Starting phenix.real_space_refine on Thu Jul 2 03:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y7z_39027/07_2026/8y7z_39027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y7z_39027/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y7z_39027/07_2026/8y7z_39027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y7z_39027/07_2026/8y7z_39027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y7z_39027/07_2026/8y7z_39027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y7z_39027/07_2026/8y7z_39027.map" } 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): 0.01s 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: 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: 1.41, per 1000 atoms: 0.22 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: 0.48 Conformation dependent library (CDL) restraints added in 237.5 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: 0.74 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: 1.10 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 9019 1.78 - 3.55: 242 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=" 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 angle pdb=" O4 DT D 12 " pdb=" C4 DT D 12 " pdb=" C5 DT D 12 " ideal model delta sigma weight residual 124.90 122.04 2.86 7.00e-01 2.04e+00 1.67e+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: 742 0.040 - 0.080: 210 0.080 - 0.120: 75 0.120 - 0.160: 18 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 2.46 2.28 0.18 2.00e-01 2.50e+01 7.77e-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: 3.060 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- 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= 0.264 Angle : 0.677 8.885 9293 Z= 0.440 Chirality : 0.045 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 0.00399 / 0.26 ( 6722) covalent geometry : angle 0.67663 / 0.44 ( 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 : 0.162 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: 0.6826 (mm-30) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.5580 time to fit residues: 49.8339 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 : 0.134 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.170525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141033 restraints weight = 5822.818| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.43 r_work: 0.3616 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0590 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= 0.171 Angle : 0.617 8.173 9293 Z= 0.335 Chirality : 0.043 0.245 1047 Planarity : 0.005 0.046 1043 Dihedral : 19.621 163.594 1326 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.95 % Allowed : 27.63 % Favored : 68.42 % 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: -0.29 (0.32), residues: 698 helix: 0.38 (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 0.006 0.001 ARG B 138 TYR 0.018 0.002 TYR B 84 PHE 0.015 0.002 PHE B 255 TRP 0.006 0.001 TRP B 198 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 6722) covalent geometry : angle 0.61742 / 0.33 ( 9293) hydrogen bonds : bond 0.06114 / 3.99 ( 269) hydrogen bonds : angle 5.28798 / 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 104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.232 Fit side-chains REVERT: B 315 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7310 (mt-10) REVERT: B 383 MET cc_start: 0.7933 (mmm) cc_final: 0.7657 (mmm) REVERT: A 484 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7957 (tp) REVERT: A 508 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7199 (mm-30) outliers start: 24 outliers final: 10 residues processed: 98 average time/residue: 0.5264 time to fit residues: 54.2636 Evaluate side-chains 82 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 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: 0.5980 chunk 21 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.163817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133751 restraints weight = 5794.513| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.45 r_work: 0.3533 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6722 Z= 0.318 Angle : 0.753 8.049 9293 Z= 0.404 Chirality : 0.050 0.295 1047 Planarity : 0.006 0.049 1043 Dihedral : 19.609 165.503 1326 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.92 % Allowed : 26.48 % 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: -0.65 (0.31), residues: 698 helix: -0.13 (0.33), residues: 217 sheet: -0.60 (0.39), residues: 165 loop : -0.37 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 462 TYR 0.025 0.003 TYR B 84 PHE 0.018 0.003 PHE A 523 TRP 0.012 0.002 TRP A 510 HIS 0.007 0.002 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.32 ( 6722) covalent geometry : angle 0.75311 / 0.40 ( 9293) hydrogen bonds : bond 0.07032 / 4.83 ( 269) hydrogen bonds : angle 5.63031 / 4.14 ( 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: 36 poor density : 76 time to evaluate : 0.241 Fit side-chains REVERT: B 222 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6691 (mm-30) REVERT: B 315 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7367 (mt-10) REVERT: B 330 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7046 (tp30) REVERT: B 383 MET cc_start: 0.7952 (mmm) cc_final: 0.7750 (mmm) REVERT: A 484 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8071 (tp) outliers start: 36 outliers final: 17 residues processed: 102 average time/residue: 0.5076 time to fit residues: 54.6242 Evaluate side-chains 91 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU 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 348 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 Chi-restraints excluded: chain A residue 514 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: 0.9990 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.168244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138739 restraints weight = 5811.458| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.42 r_work: 0.3588 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6722 Z= 0.180 Angle : 0.623 7.706 9293 Z= 0.338 Chirality : 0.044 0.292 1047 Planarity : 0.005 0.043 1043 Dihedral : 19.621 163.357 1326 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: -0.43 (0.32), residues: 698 helix: 0.24 (0.34), residues: 218 sheet: -0.63 (0.39), residues: 165 loop : -0.28 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 138 TYR 0.022 0.002 TYR B 84 PHE 0.020 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 0.00396 / 0.18 ( 6722) covalent geometry : angle 0.62337 / 0.34 ( 9293) hydrogen bonds : bond 0.05956 / 3.84 ( 269) hydrogen bonds : angle 5.40254 / 3.98 ( 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 : 0.202 Fit side-chains REVERT: B 121 ASN cc_start: 0.7535 (t0) cc_final: 0.7281 (t0) REVERT: B 315 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7319 (mt-10) REVERT: B 383 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7740 (mmm) REVERT: A 442 ARG cc_start: 0.6935 (mtt-85) cc_final: 0.6720 (mtt-85) REVERT: A 484 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8131 (tp) outliers start: 37 outliers final: 13 residues processed: 103 average time/residue: 0.4747 time to fit residues: 51.4454 Evaluate side-chains 90 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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 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 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: 0.0470 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.0370 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.168910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139347 restraints weight = 5866.959| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.44 r_work: 0.3597 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6722 Z= 0.168 Angle : 0.614 8.055 9293 Z= 0.330 Chirality : 0.044 0.274 1047 Planarity : 0.005 0.047 1043 Dihedral : 19.497 162.858 1326 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.76 % Allowed : 26.64 % 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: -0.32 (0.32), residues: 698 helix: 0.39 (0.34), residues: 218 sheet: -0.59 (0.39), residues: 165 loop : -0.26 (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 0.020 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 0.00367 / 0.17 ( 6722) covalent geometry : angle 0.61429 / 0.33 ( 9293) hydrogen bonds : bond 0.05858 / 3.83 ( 269) hydrogen bonds : angle 5.31463 / 3.93 ( 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 111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.145 Fit side-chains REVERT: B 121 ASN cc_start: 0.7498 (t0) cc_final: 0.7109 (t0) REVERT: B 315 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7314 (mt-10) REVERT: B 330 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6972 (tp30) REVERT: B 383 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7731 (mmm) REVERT: A 442 ARG cc_start: 0.6900 (mtt-85) cc_final: 0.6693 (mtt-85) REVERT: A 484 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8099 (tp) outliers start: 35 outliers final: 18 residues processed: 101 average time/residue: 0.4366 time to fit residues: 46.5361 Evaluate side-chains 96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.168348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138824 restraints weight = 5857.325| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.43 r_work: 0.3590 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1075 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= 0.181 Angle : 0.615 7.880 9293 Z= 0.331 Chirality : 0.044 0.264 1047 Planarity : 0.005 0.050 1043 Dihedral : 19.443 162.897 1326 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.20 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: -0.34 (0.32), residues: 698 helix: 0.39 (0.34), residues: 218 sheet: -0.60 (0.39), residues: 165 loop : -0.28 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 138 TYR 0.024 0.002 TYR B 84 PHE 0.017 0.002 PHE B 255 TRP 0.006 0.001 TRP B 198 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 6722) covalent geometry : angle 0.61509 / 0.33 ( 9293) hydrogen bonds : bond 0.05814 / 3.83 ( 269) hydrogen bonds : angle 5.29856 / 3.92 ( 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 106 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.199 Fit side-chains REVERT: B 121 ASN cc_start: 0.7517 (t0) cc_final: 0.7152 (t0) REVERT: B 298 ARG cc_start: 0.6737 (ttp-110) cc_final: 0.6390 (mtp180) REVERT: B 315 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7322 (mt-10) REVERT: B 330 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7016 (tp30) REVERT: B 383 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7738 (mmm) REVERT: B 457 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7853 (ttmt) REVERT: A 484 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 512 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6413 (tmtp) outliers start: 31 outliers final: 18 residues processed: 98 average time/residue: 0.4876 time to fit residues: 50.2600 Evaluate side-chains 96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 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 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 484 LEU Chi-restraints excluded: chain A residue 512 LYS 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: 0.9980 chunk 6 optimal weight: 0.4980 chunk 61 optimal weight: 0.0870 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.169844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140452 restraints weight = 5845.541| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.43 r_work: 0.3606 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6722 Z= 0.158 Angle : 0.601 8.079 9293 Z= 0.322 Chirality : 0.043 0.261 1047 Planarity : 0.005 0.052 1043 Dihedral : 19.404 162.400 1326 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -0.28 (0.32), residues: 698 helix: 0.47 (0.34), residues: 217 sheet: -0.57 (0.39), residues: 165 loop : -0.27 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 138 TYR 0.025 0.002 TYR B 341 PHE 0.018 0.002 PHE B 257 TRP 0.006 0.001 TRP B 198 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 6722) covalent geometry : angle 0.60099 / 0.32 ( 9293) hydrogen bonds : bond 0.05670 / 3.69 ( 269) hydrogen bonds : angle 5.22841 / 3.86 ( 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 111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.217 Fit side-chains REVERT: B 110 LEU cc_start: 0.7633 (mp) cc_final: 0.7378 (mp) REVERT: B 121 ASN cc_start: 0.7448 (t0) cc_final: 0.7110 (t0) REVERT: B 315 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7296 (mt-10) REVERT: B 330 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: B 383 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7712 (mmm) REVERT: B 457 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7837 (ttmt) REVERT: A 484 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8081 (tp) REVERT: A 512 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6470 (tmtp) outliers start: 31 outliers final: 18 residues processed: 103 average time/residue: 0.4769 time to fit residues: 51.7848 Evaluate side-chains 96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 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 352 SER 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: 7.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 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 = 0.4000 r_free = 0.4000 target = 0.171281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142151 restraints weight = 5817.237| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.43 r_work: 0.3627 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6722 Z= 0.144 Angle : 0.586 8.730 9293 Z= 0.315 Chirality : 0.042 0.260 1047 Planarity : 0.005 0.056 1043 Dihedral : 19.330 161.884 1326 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.10 % Allowed : 27.80 % Favored : 67.11 % 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: -0.19 (0.32), residues: 698 helix: 0.60 (0.34), residues: 217 sheet: -0.58 (0.39), residues: 169 loop : -0.23 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 138 TYR 0.023 0.002 TYR B 84 PHE 0.018 0.002 PHE B 255 TRP 0.006 0.001 TRP B 198 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6722) covalent geometry : angle 0.58649 / 0.32 ( 9293) hydrogen bonds : bond 0.05550 / 3.60 ( 269) hydrogen bonds : angle 5.15437 / 3.82 ( 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 111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.152 Fit side-chains REVERT: B 110 LEU cc_start: 0.7689 (mp) cc_final: 0.7445 (mp) REVERT: B 121 ASN cc_start: 0.7451 (t0) cc_final: 0.7116 (t0) REVERT: B 131 GLN cc_start: 0.6740 (tt0) cc_final: 0.6528 (tt0) REVERT: B 298 ARG cc_start: 0.6688 (ttp-110) cc_final: 0.6276 (ttp-170) REVERT: B 315 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7268 (mt-10) REVERT: B 330 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: B 383 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7680 (mmm) REVERT: A 484 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 508 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 512 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6453 (tmtp) outliers start: 31 outliers final: 18 residues processed: 102 average time/residue: 0.5371 time to fit residues: 57.5905 Evaluate side-chains 100 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 403 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 461 GLU 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 352 SER Chi-restraints excluded: chain A residue 475 THR 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: 0.5980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 68 optimal weight: 0.0040 chunk 3 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN A 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.172146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143071 restraints weight = 5877.029| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.42 r_work: 0.3634 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6722 Z= 0.138 Angle : 0.583 9.043 9293 Z= 0.312 Chirality : 0.042 0.262 1047 Planarity : 0.005 0.058 1043 Dihedral : 19.300 161.654 1326 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.77 % Allowed : 28.12 % Favored : 67.11 % 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: -0.15 (0.32), residues: 698 helix: 0.66 (0.34), residues: 218 sheet: -0.57 (0.39), residues: 169 loop : -0.21 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 138 TYR 0.023 0.002 TYR B 84 PHE 0.017 0.002 PHE B 255 TRP 0.005 0.001 TRP B 198 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 6722) covalent geometry : angle 0.58303 / 0.31 ( 9293) hydrogen bonds : bond 0.05520 / 3.59 ( 269) hydrogen bonds : angle 5.09711 / 3.77 ( 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 111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.154 Fit side-chains REVERT: B 110 LEU cc_start: 0.7759 (mp) cc_final: 0.7529 (mp) REVERT: B 121 ASN cc_start: 0.7456 (t0) cc_final: 0.7118 (t0) REVERT: B 131 GLN cc_start: 0.6735 (tt0) cc_final: 0.6518 (tt0) REVERT: B 289 HIS cc_start: 0.7559 (t70) cc_final: 0.7268 (t70) REVERT: B 315 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7263 (mt-10) REVERT: B 330 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7002 (tp30) REVERT: B 383 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7683 (mmm) REVERT: A 484 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8034 (tp) REVERT: A 508 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7122 (mm-30) REVERT: A 512 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6444 (tmtp) outliers start: 29 outliers final: 19 residues processed: 102 average time/residue: 0.5386 time to fit residues: 57.8389 Evaluate side-chains 104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 150 LEU 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 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 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 352 SER Chi-restraints excluded: chain A residue 475 THR 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: 0.8980 chunk 61 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN A 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139156 restraints weight = 5780.243| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.40 r_work: 0.3588 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6722 Z= 0.197 Angle : 0.632 8.710 9293 Z= 0.337 Chirality : 0.044 0.279 1047 Planarity : 0.005 0.060 1043 Dihedral : 19.304 162.753 1326 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.11 % Allowed : 28.78 % Favored : 67.11 % 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: -0.29 (0.32), residues: 698 helix: 0.47 (0.34), residues: 218 sheet: -0.57 (0.39), residues: 165 loop : -0.29 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 138 TYR 0.027 0.002 TYR B 84 PHE 0.017 0.002 PHE B 257 TRP 0.007 0.001 TRP A 510 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 ( 6722) covalent geometry : angle 0.63169 / 0.34 ( 9293) hydrogen bonds : bond 0.05721 / 3.77 ( 269) hydrogen bonds : angle 5.22272 / 3.87 ( 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 106 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.232 Fit side-chains REVERT: B 121 ASN cc_start: 0.7476 (t0) cc_final: 0.7138 (t0) REVERT: B 131 GLN cc_start: 0.6774 (tt0) cc_final: 0.6554 (tt0) REVERT: B 315 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 330 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: A 484 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 508 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7183 (mm-30) outliers start: 25 outliers final: 17 residues processed: 99 average time/residue: 0.5630 time to fit residues: 58.7035 Evaluate side-chains 96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 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 352 SER Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.170712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141355 restraints weight = 5523.367| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.69 r_work: 0.3493 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6722 Z= 0.140 Angle : 0.595 9.002 9293 Z= 0.317 Chirality : 0.042 0.276 1047 Planarity : 0.005 0.059 1043 Dihedral : 19.314 161.664 1326 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.11 % Allowed : 28.45 % 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: -0.13 (0.32), residues: 698 helix: 0.68 (0.34), residues: 217 sheet: -0.53 (0.39), residues: 169 loop : -0.22 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 298 TYR 0.022 0.002 TYR B 84 PHE 0.017 0.002 PHE B 255 TRP 0.005 0.001 TRP A 543 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 6722) covalent geometry : angle 0.59477 / 0.32 ( 9293) hydrogen bonds : bond 0.05537 / 3.57 ( 269) hydrogen bonds : angle 5.10126 / 3.77 ( 746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.07 seconds wall clock time: 40 minutes 35.08 seconds (2435.08 seconds total)