Starting phenix.real_space_refine on Sat Jul 4 03:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf2_45527/07_2026/9cf2_45527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf2_45527/07_2026/9cf2_45527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cf2_45527/07_2026/9cf2_45527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf2_45527/07_2026/9cf2_45527.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf2_45527/07_2026/9cf2_45527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf2_45527/07_2026/9cf2_45527.cif" } resolution = 3.15 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= 0.002 sd= 0.030 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 121 5.49 5 S 35 5.16 5 C 5804 2.51 5 N 1707 2.21 5 O 2071 1.98 5 H 8649 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 18387 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2426 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 151} Chain: "N" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 349 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 12097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 12097 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 26, 'TRANS': 699} Chain breaks: 1 Chain: "T" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 830 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "W" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1787 Classifications: {'DNA': 15, 'RNA': 41} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 7, 'rna3p': 48} Chain: "X" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 449 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 449 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Time building chain proxies: 2.64, per 1000 atoms: 0.14 Number of scatterers: 18387 At special positions: 0 Unit cell: (80.025, 120.45, 122.925, 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 35 16.00 P 121 15.00 O 2071 8.00 N 1707 7.00 C 5804 6.00 H 8649 1.00 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: 1.69 Conformation dependent library (CDL) restraints added in 426.0 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 51.6% alpha, 11.3% beta 48 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'B' and resid 27 through 40 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.677A pdb=" N LEU B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 119 through 122 Processing helix chain 'P' and resid 123 through 155 Processing helix chain 'P' and resid 159 through 164 removed outlier: 3.851A pdb=" N LEU P 163 " --> pdb=" O ALA P 159 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE P 164 " --> pdb=" O PHE P 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 159 through 164' Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.614A pdb=" N LEU P 176 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 187 Processing helix chain 'P' and resid 188 through 210 removed outlier: 3.801A pdb=" N HIS P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP P 203 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA P 204 " --> pdb=" O LYS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 255 removed outlier: 3.756A pdb=" N ALA P 228 " --> pdb=" O LEU P 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS P 229 " --> pdb=" O TYR P 225 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN P 244 " --> pdb=" O ALA P 240 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG P 245 " --> pdb=" O HIS P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 270 removed outlier: 3.547A pdb=" N ALA P 269 " --> pdb=" O LYS P 265 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN P 270 " --> pdb=" O GLU P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 285 through 298 Processing helix chain 'P' and resid 308 through 320 Processing helix chain 'P' and resid 328 through 331 Processing helix chain 'P' and resid 332 through 340 removed outlier: 4.203A pdb=" N VAL P 338 " --> pdb=" O PHE P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 343 No H-bonds generated for 'chain 'P' and resid 341 through 343' Processing helix chain 'P' and resid 344 through 358 Processing helix chain 'P' and resid 380 through 388 Processing helix chain 'P' and resid 396 through 398 No H-bonds generated for 'chain 'P' and resid 396 through 398' Processing helix chain 'P' and resid 399 through 406 removed outlier: 3.602A pdb=" N TRP P 404 " --> pdb=" O LYS P 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 419 through 423 Processing helix chain 'P' and resid 466 through 470 Processing helix chain 'P' and resid 471 through 476 Processing helix chain 'P' and resid 477 through 479 No H-bonds generated for 'chain 'P' and resid 477 through 479' Processing helix chain 'P' and resid 512 through 530 removed outlier: 5.274A pdb=" N CYS P 518 " --> pdb=" O ASP P 514 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER P 519 " --> pdb=" O ARG P 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 531 through 542 Processing helix chain 'P' and resid 550 through 573 removed outlier: 4.959A pdb=" N ASP P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE P 567 " --> pdb=" O SER P 563 " (cutoff:3.500A) Processing helix chain 'P' and resid 623 through 639 removed outlier: 3.838A pdb=" N SER P 627 " --> pdb=" O ILE P 623 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN P 639 " --> pdb=" O GLN P 635 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 645 removed outlier: 3.964A pdb=" N GLU P 645 " --> pdb=" O LYS P 641 " (cutoff:3.500A) Processing helix chain 'P' and resid 648 through 665 removed outlier: 3.761A pdb=" N GLU P 664 " --> pdb=" O LYS P 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 669 through 679 Processing helix chain 'P' and resid 680 through 684 Processing helix chain 'P' and resid 686 through 713 Processing helix chain 'P' and resid 736 through 747 Processing helix chain 'P' and resid 780 through 784 Processing helix chain 'P' and resid 818 through 837 Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.649A pdb=" N ARG B 53 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 95 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET B 98 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 126 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 19 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA B 10 " --> pdb=" O PRO B 14 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 16 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 158 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 9 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL B 156 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 107 through 113 removed outlier: 5.132A pdb=" N THR P 429 " --> pdb=" O LEU P 440 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLN P 442 " --> pdb=" O GLN P 427 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN P 427 " --> pdb=" O GLN P 442 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU P 430 " --> pdb=" O VAL P 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'P' and resid 507 through 511 removed outlier: 6.244A pdb=" N VAL P 483 " --> pdb=" O VAL P 720 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLY P 722 " --> pdb=" O VAL P 483 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N MET P 485 " --> pdb=" O GLY P 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 592 through 593 Processing sheet with id=AA6, first strand: chain 'P' and resid 770 through 771 Processing sheet with id=AA7, first strand: chain 'P' and resid 775 through 777 350 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8632 1.03 - 1.23: 83 1.23 - 1.42: 4392 1.42 - 1.62: 5685 1.62 - 1.81: 53 Bond restraints: 18845 Sorted by residual: bond pdb=" C3' DT T 1 " pdb=" C2' DT T 1 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT Y 13 " pdb=" C2' DT Y 13 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT T 0 " pdb=" C2' DT T 0 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.87e+00 bond pdb=" C3' DA X 11 " pdb=" C2' DA X 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.54e+00 bond pdb=" C3' DA X 20 " pdb=" C2' DA X 20 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.11e+00 ... (remaining 18840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 33841 2.56 - 5.13: 233 5.13 - 7.69: 2 7.69 - 10.26: 8 10.26 - 12.82: 4 Bond angle restraints: 34088 Sorted by residual: angle pdb=" N3 DT W 49 " pdb=" C4 DT W 49 " pdb=" O4 DT W 49 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N ILE P 580 " pdb=" CA ILE P 580 " pdb=" C ILE P 580 " ideal model delta sigma weight residual 113.71 109.43 4.28 9.50e-01 1.11e+00 2.03e+01 angle pdb=" N3 DT T 0 " pdb=" C4 DT T 0 " pdb=" O4 DT T 0 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT Y 8 " pdb=" C4 DT Y 8 " pdb=" O4 DT Y 8 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4' DC T -15 " pdb=" C1' DC T -15 " pdb=" N1 DC T -15 " ideal model delta sigma weight residual 108.00 111.07 -3.07 7.00e-01 2.04e+00 1.93e+01 ... (remaining 34083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 8121 35.18 - 70.36: 458 70.36 - 105.54: 27 105.54 - 140.72: 7 140.72 - 175.90: 4 Dihedral angle restraints: 8617 sinusoidal: 5491 harmonic: 3126 Sorted by residual: dihedral pdb=" O4' U W 15 " pdb=" C1' U W 15 " pdb=" N1 U W 15 " pdb=" C2 U W 15 " ideal model delta sinusoidal sigma weight residual -128.00 39.23 -167.23 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" O4' U W 17 " pdb=" C1' U W 17 " pdb=" N1 U W 17 " pdb=" C2 U W 17 " ideal model delta sinusoidal sigma weight residual -128.00 27.16 -155.16 1 1.70e+01 3.46e-03 6.34e+01 dihedral pdb=" CA TYR P 600 " pdb=" C TYR P 600 " pdb=" N TYR P 601 " pdb=" CA TYR P 601 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1452 0.085 - 0.170: 130 0.170 - 0.254: 4 0.254 - 0.339: 1 0.339 - 0.424: 3 Chirality restraints: 1590 Sorted by residual: chirality pdb=" P DT T -1 " pdb=" OP1 DT T -1 " pdb=" OP2 DT T -1 " pdb=" O5' DT T -1 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" P A W 29 " pdb=" OP1 A W 29 " pdb=" OP2 A W 29 " pdb=" O5' A W 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" P DT T 0 " pdb=" OP1 DT T 0 " pdb=" OP2 DT T 0 " pdb=" O5' DT T 0 " both_signs ideal model delta sigma weight residual True 2.34 -2.69 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 1587 not shown) Planarity restraints: 2323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C W 36 " 0.017 2.00e-02 2.50e+03 7.81e-03 1.68e+00 pdb=" N1 C W 36 " -0.018 2.00e-02 2.50e+03 pdb=" C2 C W 36 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C W 36 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C W 36 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C W 36 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C W 36 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C W 36 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C W 36 " -0.003 2.00e-02 2.50e+03 pdb=" H5 C W 36 " 0.002 2.00e-02 2.50e+03 pdb=" H6 C W 36 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN P 287 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO P 288 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO P 288 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 288 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN P 530 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO P 531 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO P 531 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO P 531 " -0.017 5.00e-02 4.00e+02 ... (remaining 2320 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 279 2.07 - 2.70: 27517 2.70 - 3.34: 51405 3.34 - 3.97: 65593 3.97 - 4.60: 104126 Nonbonded interactions: 248920 Sorted by model distance: nonbonded pdb=" OH TYR P 225 " pdb=" OD2 ASP P 380 " model vdw 1.441 2.800 nonbonded pdb="HO2' U W 31 " pdb=" OP2 A W 32 " model vdw 1.562 2.450 nonbonded pdb=" O THR P 759 " pdb="HD21 ASN P 825 " model vdw 1.568 2.450 nonbonded pdb="HO2' A W 29 " pdb=" O5' U W 30 " model vdw 1.592 2.450 nonbonded pdb="HH22 ARG P 818 " pdb=" OP2 DT Y 13 " model vdw 1.618 2.450 ... (remaining 248915 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: 1.610 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: 0.110 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 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 0.039 10196 Z= 0.323 Angle : 0.686 12.824 14269 Z= 0.529 Chirality : 0.050 0.424 1590 Planarity : 0.003 0.032 1391 Dihedral : 18.512 175.903 4334 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 2.60 (0.30), residues: 882 helix: 3.23 (0.28), residues: 364 sheet: 1.10 (0.60), residues: 79 loop : 0.62 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 282 TYR 0.006 0.001 TYR P 141 PHE 0.008 0.001 PHE P 158 TRP 0.002 0.000 TRP P 816 HIS 0.001 0.000 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.32 (10196) covalent geometry : angle 0.68639 / 0.53 (14269) hydrogen bonds : bond 0.15325 / 10.17 ( 464) hydrogen bonds : angle 5.82944 / 4.03 ( 1220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 VAL cc_start: 0.7288 (t) cc_final: 0.6882 (t) REVERT: B 106 ASN cc_start: 0.7067 (m-40) cc_final: 0.6712 (m-40) REVERT: P 112 THR cc_start: 0.7345 (t) cc_final: 0.7082 (p) REVERT: P 160 PHE cc_start: 0.7614 (t80) cc_final: 0.7353 (t80) REVERT: P 171 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6326 (mm-30) REVERT: P 195 ARG cc_start: 0.6956 (ttm170) cc_final: 0.6688 (ttm-80) REVERT: P 202 LYS cc_start: 0.7587 (tttt) cc_final: 0.7273 (ttpp) REVERT: P 205 TYR cc_start: 0.7738 (t80) cc_final: 0.7338 (t80) REVERT: P 212 THR cc_start: 0.7622 (m) cc_final: 0.7313 (p) REVERT: P 254 PHE cc_start: 0.7554 (t80) cc_final: 0.7342 (t80) REVERT: P 310 LYS cc_start: 0.8223 (tttt) cc_final: 0.8000 (ttpp) REVERT: P 395 LEU cc_start: 0.8320 (tp) cc_final: 0.8104 (tt) REVERT: P 422 LYS cc_start: 0.7939 (mttt) cc_final: 0.7699 (mttp) REVERT: P 484 LEU cc_start: 0.7091 (mt) cc_final: 0.6859 (mp) REVERT: P 503 ASP cc_start: 0.7082 (p0) cc_final: 0.6626 (p0) REVERT: P 504 LYS cc_start: 0.7742 (tttt) cc_final: 0.7405 (ttpp) REVERT: P 540 TYR cc_start: 0.7535 (t80) cc_final: 0.7213 (t80) REVERT: P 556 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6940 (mt-10) REVERT: P 584 TYR cc_start: 0.8378 (m-80) cc_final: 0.8155 (m-80) REVERT: P 656 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7454 (mt-10) REVERT: P 672 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8083 (mtpt) REVERT: P 699 ASP cc_start: 0.6625 (m-30) cc_final: 0.6383 (m-30) REVERT: P 752 TYR cc_start: 0.7933 (m-80) cc_final: 0.7709 (m-80) REVERT: P 769 ASP cc_start: 0.7161 (p0) cc_final: 0.6800 (p0) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2859 time to fit residues: 101.2588 Evaluate side-chains 233 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 300 ASN P 353 GLN P 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.151275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125720 restraints weight = 37032.255| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.79 r_work: 0.3490 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10196 Z= 0.339 Angle : 0.696 9.604 14269 Z= 0.416 Chirality : 0.050 0.271 1590 Planarity : 0.005 0.074 1391 Dihedral : 23.036 178.126 2476 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.88 % Allowed : 8.21 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.28), residues: 882 helix: 2.29 (0.26), residues: 368 sheet: 0.42 (0.54), residues: 88 loop : 0.39 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 839 TYR 0.020 0.002 TYR P 141 PHE 0.021 0.002 PHE B 111 TRP 0.007 0.002 TRP P 816 HIS 0.007 0.001 HIS P 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.34 (10196) covalent geometry : angle 0.69581 / 0.42 (14269) hydrogen bonds : bond 0.06125 / 4.10 ( 464) hydrogen bonds : angle 4.89854 / 3.37 ( 1220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 242 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 VAL cc_start: 0.7274 (t) cc_final: 0.7012 (t) REVERT: B 35 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8263 (ttp80) REVERT: B 106 ASN cc_start: 0.7869 (m-40) cc_final: 0.7505 (m-40) REVERT: P 160 PHE cc_start: 0.7924 (t80) cc_final: 0.7556 (t80) REVERT: P 202 LYS cc_start: 0.8329 (tttt) cc_final: 0.8129 (ttpp) REVERT: P 212 THR cc_start: 0.8243 (m) cc_final: 0.7922 (p) REVERT: P 313 THR cc_start: 0.7947 (m) cc_final: 0.7745 (p) REVERT: P 331 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7505 (mt-10) REVERT: P 380 ASP cc_start: 0.7032 (t0) cc_final: 0.6735 (t0) REVERT: P 395 LEU cc_start: 0.8481 (tp) cc_final: 0.8238 (tt) REVERT: P 399 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7081 (mm-30) REVERT: P 422 LYS cc_start: 0.8452 (mttt) cc_final: 0.8191 (mttp) REVERT: P 484 LEU cc_start: 0.8309 (mt) cc_final: 0.8041 (mp) REVERT: P 504 LYS cc_start: 0.8390 (tttt) cc_final: 0.8114 (ttmm) REVERT: P 536 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7553 (mm-30) REVERT: P 540 TYR cc_start: 0.8109 (t80) cc_final: 0.7848 (t80) REVERT: P 565 LYS cc_start: 0.8485 (pttt) cc_final: 0.8145 (pttm) REVERT: P 584 TYR cc_start: 0.8738 (m-80) cc_final: 0.8326 (m-80) REVERT: P 599 LEU cc_start: 0.8115 (tp) cc_final: 0.7903 (tt) REVERT: P 603 ASN cc_start: 0.8161 (m-40) cc_final: 0.7955 (m-40) REVERT: P 637 MET cc_start: 0.8864 (ttt) cc_final: 0.8624 (ttm) REVERT: P 653 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7351 (mtp180) REVERT: P 656 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7702 (mt-10) REVERT: P 672 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8391 (mtpt) REVERT: P 695 LYS cc_start: 0.8031 (tppt) cc_final: 0.7441 (tptm) REVERT: P 699 ASP cc_start: 0.7888 (m-30) cc_final: 0.7634 (m-30) REVERT: P 701 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7616 (t0) REVERT: P 769 ASP cc_start: 0.7650 (p0) cc_final: 0.7436 (p0) REVERT: P 787 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7545 (mm-40) REVERT: P 819 ASP cc_start: 0.7776 (m-30) cc_final: 0.7486 (m-30) outliers start: 7 outliers final: 1 residues processed: 246 average time/residue: 0.2578 time to fit residues: 80.7246 Evaluate side-chains 224 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 701 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 HIS ** P 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.150861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125373 restraints weight = 36876.530| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.71 r_work: 0.3484 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 10196 Z= 0.212 Angle : 0.592 6.514 14269 Z= 0.364 Chirality : 0.045 0.225 1590 Planarity : 0.004 0.053 1391 Dihedral : 23.125 175.381 2476 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.01 % Allowed : 9.72 % Favored : 89.27 % 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: 1.43 (0.28), residues: 882 helix: 2.01 (0.26), residues: 368 sheet: 0.27 (0.54), residues: 91 loop : 0.25 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 818 TYR 0.013 0.002 TYR P 386 PHE 0.018 0.002 PHE P 254 TRP 0.007 0.001 TRP P 816 HIS 0.004 0.001 HIS P 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (10196) covalent geometry : angle 0.59228 / 0.36 (14269) hydrogen bonds : bond 0.05455 / 3.65 ( 464) hydrogen bonds : angle 4.70373 / 3.23 ( 1220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 VAL cc_start: 0.7358 (t) cc_final: 0.7102 (t) REVERT: B 35 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8274 (ttp80) REVERT: B 106 ASN cc_start: 0.7922 (m-40) cc_final: 0.7592 (m-40) REVERT: P 114 ILE cc_start: 0.8336 (mm) cc_final: 0.8128 (tt) REVERT: P 160 PHE cc_start: 0.7909 (t80) cc_final: 0.7463 (t80) REVERT: P 202 LYS cc_start: 0.8357 (tttt) cc_final: 0.8058 (ttpp) REVERT: P 212 THR cc_start: 0.8221 (m) cc_final: 0.7909 (p) REVERT: P 255 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8110 (mmtp) REVERT: P 259 LYS cc_start: 0.8003 (mttt) cc_final: 0.7790 (mtpt) REVERT: P 331 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7485 (mt-10) REVERT: P 380 ASP cc_start: 0.6908 (t0) cc_final: 0.6643 (t0) REVERT: P 395 LEU cc_start: 0.8490 (tp) cc_final: 0.8239 (tt) REVERT: P 399 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6997 (mm-30) REVERT: P 422 LYS cc_start: 0.8435 (mttt) cc_final: 0.8172 (mttp) REVERT: P 504 LYS cc_start: 0.8429 (tttt) cc_final: 0.8149 (ttpt) REVERT: P 536 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7584 (mm-30) REVERT: P 565 LYS cc_start: 0.8469 (pttt) cc_final: 0.8191 (pttm) REVERT: P 637 MET cc_start: 0.8836 (ttt) cc_final: 0.8587 (ttm) REVERT: P 653 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7450 (mtp180) REVERT: P 656 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7724 (mt-10) REVERT: P 660 LYS cc_start: 0.8878 (tttt) cc_final: 0.8653 (tttt) REVERT: P 672 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8424 (mtpt) REVERT: P 695 LYS cc_start: 0.8009 (tppt) cc_final: 0.7413 (tptm) REVERT: P 699 ASP cc_start: 0.7951 (m-30) cc_final: 0.7666 (m-30) REVERT: P 769 ASP cc_start: 0.7633 (p0) cc_final: 0.7428 (p0) REVERT: P 787 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7591 (mm-40) REVERT: P 819 ASP cc_start: 0.7762 (m-30) cc_final: 0.7460 (m-30) outliers start: 8 outliers final: 7 residues processed: 223 average time/residue: 0.2673 time to fit residues: 76.1713 Evaluate side-chains 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 221 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 476 LYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 729 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 0.0370 chunk 97 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 GLN P 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.150616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125061 restraints weight = 36917.395| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.72 r_work: 0.3482 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10196 Z= 0.182 Angle : 0.575 5.449 14269 Z= 0.354 Chirality : 0.043 0.212 1590 Planarity : 0.004 0.050 1391 Dihedral : 23.168 175.081 2476 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.14 % Allowed : 8.96 % Favored : 89.90 % 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: 1.39 (0.28), residues: 882 helix: 2.05 (0.26), residues: 370 sheet: 0.24 (0.53), residues: 86 loop : 0.13 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 758 TYR 0.012 0.001 TYR P 141 PHE 0.013 0.001 PHE P 254 TRP 0.007 0.001 TRP P 816 HIS 0.027 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (10196) covalent geometry : angle 0.57472 / 0.35 (14269) hydrogen bonds : bond 0.04841 / 3.22 ( 464) hydrogen bonds : angle 4.52349 / 3.11 ( 1220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8282 (ttp80) REVERT: B 106 ASN cc_start: 0.7944 (m-40) cc_final: 0.7640 (m-40) REVERT: P 202 LYS cc_start: 0.8311 (tttt) cc_final: 0.8011 (ttpp) REVERT: P 212 THR cc_start: 0.8218 (m) cc_final: 0.7891 (p) REVERT: P 255 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8068 (mmtp) REVERT: P 380 ASP cc_start: 0.6906 (t0) cc_final: 0.6630 (t0) REVERT: P 395 LEU cc_start: 0.8492 (tp) cc_final: 0.8242 (tt) REVERT: P 399 GLU cc_start: 0.7619 (mm-30) cc_final: 0.6949 (mm-30) REVERT: P 422 LYS cc_start: 0.8472 (mttt) cc_final: 0.8211 (mttp) REVERT: P 504 LYS cc_start: 0.8423 (tttt) cc_final: 0.8138 (ttpt) REVERT: P 536 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7568 (mm-30) REVERT: P 565 LYS cc_start: 0.8476 (pttt) cc_final: 0.8195 (pttm) REVERT: P 637 MET cc_start: 0.8841 (ttt) cc_final: 0.8584 (ttm) REVERT: P 653 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7456 (mtp180) REVERT: P 656 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7775 (mt-10) REVERT: P 660 LYS cc_start: 0.8869 (tttt) cc_final: 0.8632 (tttt) REVERT: P 672 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8475 (mtpt) REVERT: P 695 LYS cc_start: 0.8014 (tppt) cc_final: 0.7385 (tptm) REVERT: P 699 ASP cc_start: 0.7958 (m-30) cc_final: 0.7670 (m-30) REVERT: P 787 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7589 (mm-40) REVERT: P 819 ASP cc_start: 0.7777 (m-30) cc_final: 0.7468 (m-30) outliers start: 9 outliers final: 7 residues processed: 217 average time/residue: 0.2869 time to fit residues: 79.4137 Evaluate side-chains 222 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 729 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125946 restraints weight = 36860.579| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.72 r_work: 0.3494 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10196 Z= 0.140 Angle : 0.542 4.531 14269 Z= 0.336 Chirality : 0.041 0.190 1590 Planarity : 0.004 0.040 1391 Dihedral : 23.198 174.308 2476 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.26 % Allowed : 9.09 % Favored : 89.65 % 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: 1.47 (0.28), residues: 882 helix: 2.13 (0.26), residues: 376 sheet: 0.13 (0.53), residues: 86 loop : 0.16 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 703 TYR 0.013 0.001 TYR B 46 PHE 0.013 0.001 PHE B 65 TRP 0.007 0.001 TRP P 816 HIS 0.011 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (10196) covalent geometry : angle 0.54156 / 0.34 (14269) hydrogen bonds : bond 0.04480 / 2.98 ( 464) hydrogen bonds : angle 4.36833 / 3.01 ( 1220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8273 (ttp80) REVERT: B 106 ASN cc_start: 0.7949 (m-40) cc_final: 0.7649 (m-40) REVERT: P 202 LYS cc_start: 0.8275 (tttt) cc_final: 0.8000 (ttpp) REVERT: P 212 THR cc_start: 0.8206 (m) cc_final: 0.7901 (p) REVERT: P 255 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8064 (mmtp) REVERT: P 380 ASP cc_start: 0.6818 (t0) cc_final: 0.6390 (t0) REVERT: P 395 LEU cc_start: 0.8493 (tp) cc_final: 0.8242 (tt) REVERT: P 399 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6864 (mm-30) REVERT: P 422 LYS cc_start: 0.8459 (mttt) cc_final: 0.8206 (mttp) REVERT: P 504 LYS cc_start: 0.8438 (tttt) cc_final: 0.8167 (ttpt) REVERT: P 536 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7563 (mm-30) REVERT: P 565 LYS cc_start: 0.8467 (pttt) cc_final: 0.8196 (pttm) REVERT: P 582 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7328 (tm-30) REVERT: P 637 MET cc_start: 0.8807 (ttt) cc_final: 0.8544 (ttm) REVERT: P 653 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7437 (mtp180) REVERT: P 656 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7773 (mt-10) REVERT: P 660 LYS cc_start: 0.8865 (tttt) cc_final: 0.8629 (tttt) REVERT: P 672 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8476 (mtpt) REVERT: P 695 LYS cc_start: 0.8009 (tppt) cc_final: 0.7317 (tptm) REVERT: P 699 ASP cc_start: 0.7960 (m-30) cc_final: 0.7716 (m-30) REVERT: P 787 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7592 (mm-40) REVERT: P 819 ASP cc_start: 0.7734 (m-30) cc_final: 0.7406 (m-30) outliers start: 10 outliers final: 9 residues processed: 225 average time/residue: 0.2896 time to fit residues: 83.4805 Evaluate side-chains 226 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 177 VAL Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 729 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.149591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124803 restraints weight = 36838.991| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.71 r_work: 0.3455 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10196 Z= 0.252 Angle : 0.603 5.516 14269 Z= 0.365 Chirality : 0.044 0.217 1590 Planarity : 0.005 0.052 1391 Dihedral : 23.292 176.616 2476 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.26 % Allowed : 10.61 % Favored : 88.13 % 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: 1.26 (0.28), residues: 882 helix: 1.91 (0.26), residues: 380 sheet: -0.01 (0.52), residues: 91 loop : 0.10 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 818 TYR 0.019 0.002 TYR B 46 PHE 0.022 0.002 PHE P 589 TRP 0.006 0.001 TRP P 816 HIS 0.007 0.002 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (10196) covalent geometry : angle 0.60345 / 0.37 (14269) hydrogen bonds : bond 0.05045 / 3.42 ( 464) hydrogen bonds : angle 4.41381 / 3.04 ( 1220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8309 (ttp80) REVERT: B 106 ASN cc_start: 0.8016 (m-40) cc_final: 0.7787 (m-40) REVERT: P 202 LYS cc_start: 0.8360 (tttt) cc_final: 0.8061 (ttpp) REVERT: P 212 THR cc_start: 0.8241 (m) cc_final: 0.7932 (p) REVERT: P 255 LYS cc_start: 0.8403 (mmmt) cc_final: 0.8079 (mmtp) REVERT: P 380 ASP cc_start: 0.6938 (t0) cc_final: 0.6520 (t0) REVERT: P 395 LEU cc_start: 0.8532 (tp) cc_final: 0.8283 (tt) REVERT: P 399 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6894 (mm-30) REVERT: P 422 LYS cc_start: 0.8506 (mttt) cc_final: 0.8256 (mttp) REVERT: P 504 LYS cc_start: 0.8435 (tttt) cc_final: 0.8154 (ttpt) REVERT: P 536 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7541 (mm-30) REVERT: P 565 LYS cc_start: 0.8493 (pttt) cc_final: 0.8214 (pttm) REVERT: P 582 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7491 (tm-30) REVERT: P 637 MET cc_start: 0.8831 (ttt) cc_final: 0.8566 (ttm) REVERT: P 653 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7472 (mtp180) REVERT: P 656 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7828 (mt-10) REVERT: P 660 LYS cc_start: 0.8842 (tttt) cc_final: 0.8598 (tttt) REVERT: P 672 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8474 (mtpt) REVERT: P 695 LYS cc_start: 0.8046 (tppt) cc_final: 0.7440 (tptm) REVERT: P 699 ASP cc_start: 0.8024 (m-30) cc_final: 0.7734 (m-30) REVERT: P 819 ASP cc_start: 0.7888 (m-30) cc_final: 0.7574 (m-30) outliers start: 10 outliers final: 8 residues processed: 220 average time/residue: 0.2849 time to fit residues: 79.6758 Evaluate side-chains 223 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 729 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123390 restraints weight = 37149.177| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.73 r_work: 0.3439 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10196 Z= 0.261 Angle : 0.617 5.557 14269 Z= 0.372 Chirality : 0.045 0.244 1590 Planarity : 0.005 0.052 1391 Dihedral : 23.442 176.294 2476 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.26 % Allowed : 10.73 % Favored : 88.01 % 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: 1.06 (0.27), residues: 882 helix: 1.75 (0.26), residues: 381 sheet: -0.01 (0.53), residues: 86 loop : -0.04 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 818 TYR 0.025 0.002 TYR P 600 PHE 0.026 0.002 PHE B 81 TRP 0.006 0.001 TRP P 816 HIS 0.008 0.002 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.26 (10196) covalent geometry : angle 0.61749 / 0.37 (14269) hydrogen bonds : bond 0.05262 / 3.59 ( 464) hydrogen bonds : angle 4.47586 / 3.08 ( 1220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8309 (ttp80) REVERT: B 106 ASN cc_start: 0.8037 (m-40) cc_final: 0.7837 (m-40) REVERT: P 202 LYS cc_start: 0.8381 (tttt) cc_final: 0.8099 (ttpp) REVERT: P 212 THR cc_start: 0.8244 (m) cc_final: 0.7937 (p) REVERT: P 255 LYS cc_start: 0.8428 (mmmt) cc_final: 0.8108 (mmtp) REVERT: P 380 ASP cc_start: 0.6966 (t0) cc_final: 0.6753 (t0) REVERT: P 395 LEU cc_start: 0.8561 (tp) cc_final: 0.8328 (tt) REVERT: P 399 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6929 (mm-30) REVERT: P 422 LYS cc_start: 0.8535 (mttt) cc_final: 0.8279 (mttp) REVERT: P 504 LYS cc_start: 0.8444 (tttt) cc_final: 0.8181 (ttpt) REVERT: P 536 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7574 (mm-30) REVERT: P 565 LYS cc_start: 0.8486 (pttt) cc_final: 0.8226 (pttm) REVERT: P 582 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7528 (tm-30) REVERT: P 636 ILE cc_start: 0.8659 (mt) cc_final: 0.8447 (tt) REVERT: P 637 MET cc_start: 0.8842 (ttt) cc_final: 0.8541 (ttm) REVERT: P 653 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7505 (mtp180) REVERT: P 660 LYS cc_start: 0.8837 (tttt) cc_final: 0.8597 (tttt) REVERT: P 672 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8475 (mtpt) REVERT: P 695 LYS cc_start: 0.8084 (tppt) cc_final: 0.7507 (tptm) REVERT: P 699 ASP cc_start: 0.8035 (m-30) cc_final: 0.7766 (m-30) REVERT: P 817 ASN cc_start: 0.7994 (t0) cc_final: 0.7777 (t0) REVERT: P 819 ASP cc_start: 0.7930 (m-30) cc_final: 0.7607 (m-30) REVERT: P 835 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7244 (mt-10) outliers start: 10 outliers final: 9 residues processed: 227 average time/residue: 0.2966 time to fit residues: 85.8170 Evaluate side-chains 229 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 220 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 177 VAL Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 729 THR Chi-restraints excluded: chain P residue 836 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123988 restraints weight = 36823.707| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.67 r_work: 0.3456 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10196 Z= 0.179 Angle : 0.570 4.633 14269 Z= 0.349 Chirality : 0.042 0.210 1590 Planarity : 0.004 0.043 1391 Dihedral : 23.420 174.805 2476 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.14 % Allowed : 11.24 % Favored : 87.63 % 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: 1.14 (0.28), residues: 882 helix: 1.84 (0.26), residues: 380 sheet: 0.13 (0.55), residues: 81 loop : -0.05 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 282 TYR 0.014 0.001 TYR P 218 PHE 0.009 0.001 PHE B 20 TRP 0.007 0.001 TRP P 816 HIS 0.006 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (10196) covalent geometry : angle 0.56980 / 0.35 (14269) hydrogen bonds : bond 0.04721 / 3.17 ( 464) hydrogen bonds : angle 4.39196 / 3.03 ( 1220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ASN cc_start: 0.8021 (m-40) cc_final: 0.7817 (m-40) REVERT: P 202 LYS cc_start: 0.8359 (tttt) cc_final: 0.8084 (ttpp) REVERT: P 212 THR cc_start: 0.8228 (m) cc_final: 0.7928 (p) REVERT: P 255 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8059 (mmtp) REVERT: P 342 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: P 380 ASP cc_start: 0.6891 (t0) cc_final: 0.6638 (t0) REVERT: P 395 LEU cc_start: 0.8579 (tp) cc_final: 0.8338 (tt) REVERT: P 399 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6914 (mm-30) REVERT: P 422 LYS cc_start: 0.8516 (mttt) cc_final: 0.8238 (mttm) REVERT: P 504 LYS cc_start: 0.8454 (tttt) cc_final: 0.8177 (ttpt) REVERT: P 536 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7576 (mm-30) REVERT: P 565 LYS cc_start: 0.8453 (pttt) cc_final: 0.8204 (pttm) REVERT: P 582 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7510 (tm-30) REVERT: P 636 ILE cc_start: 0.8632 (mt) cc_final: 0.8429 (tt) REVERT: P 637 MET cc_start: 0.8812 (ttt) cc_final: 0.8509 (ttm) REVERT: P 653 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7492 (mtp180) REVERT: P 660 LYS cc_start: 0.8798 (tttt) cc_final: 0.8556 (tttt) REVERT: P 672 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8481 (mtpt) REVERT: P 695 LYS cc_start: 0.8051 (tppt) cc_final: 0.7436 (tptm) REVERT: P 699 ASP cc_start: 0.8005 (m-30) cc_final: 0.7717 (m-30) REVERT: P 819 ASP cc_start: 0.7871 (m-30) cc_final: 0.7546 (m-30) REVERT: P 835 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7224 (mt-10) outliers start: 9 outliers final: 7 residues processed: 221 average time/residue: 0.3010 time to fit residues: 84.4632 Evaluate side-chains 224 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 177 VAL Chi-restraints excluded: chain P residue 342 GLU Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 729 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 GLN P 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.144085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119162 restraints weight = 37051.861| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.78 r_work: 0.3394 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 10196 Z= 0.395 Angle : 0.702 6.516 14269 Z= 0.413 Chirality : 0.050 0.266 1590 Planarity : 0.005 0.060 1391 Dihedral : 23.567 179.156 2476 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.01 % Allowed : 11.49 % Favored : 87.50 % 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: 0.63 (0.27), residues: 882 helix: 1.38 (0.25), residues: 381 sheet: -0.25 (0.50), residues: 88 loop : -0.26 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 818 TYR 0.024 0.003 TYR P 141 PHE 0.021 0.002 PHE P 235 TRP 0.011 0.002 TRP P 816 HIS 0.007 0.002 HIS P 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00845 / 0.39 (10196) covalent geometry : angle 0.70183 / 0.41 (14269) hydrogen bonds : bond 0.06133 / 4.27 ( 464) hydrogen bonds : angle 4.62861 / 3.20 ( 1220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 225 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 106 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6881 (ttt-90) REVERT: P 202 LYS cc_start: 0.8412 (tttt) cc_final: 0.8116 (ttpp) REVERT: P 212 THR cc_start: 0.8245 (m) cc_final: 0.7949 (p) REVERT: P 255 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8108 (mmtp) REVERT: P 342 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: P 359 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7827 (mp0) REVERT: P 371 THR cc_start: 0.8623 (t) cc_final: 0.8401 (p) REVERT: P 380 ASP cc_start: 0.7136 (t0) cc_final: 0.6804 (t0) REVERT: P 395 LEU cc_start: 0.8642 (tp) cc_final: 0.8391 (tt) REVERT: P 399 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7028 (mm-30) REVERT: P 422 LYS cc_start: 0.8542 (mttt) cc_final: 0.8270 (mttm) REVERT: P 504 LYS cc_start: 0.8467 (tttt) cc_final: 0.8188 (ttpt) REVERT: P 536 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7590 (mm-30) REVERT: P 540 TYR cc_start: 0.8260 (t80) cc_final: 0.7915 (t80) REVERT: P 565 LYS cc_start: 0.8495 (pttt) cc_final: 0.8240 (pttm) REVERT: P 582 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7529 (tm-30) REVERT: P 604 LEU cc_start: 0.8383 (tt) cc_final: 0.8084 (tp) REVERT: P 615 GLN cc_start: 0.6991 (mm110) cc_final: 0.6784 (mm110) REVERT: P 636 ILE cc_start: 0.8677 (mt) cc_final: 0.8456 (tt) REVERT: P 637 MET cc_start: 0.8857 (ttt) cc_final: 0.8566 (ttm) REVERT: P 653 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7549 (mtp180) REVERT: P 660 LYS cc_start: 0.8860 (tttt) cc_final: 0.8616 (tttt) REVERT: P 672 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8484 (mtpt) REVERT: P 695 LYS cc_start: 0.8115 (tppt) cc_final: 0.7555 (tptm) REVERT: P 699 ASP cc_start: 0.8043 (m-30) cc_final: 0.7789 (m-30) REVERT: P 786 LYS cc_start: 0.8583 (mptt) cc_final: 0.8243 (mptt) REVERT: P 819 ASP cc_start: 0.8043 (m-30) cc_final: 0.7726 (m-30) REVERT: P 835 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7266 (mt-10) outliers start: 8 outliers final: 7 residues processed: 227 average time/residue: 0.2837 time to fit residues: 81.9222 Evaluate side-chains 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 177 VAL Chi-restraints excluded: chain P residue 342 GLU Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.147570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122640 restraints weight = 36838.387| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.69 r_work: 0.3437 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10196 Z= 0.152 Angle : 0.578 4.503 14269 Z= 0.351 Chirality : 0.042 0.201 1590 Planarity : 0.005 0.046 1391 Dihedral : 23.546 173.737 2476 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.01 % Allowed : 11.99 % Favored : 86.99 % 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: 0.96 (0.28), residues: 882 helix: 1.68 (0.26), residues: 381 sheet: 0.07 (0.55), residues: 81 loop : -0.16 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 282 TYR 0.013 0.001 TYR P 205 PHE 0.008 0.001 PHE B 20 TRP 0.007 0.001 TRP P 816 HIS 0.005 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (10196) covalent geometry : angle 0.57753 / 0.35 (14269) hydrogen bonds : bond 0.04705 / 3.16 ( 464) hydrogen bonds : angle 4.39253 / 3.03 ( 1220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 221 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 202 LYS cc_start: 0.8369 (tttt) cc_final: 0.8096 (ttpp) REVERT: P 212 THR cc_start: 0.8225 (m) cc_final: 0.7932 (p) REVERT: P 255 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8039 (mmtp) REVERT: P 380 ASP cc_start: 0.6924 (t0) cc_final: 0.6664 (t0) REVERT: P 395 LEU cc_start: 0.8599 (tp) cc_final: 0.8361 (tt) REVERT: P 399 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6941 (mm-30) REVERT: P 422 LYS cc_start: 0.8515 (mttt) cc_final: 0.8286 (mttt) REVERT: P 504 LYS cc_start: 0.8474 (tttt) cc_final: 0.8192 (ttpt) REVERT: P 536 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7572 (mm-30) REVERT: P 565 LYS cc_start: 0.8449 (pttt) cc_final: 0.8194 (pttm) REVERT: P 582 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7484 (tm-30) REVERT: P 613 TYR cc_start: 0.5326 (OUTLIER) cc_final: 0.4977 (t80) REVERT: P 615 GLN cc_start: 0.6930 (mm110) cc_final: 0.6725 (mm110) REVERT: P 636 ILE cc_start: 0.8629 (mt) cc_final: 0.8415 (tt) REVERT: P 637 MET cc_start: 0.8802 (ttt) cc_final: 0.8505 (ttm) REVERT: P 653 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7504 (mtp180) REVERT: P 660 LYS cc_start: 0.8800 (tttt) cc_final: 0.8574 (tttt) REVERT: P 672 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8476 (mtpt) REVERT: P 695 LYS cc_start: 0.8047 (tppt) cc_final: 0.7445 (tptm) REVERT: P 699 ASP cc_start: 0.8005 (m-30) cc_final: 0.7718 (m-30) REVERT: P 786 LYS cc_start: 0.8571 (mptt) cc_final: 0.8243 (mptt) REVERT: P 819 ASP cc_start: 0.7905 (m-30) cc_final: 0.7577 (m-30) REVERT: P 835 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7238 (mt-10) outliers start: 8 outliers final: 5 residues processed: 224 average time/residue: 0.2867 time to fit residues: 82.3556 Evaluate side-chains 225 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 219 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 177 VAL Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 613 TYR Chi-restraints excluded: chain P residue 643 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 701 ASN P 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.146923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121955 restraints weight = 37014.624| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.69 r_work: 0.3432 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10196 Z= 0.201 Angle : 0.589 5.345 14269 Z= 0.355 Chirality : 0.043 0.206 1590 Planarity : 0.005 0.048 1391 Dihedral : 23.548 175.253 2476 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.14 % Allowed : 12.12 % Favored : 86.74 % 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: 0.98 (0.28), residues: 882 helix: 1.74 (0.26), residues: 381 sheet: 0.03 (0.55), residues: 81 loop : -0.19 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 282 TYR 0.015 0.001 TYR P 141 PHE 0.014 0.001 PHE B 111 TRP 0.006 0.001 TRP P 816 HIS 0.005 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (10196) covalent geometry : angle 0.58915 / 0.36 (14269) hydrogen bonds : bond 0.04791 / 3.22 ( 464) hydrogen bonds : angle 4.39856 / 3.03 ( 1220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4945.31 seconds wall clock time: 84 minutes 35.68 seconds (5075.68 seconds total)