85) REVERT: B 436 MET cc_start: 0.8288 (mmm) cc_final: 0.7989 (mmt) outliers start: 24 outliers final: 20 residues processed: 88 average time/residue: 0.0917 time to fit residues: 10.9570 Evaluate side-chains 91 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 328 CYS 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 430 SER Chi-restraints excluded: chain A residue 455 CYS 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 242 LEU 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 Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 HIS ** A 469 GLN ** 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 = 0.3959 r_free = 0.3959 target = 0.166748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133708 restraints weight = 8849.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136243 restraints weight = 5144.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137884 restraints weight = 3639.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138885 restraints weight = 2937.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139389 restraints weight = 2583.747| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7733 Z= 0.273 Angle : 0.691 7.665 10770 Z= 0.347 Chirality : 0.043 0.168 1235 Planarity : 0.005 0.048 1178 Dihedral : 10.203 165.800 1579 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.31 % Allowed : 20.65 % Favored : 75.04 % 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: 0.11 (0.29), residues: 760 helix: 1.87 (0.30), residues: 290 sheet: 0.33 (0.50), residues: 100 loop : -1.56 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 77 TYR 0.020 0.002 TYR B 45 PHE 0.018 0.002 PHE B 63 TRP 0.010 0.002 TRP B 409 HIS 0.009 0.002 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 ( 7733) covalent geometry : angle 0.69073 / 0.35 (10770) hydrogen bonds : bond 0.04772 / 3.27 ( 338) hydrogen bonds : angle 4.75070 / 3.39 ( 926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1341.81 seconds wall clock time: 23 minutes 56.43 seconds (1436.43 seconds total)