Starting phenix.real_space_refine on Tue Aug 4 19:39:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y7z_39027/08_2026/8y7z_39027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y7z_39027/08_2026/8y7z_39027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y7z_39027/08_2026/8y7z_39027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y7z_39027/08_2026/8y7z_39027.map" model { file = "/net/cci-nas-00/data/ceres_data/8y7z_39027/08_2026/8y7z_39027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y7z_39027/08_2026/8y7z_39027.cif" } resolution = 2.57 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= -0.001 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4007 2.51 5 N 1117 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6488 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "A" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2005 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.39, per 1000 atoms: 0.21 Number of scatterers: 6488 At special positions: 0 Unit cell: (68.641, 79.392, 106.683, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 41 15.00 Mg 1 11.99 O 1300 8.00 N 1117 7.00 C 4007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 304.0 milliseconds 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 11 sheets defined 37.6% alpha, 24.3% beta 15 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.847A pdb=" N CYS B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.618A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 95 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.826A pdb=" N HIS B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.788A pdb=" N ARG B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.769A pdb=" N LYS B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 184 through 190 removed outlier: 3.966A pdb=" N LEU B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.834A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 294 removed outlier: 3.550A pdb=" N SER B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.719A pdb=" N PHE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 4.717A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 459 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.555A pdb=" N ILE A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 513 through 519 removed outlier: 4.878A pdb=" N GLU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 549 Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.401A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 223 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N HIS B 306 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 225 " --> pdb=" O HIS B 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.533A pdb=" N ARG B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.493A pdb=" N CYS B 107 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR B 54 " --> pdb=" O CYS B 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.407A pdb=" N ARG B 51 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 147 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 53 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR B 149 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 55 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 146 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE B 183 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 148 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.544A pdb=" N TYR B 160 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AA7, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 337 removed outlier: 4.017A pdb=" N HIS A 444 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AB1, first strand: chain 'A' and resid 370 through 373 removed outlier: 7.031A pdb=" N GLY A 382 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N ARG A 344 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 343 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR A 403 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS A 345 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLN A 401 " --> pdb=" O CYS A 345 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 347 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 399 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR A 349 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 558 through 561 removed outlier: 3.560A pdb=" N ALA A 569 " --> pdb=" O CYS A 561 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.56 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: 1866 1.34 - 1.45: 1407 1.45 - 1.57: 3336 1.57 - 1.69: 81 1.69 - 1.81: 32 Bond restraints: 6722 Sorted by residual: bond pdb=" C3' DC D 17 " pdb=" C2' DC D 17 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.71e+00 bond pdb=" C3' DA D 18 " pdb=" C2' DA D 18 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.24e+00 bond pdb=" O4' DT D 12 " pdb=" C1' DT D 12 " ideal model delta sigma weight residual 1.420 1.395 0.025 1.10e-02 8.26e+03 5.18e+00 bond pdb=" C3' DG D 19 " pdb=" O3' DG D 19 " ideal model delta sigma weight residual 1.435 1.407 0.028 1.30e-02 5.92e+03 4.54e+00 bond pdb=" C4' DC D 13 " pdb=" C3' DC D 13 " ideal model delta sigma weight residual 1.529 1.509 0.020 1.00e-02 1.00e+04 3.84e+00 ... (remaining 6717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 8966 1.78 - 3.55: 295 3.55 - 5.33: 24 5.33 - 7.11: 6 7.11 - 8.88: 2 Bond angle restraints: 9293 Sorted by residual: angle pdb=" O4' DT D 12 " pdb=" C1' DT D 12 " pdb=" N1 DT D 12 " ideal model delta sigma weight residual 108.00 112.58 -4.58 7.00e-01 2.04e+00 4.29e+01 angle pdb=" N3 DT D 14 " pdb=" C4 DT D 14 " pdb=" O4 DT D 14 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" O4' C C 5 " pdb=" C1' C C 5 " pdb=" N1 C C 5 " ideal model delta sigma weight residual 108.20 111.73 -3.53 8.00e-01 1.56e+00 1.95e+01 angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT D 23 " pdb=" C4 DT D 23 " pdb=" O4 DT D 23 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 9288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 3680 32.78 - 65.56: 299 65.56 - 98.34: 20 98.34 - 131.13: 0 131.13 - 163.91: 2 Dihedral angle restraints: 4001 sinusoidal: 1942 harmonic: 2059 Sorted by residual: dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N PRO B 47 " pdb=" CA PRO B 47 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" C4' DT D 23 " pdb=" C3' DT D 23 " pdb=" O3' DT D 23 " pdb=" P DA D 24 " ideal model delta sinusoidal sigma weight residual 220.00 56.09 163.91 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA D 18 " pdb=" C3' DA D 18 " pdb=" O3' DA D 18 " pdb=" P DG D 19 " ideal model delta sinusoidal sigma weight residual 220.00 65.62 154.38 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 3998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 721 0.040 - 0.080: 208 0.080 - 0.120: 80 0.120 - 0.160: 36 0.160 - 0.200: 2 Chirality restraints: 1047 Sorted by residual: chirality pdb=" CB VAL B 247 " pdb=" CA VAL B 247 " pdb=" CG1 VAL B 247 " pdb=" CG2 VAL B 247 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1' A C 20 " pdb=" O4' A C 20 " pdb=" C2' A C 20 " pdb=" N9 A C 20 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" C3' DA D 18 " pdb=" C4' DA D 18 " pdb=" O3' DA D 18 " pdb=" C2' DA D 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 1044 not shown) Planarity restraints: 1043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT D 12 " -0.027 2.00e-02 2.50e+03 1.44e-02 5.21e+00 pdb=" N1 DT D 12 " 0.036 2.00e-02 2.50e+03 pdb=" C2 DT D 12 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT D 12 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT D 12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT D 12 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT D 12 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DT D 12 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT D 12 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DT D 12 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 5 " 0.026 2.00e-02 2.50e+03 1.38e-02 4.31e+00 pdb=" N1 C C 5 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C C 5 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C C 5 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C C 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C C 5 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C C 5 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C C 5 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 5 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 4 " -0.027 2.00e-02 2.50e+03 1.35e-02 4.11e+00 pdb=" N1 C C 4 " 0.027 2.00e-02 2.50e+03 pdb=" C2 C C 4 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C C 4 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C C 4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C C 4 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C C 4 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C C 4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C C 4 " 0.006 2.00e-02 2.50e+03 ... (remaining 1040 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 57 2.55 - 3.13: 4821 3.13 - 3.72: 11324 3.72 - 4.31: 16395 4.31 - 4.90: 25575 Nonbonded interactions: 58172 Sorted by model distance: nonbonded pdb=" OP1 A C 1 " pdb="MG MG B 501 " model vdw 1.958 2.170 nonbonded pdb=" ND2 ASN B 434 " pdb="MG MG B 501 " model vdw 2.059 2.250 nonbonded pdb=" N2 G C 11 " pdb=" O2 DC D 13 " model vdw 2.138 2.496 nonbonded pdb=" O THR B 242 " pdb=" OG1 THR B 262 " model vdw 2.142 3.040 nonbonded pdb=" N2 G C 16 " pdb=" O2 DC D 8 " model vdw 2.147 2.496 ... (remaining 58167 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.010 Process input model: 7.340 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6722 Z= 0.268 Angle : 0.704 8.885 9293 Z= 0.468 Chirality : 0.049 0.200 1047 Planarity : 0.004 0.042 1043 Dihedral : 20.761 163.906 2675 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.33 % Allowed : 28.62 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.32), residues: 698 helix: 0.40 (0.35), residues: 217 sheet: -0.45 (0.38), residues: 166 loop : -0.41 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 138 TYR 0.021 0.002 TYR B 84 PHE 0.012 0.002 PHE B 257 TRP 0.007 0.001 TRP B 198 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.27 ( 6722) covalent geometry : angle 0.70371 / 0.47 ( 9293) hydrogen bonds : bond 0.08523 / 6.22 ( 269) hydrogen bonds : angle 5.44428 / 3.97 ( 746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.212 Fit side-chains REVERT: B 299 MET cc_start: 0.7363 (mmt) cc_final: 0.6900 (mmm) REVERT: A 508 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6825 (mm-30) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.4913 time to fit residues: 44.0992 Evaluate side-chains 75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 437 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.170780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141196 restraints weight = 5827.863| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.43 r_work: 0.3617 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6722 Z= 0.167 Angle : 0.621 8.388 9293 Z= 0.335 Chirality : 0.044 0.262 1047 Planarity : 0.005 0.043 1043 Dihedral : 19.578 164.166 1326 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.11 % Allowed : 26.97 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.32), residues: 698 helix: 0.40 (0.34), residues: 217 sheet: -0.48 (0.39), residues: 165 loop : -0.27 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 138 TYR 0.018 0.002 TYR B 84 PHE 0.016 0.002 PHE B 255 TRP 0.006 0.001 TRP B 198 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 6722) covalent geometry : angle 0.62090 / 0.33 ( 9293) hydrogen bonds : bond 0.06181 / 4.00 ( 269) hydrogen bonds : angle 5.28576 / 3.88 ( 746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.223 Fit side-chains REVERT: B 315 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 383 MET cc_start: 0.7921 (mmm) cc_final: 0.7655 (mmm) REVERT: A 484 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A 508 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7213 (mm-30) outliers start: 25 outliers final: 11 residues processed: 101 average time/residue: 0.4414 time to fit residues: 46.9030 Evaluate side-chains 84 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 0.0040 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.164474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134350 restraints weight = 5793.729| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.43 r_work: 0.3538 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 6722 Z= 0.296 Angle : 0.746 7.921 9293 Z= 0.396 Chirality : 0.050 0.317 1047 Planarity : 0.006 0.048 1043 Dihedral : 19.559 165.812 1326 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.09 % Allowed : 26.15 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.31), residues: 698 helix: -0.07 (0.33), residues: 217 sheet: -0.57 (0.39), residues: 165 loop : -0.34 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 138 TYR 0.024 0.003 TYR B 84 PHE 0.017 0.003 PHE A 523 TRP 0.011 0.002 TRP A 510 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.30 ( 6722) covalent geometry : angle 0.74620 / 0.40 ( 9293) hydrogen bonds : bond 0.06886 / 4.70 ( 269) hydrogen bonds : angle 5.58224 / 4.11 ( 746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.213 Fit side-chains REVERT: B 121 ASN cc_start: 0.7630 (t0) cc_final: 0.7341 (t0) REVERT: B 222 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: B 315 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7361 (mt-10) REVERT: B 330 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: B 383 MET cc_start: 0.7954 (mmm) cc_final: 0.7748 (mmm) REVERT: A 484 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (tp) outliers start: 37 outliers final: 14 residues processed: 101 average time/residue: 0.4905 time to fit residues: 52.2316 Evaluate side-chains 89 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137837 restraints weight = 5823.293| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.43 r_work: 0.3578 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6722 Z= 0.196 Angle : 0.643 7.807 9293 Z= 0.345 Chirality : 0.045 0.314 1047 Planarity : 0.005 0.043 1043 Dihedral : 19.554 164.388 1326 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.09 % Allowed : 25.82 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.32), residues: 698 helix: 0.21 (0.33), residues: 218 sheet: -0.63 (0.39), residues: 165 loop : -0.29 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 138 TYR 0.023 0.002 TYR B 84 PHE 0.020 0.002 PHE B 255 TRP 0.008 0.001 TRP B 198 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 6722) covalent geometry : angle 0.64328 / 0.35 ( 9293) hydrogen bonds : bond 0.06076 / 3.96 ( 269) hydrogen bonds : angle 5.42532 / 4.00 ( 746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.237 Fit side-chains REVERT: B 121 ASN cc_start: 0.7527 (t0) cc_final: 0.7161 (t0) REVERT: B 222 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6464 (mm-30) REVERT: B 315 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7344 (mt-10) REVERT: B 383 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7737 (mmm) REVERT: A 484 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8135 (tp) outliers start: 37 outliers final: 14 residues processed: 102 average time/residue: 0.4966 time to fit residues: 53.4025 Evaluate side-chains 93 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.165845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135871 restraints weight = 5873.133| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.44 r_work: 0.3555 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6722 Z= 0.236 Angle : 0.683 7.502 9293 Z= 0.363 Chirality : 0.047 0.319 1047 Planarity : 0.005 0.045 1043 Dihedral : 19.498 164.752 1326 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.58 % Allowed : 25.66 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.32), residues: 698 helix: 0.09 (0.33), residues: 217 sheet: -0.62 (0.39), residues: 165 loop : -0.30 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 138 TYR 0.026 0.002 TYR B 84 PHE 0.020 0.002 PHE B 255 TRP 0.008 0.002 TRP B 198 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 ( 6722) covalent geometry : angle 0.68283 / 0.36 ( 9293) hydrogen bonds : bond 0.06288 / 4.20 ( 269) hydrogen bonds : angle 5.46845 / 4.04 ( 746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.153 Fit side-chains REVERT: B 121 ASN cc_start: 0.7518 (t0) cc_final: 0.7173 (t0) REVERT: B 222 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: B 315 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7346 (mt-10) REVERT: B 330 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: B 383 MET cc_start: 0.7894 (mmm) cc_final: 0.7662 (mmm) REVERT: A 484 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8160 (tp) outliers start: 40 outliers final: 19 residues processed: 106 average time/residue: 0.5419 time to fit residues: 60.4727 Evaluate side-chains 97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137908 restraints weight = 5867.532| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.44 r_work: 0.3580 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6722 Z= 0.191 Angle : 0.638 7.675 9293 Z= 0.341 Chirality : 0.045 0.306 1047 Planarity : 0.005 0.052 1043 Dihedral : 19.444 164.051 1326 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.76 % Allowed : 26.81 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.32), residues: 698 helix: 0.26 (0.33), residues: 218 sheet: -0.64 (0.39), residues: 165 loop : -0.28 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 138 TYR 0.023 0.002 TYR B 84 PHE 0.021 0.002 PHE B 255 TRP 0.008 0.001 TRP B 198 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 6722) covalent geometry : angle 0.63775 / 0.34 ( 9293) hydrogen bonds : bond 0.05967 / 3.92 ( 269) hydrogen bonds : angle 5.38307 / 3.98 ( 746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.170 Fit side-chains REVERT: B 121 ASN cc_start: 0.7457 (t0) cc_final: 0.7105 (t0) REVERT: B 222 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6539 (mm-30) REVERT: B 298 ARG cc_start: 0.6789 (ttp-110) cc_final: 0.6359 (ttp-170) REVERT: B 315 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7308 (mt-10) REVERT: B 330 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: B 383 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7739 (mmm) REVERT: B 457 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7835 (ttmt) REVERT: A 484 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8126 (tp) outliers start: 35 outliers final: 20 residues processed: 104 average time/residue: 0.5265 time to fit residues: 57.7459 Evaluate side-chains 100 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.138001 restraints weight = 5840.286| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.43 r_work: 0.3582 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6722 Z= 0.190 Angle : 0.639 8.080 9293 Z= 0.340 Chirality : 0.045 0.288 1047 Planarity : 0.005 0.054 1043 Dihedral : 19.380 163.961 1326 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.43 % Allowed : 26.97 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.32), residues: 698 helix: 0.30 (0.34), residues: 218 sheet: -0.64 (0.39), residues: 165 loop : -0.29 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 138 TYR 0.024 0.002 TYR B 84 PHE 0.022 0.002 PHE B 255 TRP 0.007 0.001 TRP B 198 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 ( 6722) covalent geometry : angle 0.63870 / 0.34 ( 9293) hydrogen bonds : bond 0.05907 / 3.90 ( 269) hydrogen bonds : angle 5.35895 / 3.96 ( 746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.231 Fit side-chains REVERT: B 121 ASN cc_start: 0.7438 (t0) cc_final: 0.7077 (t0) REVERT: B 298 ARG cc_start: 0.6766 (ttp-110) cc_final: 0.6324 (ttp-170) REVERT: B 315 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 330 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: B 383 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7738 (mmm) REVERT: B 457 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7830 (ttmt) REVERT: A 484 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8139 (tp) REVERT: A 512 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6433 (tmtp) outliers start: 33 outliers final: 21 residues processed: 102 average time/residue: 0.4998 time to fit residues: 53.6189 Evaluate side-chains 99 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 39 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142733 restraints weight = 5821.052| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.42 r_work: 0.3632 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6722 Z= 0.137 Angle : 0.588 8.672 9293 Z= 0.315 Chirality : 0.042 0.277 1047 Planarity : 0.005 0.055 1043 Dihedral : 19.286 162.723 1326 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.93 % Allowed : 27.47 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.32), residues: 698 helix: 0.53 (0.34), residues: 218 sheet: -0.61 (0.39), residues: 169 loop : -0.20 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 138 TYR 0.022 0.002 TYR B 341 PHE 0.023 0.002 PHE B 255 TRP 0.007 0.001 TRP B 198 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 6722) covalent geometry : angle 0.58775 / 0.31 ( 9293) hydrogen bonds : bond 0.05647 / 3.65 ( 269) hydrogen bonds : angle 5.21587 / 3.87 ( 746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.156 Fit side-chains REVERT: B 121 ASN cc_start: 0.7406 (t0) cc_final: 0.7049 (t0) REVERT: B 330 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: B 383 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7683 (mmm) REVERT: B 457 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7777 (ttmt) REVERT: A 484 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8097 (tp) REVERT: A 508 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 512 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6473 (tmtp) outliers start: 30 outliers final: 17 residues processed: 100 average time/residue: 0.4864 time to fit residues: 51.1156 Evaluate side-chains 97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.168958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139356 restraints weight = 5865.404| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.44 r_work: 0.3597 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6722 Z= 0.177 Angle : 0.625 8.426 9293 Z= 0.332 Chirality : 0.044 0.284 1047 Planarity : 0.005 0.057 1043 Dihedral : 19.249 163.608 1326 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.10 % Allowed : 27.30 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.32), residues: 698 helix: 0.45 (0.34), residues: 218 sheet: -0.58 (0.39), residues: 165 loop : -0.28 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 138 TYR 0.026 0.002 TYR B 84 PHE 0.021 0.002 PHE B 255 TRP 0.006 0.001 TRP A 510 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 6722) covalent geometry : angle 0.62506 / 0.33 ( 9293) hydrogen bonds : bond 0.05653 / 3.72 ( 269) hydrogen bonds : angle 5.24184 / 3.88 ( 746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.151 Fit side-chains REVERT: B 110 LEU cc_start: 0.7641 (mp) cc_final: 0.7385 (mp) REVERT: B 121 ASN cc_start: 0.7394 (t0) cc_final: 0.7076 (t0) REVERT: B 222 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6176 (mm-30) REVERT: B 330 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6951 (tp30) REVERT: B 457 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7794 (ttmt) REVERT: A 484 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8102 (tp) REVERT: A 508 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 512 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6508 (tmtp) outliers start: 31 outliers final: 19 residues processed: 100 average time/residue: 0.4957 time to fit residues: 52.0893 Evaluate side-chains 100 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137275 restraints weight = 5781.044| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.43 r_work: 0.3572 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6722 Z= 0.217 Angle : 0.670 8.095 9293 Z= 0.354 Chirality : 0.046 0.311 1047 Planarity : 0.005 0.059 1043 Dihedral : 19.314 164.390 1326 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.28 % Allowed : 28.12 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.32), residues: 698 helix: 0.26 (0.33), residues: 217 sheet: -0.60 (0.39), residues: 165 loop : -0.33 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 298 TYR 0.028 0.002 TYR B 84 PHE 0.020 0.002 PHE B 255 TRP 0.008 0.002 TRP A 510 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 ( 6722) covalent geometry : angle 0.67031 / 0.35 ( 9293) hydrogen bonds : bond 0.05940 / 3.94 ( 269) hydrogen bonds : angle 5.35066 / 3.95 ( 746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.227 Fit side-chains REVERT: B 110 LEU cc_start: 0.7679 (mp) cc_final: 0.7436 (mp) REVERT: B 121 ASN cc_start: 0.7441 (t0) cc_final: 0.7122 (t0) REVERT: B 330 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: B 457 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7924 (ttmt) REVERT: A 484 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8068 (tp) outliers start: 26 outliers final: 19 residues processed: 96 average time/residue: 0.5016 time to fit residues: 50.6361 Evaluate side-chains 96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139379 restraints weight = 5837.466| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.43 r_work: 0.3594 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6722 Z= 0.177 Angle : 0.638 8.321 9293 Z= 0.338 Chirality : 0.044 0.315 1047 Planarity : 0.005 0.059 1043 Dihedral : 19.298 163.806 1326 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.11 % Allowed : 28.29 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.32), residues: 698 helix: 0.41 (0.34), residues: 218 sheet: -0.61 (0.39), residues: 165 loop : -0.30 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 298 TYR 0.024 0.002 TYR B 84 PHE 0.020 0.002 PHE B 255 TRP 0.005 0.001 TRP A 510 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 6722) covalent geometry : angle 0.63845 / 0.34 ( 9293) hydrogen bonds : bond 0.05731 / 3.73 ( 269) hydrogen bonds : angle 5.28134 / 3.90 ( 746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.72 seconds wall clock time: 39 minutes 13.21 seconds (2353.21 seconds total)