Starting phenix.real_space_refine on Tue Jan 14 09:58:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y7z_39027/01_2025/8y7z_39027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y7z_39027/01_2025/8y7z_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_39027/01_2025/8y7z_39027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y7z_39027/01_2025/8y7z_39027.map" model { file = "/net/cci-nas-00/data/ceres_data/8y7z_39027/01_2025/8y7z_39027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y7z_39027/01_2025/8y7z_39027.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 4.99, per 1000 atoms: 0.77 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: 1.89 Conformation dependent library (CDL) restraints added in 824.1 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: 2.53 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: 2.50 Time building geometry restraints manager: 2.09 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=" CA ASN B 121 " pdb=" CB ASN B 121 " ideal model delta sigma weight residual 1.531 1.579 -0.049 3.28e-02 9.30e+02 2.21e+00 bond pdb=" C3' DA D 18 " pdb=" O3' DA D 18 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" C3' DT D 23 " pdb=" O3' DT D 23 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.41e+00 bond pdb=" CB ASN B 296 " pdb=" CG ASN B 296 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.06e+00 bond pdb=" CG LEU B 288 " pdb=" CD2 LEU B 288 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.55e-01 ... (remaining 6717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9046 1.78 - 3.55: 215 3.55 - 5.33: 24 5.33 - 7.11: 6 7.11 - 8.88: 2 Bond angle restraints: 9293 Sorted by residual: angle pdb=" CB MET B 383 " pdb=" CG MET B 383 " pdb=" SD MET B 383 " ideal model delta sigma weight residual 112.70 121.58 -8.88 3.00e+00 1.11e-01 8.77e+00 angle pdb=" O4' DT D 12 " pdb=" C1' DT D 12 " pdb=" N1 DT D 12 " ideal model delta sigma weight residual 108.40 112.58 -4.18 1.50e+00 4.44e-01 7.77e+00 angle pdb=" C HIS A 441 " pdb=" CA HIS A 441 " pdb=" CB HIS A 441 " ideal model delta sigma weight residual 110.42 115.96 -5.54 1.99e+00 2.53e-01 7.75e+00 angle pdb=" N GLY B 209 " pdb=" CA GLY B 209 " pdb=" C GLY B 209 " ideal model delta sigma weight residual 113.18 107.21 5.97 2.37e+00 1.78e-01 6.34e+00 angle pdb=" N HIS A 441 " pdb=" CA HIS A 441 " pdb=" C HIS A 441 " ideal model delta sigma weight residual 110.80 105.57 5.23 2.13e+00 2.20e-01 6.02e+00 ... (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: 756 0.040 - 0.080: 205 0.080 - 0.120: 70 0.120 - 0.160: 14 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=" CB ILE B 225 " pdb=" CA ILE B 225 " pdb=" CG1 ILE B 225 " pdb=" CG2 ILE B 225 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.85e-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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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= 0.242 Angle : 0.657 8.885 9293 Z= 0.352 Chirality : 0.043 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 198 HIS 0.003 0.001 HIS B 166 PHE 0.012 0.002 PHE B 257 TYR 0.021 0.002 TYR B 84 ARG 0.008 0.000 ARG B 138 *********************** 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 : 0.731 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: 1.2618 time to fit residues: 112.8638 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 : 0.694 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4002 r_free = 0.4002 target = 0.171138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141667 restraints weight = 5760.763| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.43 r_work: 0.3622 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0625 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= 0.238 Angle : 0.616 8.457 9293 Z= 0.324 Chirality : 0.042 0.170 1047 Planarity : 0.005 0.040 1043 Dihedral : 19.479 164.118 1326 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.11 % Allowed : 27.30 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.32), residues: 698 helix: 0.45 (0.34), residues: 217 sheet: -0.46 (0.39), residues: 165 loop : -0.26 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 198 HIS 0.004 0.001 HIS B 60 PHE 0.016 0.002 PHE B 255 TYR 0.017 0.002 TYR B 84 ARG 0.006 0.001 ARG B 138 *********************** 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 : 0.670 Fit side-chains revert: symmetry clash REVERT: B 315 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7317 (mt-10) REVERT: B 383 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7661 (mmm) REVERT: A 484 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7977 (tp) REVERT: A 508 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7171 (mm-30) outliers start: 25 outliers final: 9 residues processed: 100 average time/residue: 1.2247 time to fit residues: 128.8861 Evaluate side-chains 85 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 383 MET 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 57 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4010 r_free = 0.4010 target = 0.171957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142823 restraints weight = 5779.521| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.43 r_work: 0.3634 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0888 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= 0.214 Angle : 0.590 8.643 9293 Z= 0.310 Chirality : 0.041 0.165 1047 Planarity : 0.004 0.038 1043 Dihedral : 19.380 164.281 1326 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.61 % Allowed : 26.81 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.32), residues: 698 helix: 0.56 (0.35), residues: 218 sheet: -0.41 (0.39), residues: 169 loop : -0.24 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 198 HIS 0.003 0.001 HIS B 60 PHE 0.014 0.002 PHE B 255 TYR 0.015 0.002 TYR B 341 ARG 0.009 0.001 ARG B 138 *********************** 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 109 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.706 Fit side-chains REVERT: B 289 HIS cc_start: 0.7555 (t70) cc_final: 0.7238 (t70) REVERT: B 315 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7302 (mt-10) REVERT: A 484 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8018 (tp) REVERT: A 508 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7176 (mm-30) outliers start: 28 outliers final: 13 residues processed: 101 average time/residue: 1.2247 time to fit residues: 130.6856 Evaluate side-chains 89 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 466 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4016 r_free = 0.4016 target = 0.172994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143870 restraints weight = 5822.823| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.44 r_work: 0.3647 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1026 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= 0.202 Angle : 0.579 8.696 9293 Z= 0.303 Chirality : 0.040 0.160 1047 Planarity : 0.004 0.039 1043 Dihedral : 19.308 164.375 1326 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.77 % Allowed : 26.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.32), residues: 698 helix: 0.71 (0.35), residues: 217 sheet: -0.35 (0.39), residues: 169 loop : -0.20 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 198 HIS 0.003 0.001 HIS B 60 PHE 0.014 0.002 PHE B 255 TYR 0.020 0.002 TYR B 84 ARG 0.010 0.001 ARG B 138 *********************** 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 110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.720 Fit side-chains REVERT: B 110 LEU cc_start: 0.7705 (mp) cc_final: 0.7491 (mp) REVERT: B 289 HIS cc_start: 0.7560 (t70) cc_final: 0.7240 (t70) REVERT: B 315 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7291 (mt-10) REVERT: B 330 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: B 334 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8018 (mm) REVERT: A 484 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7981 (tp) REVERT: A 508 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 512 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6361 (tmtp) outliers start: 29 outliers final: 16 residues processed: 101 average time/residue: 1.2577 time to fit residues: 133.9916 Evaluate side-chains 97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 334 ILE 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 403 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 0.0010 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** 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 = 0.3993 r_free = 0.3993 target = 0.172332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140747 restraints weight = 5464.067| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.48 r_work: 0.3541 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1163 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= 0.202 Angle : 0.575 8.315 9293 Z= 0.300 Chirality : 0.040 0.153 1047 Planarity : 0.004 0.044 1043 Dihedral : 19.274 164.487 1326 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.44 % Allowed : 27.30 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.32), residues: 698 helix: 0.79 (0.35), residues: 217 sheet: -0.31 (0.39), residues: 169 loop : -0.19 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 198 HIS 0.003 0.001 HIS B 166 PHE 0.017 0.002 PHE B 255 TYR 0.021 0.002 TYR B 84 ARG 0.010 0.000 ARG B 138 *********************** 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 110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.721 Fit side-chains REVERT: B 289 HIS cc_start: 0.7483 (t70) cc_final: 0.7203 (t70) REVERT: B 298 ARG cc_start: 0.6594 (ttp-110) cc_final: 0.6246 (mtp180) REVERT: B 330 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: B 334 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7867 (mm) REVERT: A 484 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 508 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 512 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6404 (tmtp) REVERT: A 528 ARG cc_start: 0.7080 (ttp-170) cc_final: 0.6220 (ptt180) outliers start: 27 outliers final: 17 residues processed: 102 average time/residue: 1.2043 time to fit residues: 129.3851 Evaluate side-chains 100 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 334 ILE 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 403 LEU 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 352 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 512 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 62 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** 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 = 0.3977 r_free = 0.3977 target = 0.170577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138550 restraints weight = 5415.729| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.53 r_work: 0.3513 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 0.036 6722 Z= 0.231 Angle : 0.593 8.919 9293 Z= 0.308 Chirality : 0.041 0.148 1047 Planarity : 0.004 0.048 1043 Dihedral : 19.251 164.761 1326 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.77 % Allowed : 27.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.32), residues: 698 helix: 0.70 (0.35), residues: 218 sheet: -0.31 (0.39), residues: 169 loop : -0.20 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 510 HIS 0.003 0.001 HIS B 166 PHE 0.015 0.002 PHE B 257 TYR 0.021 0.002 TYR B 84 ARG 0.011 0.001 ARG B 138 *********************** 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 110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.718 Fit side-chains REVERT: B 110 LEU cc_start: 0.7634 (mp) cc_final: 0.7403 (mp) REVERT: B 289 HIS cc_start: 0.7487 (t70) cc_final: 0.7206 (t70) REVERT: B 298 ARG cc_start: 0.6621 (ttp-110) cc_final: 0.6322 (mtp180) REVERT: B 307 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7959 (tttp) REVERT: B 330 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: A 367 SER cc_start: 0.7853 (m) cc_final: 0.7168 (p) REVERT: A 484 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7874 (tp) REVERT: A 508 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7190 (mm-30) REVERT: A 528 ARG cc_start: 0.7052 (ttp-170) cc_final: 0.6185 (ptt180) outliers start: 29 outliers final: 18 residues processed: 102 average time/residue: 1.2128 time to fit residues: 130.0295 Evaluate side-chains 97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 185 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 307 LYS 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 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 514 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.0000 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3961 r_free = 0.3961 target = 0.167114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137412 restraints weight = 5720.124| |-----------------------------------------------------------------------------| 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: 0.3463 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6722 Z= 0.340 Angle : 0.664 7.990 9293 Z= 0.345 Chirality : 0.044 0.159 1047 Planarity : 0.005 0.047 1043 Dihedral : 19.306 165.155 1326 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.43 % Allowed : 26.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.32), residues: 698 helix: 0.44 (0.34), residues: 216 sheet: -0.38 (0.40), residues: 165 loop : -0.26 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 510 HIS 0.005 0.001 HIS B 166 PHE 0.016 0.002 PHE B 257 TYR 0.026 0.002 TYR B 84 ARG 0.011 0.001 ARG B 138 *********************** 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 108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.739 Fit side-chains REVERT: B 222 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6388 (mm-30) REVERT: B 307 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8133 (tttp) REVERT: B 315 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7153 (mt-10) REVERT: B 330 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7060 (tp30) REVERT: A 367 SER cc_start: 0.7916 (m) cc_final: 0.7243 (p) REVERT: A 484 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8006 (tp) outliers start: 33 outliers final: 18 residues processed: 99 average time/residue: 1.2801 time to fit residues: 133.2016 Evaluate side-chains 94 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 222 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 307 LYS 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 392 GLN Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR 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 363 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3999 r_free = 0.3999 target = 0.171043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141945 restraints weight = 5771.695| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.43 r_work: 0.3622 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6722 Z= 0.224 Angle : 0.602 8.271 9293 Z= 0.315 Chirality : 0.041 0.155 1047 Planarity : 0.005 0.053 1043 Dihedral : 19.253 164.461 1326 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.93 % Allowed : 26.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.32), residues: 698 helix: 0.70 (0.35), residues: 217 sheet: -0.43 (0.40), residues: 169 loop : -0.18 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 543 HIS 0.003 0.001 HIS B 60 PHE 0.018 0.002 PHE B 257 TYR 0.027 0.002 TYR B 84 ARG 0.012 0.001 ARG B 138 *********************** 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 108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.697 Fit side-chains REVERT: B 222 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6221 (mm-30) REVERT: B 298 ARG cc_start: 0.6591 (ttp-110) cc_final: 0.6279 (mtp180) REVERT: B 307 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8075 (tttp) REVERT: B 330 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: B 457 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7791 (ttmt) REVERT: A 367 SER cc_start: 0.7902 (m) cc_final: 0.7223 (p) REVERT: A 484 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 508 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7205 (mm-30) outliers start: 30 outliers final: 16 residues processed: 99 average time/residue: 1.3683 time to fit residues: 142.5234 Evaluate side-chains 97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 222 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 307 LYS 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 401 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 457 LYS 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 363 ILE Chi-restraints excluded: chain A residue 484 LEU 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: 3.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3959 r_free = 0.3959 target = 0.166970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137010 restraints weight = 5859.742| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.45 r_work: 0.3568 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6722 Z= 0.351 Angle : 0.677 8.720 9293 Z= 0.351 Chirality : 0.044 0.155 1047 Planarity : 0.005 0.053 1043 Dihedral : 19.306 165.147 1326 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.11 % Allowed : 27.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.32), residues: 698 helix: 0.38 (0.33), residues: 217 sheet: -0.48 (0.40), residues: 165 loop : -0.25 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 510 HIS 0.004 0.001 HIS B 166 PHE 0.019 0.002 PHE B 257 TYR 0.029 0.002 TYR B 84 ARG 0.014 0.001 ARG B 138 *********************** 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 98 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.728 Fit side-chains REVERT: B 110 LEU cc_start: 0.7711 (mp) cc_final: 0.7484 (mp) REVERT: B 222 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6240 (mm-30) REVERT: B 298 ARG cc_start: 0.6651 (ttp-110) cc_final: 0.6328 (mtp180) REVERT: B 307 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8145 (tttp) REVERT: B 330 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: A 367 SER cc_start: 0.7938 (m) cc_final: 0.7273 (p) REVERT: A 484 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7997 (tp) outliers start: 25 outliers final: 17 residues processed: 90 average time/residue: 1.3509 time to fit residues: 128.3786 Evaluate side-chains 92 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 222 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 307 LYS 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 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 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** 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 = 0.3983 r_free = 0.3983 target = 0.169472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139763 restraints weight = 5822.946| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.44 r_work: 0.3601 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1244 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= 0.263 Angle : 0.628 8.868 9293 Z= 0.327 Chirality : 0.042 0.155 1047 Planarity : 0.005 0.057 1043 Dihedral : 19.267 164.636 1326 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.45 % Allowed : 28.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.32), residues: 698 helix: 0.55 (0.34), residues: 218 sheet: -0.50 (0.40), residues: 165 loop : -0.23 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 510 HIS 0.003 0.001 HIS B 166 PHE 0.017 0.002 PHE B 257 TYR 0.026 0.002 TYR B 84 ARG 0.014 0.001 ARG B 138 ********************** 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 95 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.665 Fit side-chains REVERT: B 222 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: B 298 ARG cc_start: 0.6674 (ttp-110) cc_final: 0.6369 (mtp180) REVERT: B 307 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8076 (tttp) REVERT: B 330 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6989 (tp30) REVERT: A 367 SER cc_start: 0.7929 (m) cc_final: 0.7258 (p) REVERT: A 484 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8051 (tp) REVERT: A 508 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7267 (mm-30) outliers start: 21 outliers final: 17 residues processed: 89 average time/residue: 1.3092 time to fit residues: 122.4330 Evaluate side-chains 94 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 222 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 307 LYS 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 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 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3972 r_free = 0.3972 target = 0.168131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138555 restraints weight = 5896.247| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.44 r_work: 0.3588 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6722 Z= 0.287 Angle : 0.642 8.799 9293 Z= 0.333 Chirality : 0.043 0.155 1047 Planarity : 0.005 0.058 1043 Dihedral : 19.264 164.770 1326 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.95 % Allowed : 27.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.32), residues: 698 helix: 0.50 (0.34), residues: 218 sheet: -0.51 (0.40), residues: 169 loop : -0.23 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 510 HIS 0.004 0.001 HIS B 166 PHE 0.018 0.002 PHE B 257 TYR 0.027 0.002 TYR B 84 ARG 0.014 0.001 ARG B 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5243.75 seconds wall clock time: 95 minutes 17.85 seconds (5717.85 seconds total)