Starting phenix.real_space_refine on Thu Sep 18 16:04:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf2_45527/09_2025/9cf2_45527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf2_45527/09_2025/9cf2_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cf2_45527/09_2025/9cf2_45527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf2_45527/09_2025/9cf2_45527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cf2_45527/09_2025/9cf2_45527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf2_45527/09_2025/9cf2_45527.map" } 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-2.0-5805/lib/python3.9/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: 2.96, per 1000 atoms: 0.16 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: 1.61 Conformation dependent library (CDL) restraints added in 404.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.82 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: 4.90 Time building geometry restraints manager: 2.20 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=" C1' A W 29 " pdb=" N9 A W 29 " ideal model delta sigma weight residual 1.475 1.493 -0.018 1.50e-02 4.44e+03 1.47e+00 bond pdb=" C3' A W 28 " pdb=" O3' A W 28 " ideal model delta sigma weight residual 1.417 1.434 -0.017 1.50e-02 4.44e+03 1.35e+00 bond pdb=" O5' A W 33 " pdb=" C5' A W 33 " ideal model delta sigma weight residual 1.420 1.436 -0.016 1.50e-02 4.44e+03 1.13e+00 bond pdb=" C3' DT T 1 " pdb=" C2' DT T 1 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 9.14e-01 bond pdb=" C ILE P 373 " pdb=" N PRO P 374 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.30e-02 5.92e+03 8.83e-01 ... (remaining 18840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 33906 2.56 - 5.13: 168 5.13 - 7.69: 2 7.69 - 10.26: 8 10.26 - 12.82: 4 Bond angle restraints: 34088 Sorted by residual: 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=" OP1 A W 29 " pdb=" P A W 29 " pdb=" OP2 A W 29 " ideal model delta sigma weight residual 119.60 106.78 12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" P A W 33 " pdb=" O5' A W 33 " pdb=" C5' A W 33 " ideal model delta sigma weight residual 120.90 127.10 -6.20 1.50e+00 4.44e-01 1.71e+01 angle pdb=" O3' A W 28 " pdb=" P A W 29 " pdb=" OP1 A W 29 " ideal model delta sigma weight residual 108.00 119.67 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" OP1 A W 32 " pdb=" P A W 32 " pdb=" OP2 A W 32 " ideal model delta sigma weight residual 119.60 108.64 10.96 3.00e+00 1.11e-01 1.33e+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 - 0.083: 1511 0.083 - 0.165: 71 0.165 - 0.248: 3 0.248 - 0.331: 2 0.331 - 0.413: 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 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.27e+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 2.35 -2.69 -0.34 2.00e-01 2.50e+01 2.95e+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: 2.110 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: 0.100 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.970 Find NCS groups from input model: 0.060 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 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 : 0.002 0.028 10196 Z= 0.126 Angle : 0.615 12.824 14269 Z= 0.345 Chirality : 0.042 0.413 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 aren 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 covalent geometry : bond 0.00245 (10196) covalent geometry : angle 0.61491 (14269) hydrogen bonds : bond 0.15325 ( 464) hydrogen bonds : angle 5.82944 ( 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 : 0.345 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: 0.3031 time to fit residues: 105.7148 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 : 0.424 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3882 r_free = 0.3882 target = 0.147616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122183 restraints weight = 36914.083| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.81 r_work: 0.3435 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 10196 Z= 0.376 Angle : 0.706 6.695 14269 Z= 0.403 Chirality : 0.052 0.236 1590 Planarity : 0.005 0.063 1391 Dihedral : 23.212 174.581 2476 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.76 % Allowed : 8.21 % Favored : 91.04 % 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 aren not related in a simple way. whole: 1.40 (0.28), residues: 882 helix: 1.95 (0.26), residues: 376 sheet: 0.31 (0.54), residues: 91 loop : 0.21 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 818 TYR 0.021 0.002 TYR P 141 PHE 0.027 0.002 PHE B 111 TRP 0.006 0.002 TRP P 816 HIS 0.006 0.002 HIS P 631 Details of bonding type rmsd covalent geometry : bond 0.00831 (10196) covalent geometry : angle 0.70646 (14269) hydrogen bonds : bond 0.05911 ( 464) hydrogen bonds : angle 4.74992 ( 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 248 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 242 time to evaluate : 0.456 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 27 VAL cc_start: 0.7472 (t) cc_final: 0.7223 (t) REVERT: B 35 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8319 (ttp80) REVERT: B 106 ASN cc_start: 0.8028 (m-40) cc_final: 0.7747 (m-40) REVERT: P 202 LYS cc_start: 0.8350 (tttt) cc_final: 0.8060 (ttpp) REVERT: P 212 THR cc_start: 0.8248 (m) cc_final: 0.7912 (p) REVERT: P 304 SER cc_start: 0.8854 (m) cc_final: 0.8615 (t) REVERT: P 313 THR cc_start: 0.8121 (m) cc_final: 0.7866 (p) REVERT: P 380 ASP cc_start: 0.7120 (t0) cc_final: 0.6838 (t0) REVERT: P 385 ASN cc_start: 0.7864 (t0) cc_final: 0.7663 (t0) REVERT: P 395 LEU cc_start: 0.8566 (tp) cc_final: 0.8305 (tt) REVERT: P 399 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7088 (mm-30) REVERT: P 422 LYS cc_start: 0.8481 (mttt) cc_final: 0.8211 (mttp) REVERT: P 504 LYS cc_start: 0.8389 (tttt) cc_final: 0.8121 (ttpt) REVERT: P 514 ASP cc_start: 0.8244 (t70) cc_final: 0.7880 (t0) REVERT: P 529 LEU cc_start: 0.8224 (mt) cc_final: 0.7944 (mp) REVERT: P 536 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7613 (mm-30) REVERT: P 540 TYR cc_start: 0.8219 (t80) cc_final: 0.7890 (t80) REVERT: P 565 LYS cc_start: 0.8523 (pttt) cc_final: 0.8210 (pttm) REVERT: P 653 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7438 (mtp180) REVERT: P 656 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7717 (mt-10) REVERT: P 672 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8442 (mtpt) REVERT: P 695 LYS cc_start: 0.8097 (tppt) cc_final: 0.7553 (tptm) REVERT: P 699 ASP cc_start: 0.7940 (m-30) cc_final: 0.7657 (m-30) REVERT: P 701 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7734 (t0) REVERT: P 769 ASP cc_start: 0.7615 (p0) cc_final: 0.7406 (p0) REVERT: P 787 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7575 (mm-40) REVERT: P 819 ASP cc_start: 0.7949 (m-30) cc_final: 0.7625 (m-30) REVERT: P 835 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7326 (mt-10) outliers start: 6 outliers final: 2 residues processed: 245 average time/residue: 0.3091 time to fit residues: 94.7544 Evaluate side-chains 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 476 LYS 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: 2.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS P 161 ASN P 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.148417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122796 restraints weight = 36888.889| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.72 r_work: 0.3442 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10196 Z= 0.218 Angle : 0.597 4.914 14269 Z= 0.345 Chirality : 0.043 0.161 1590 Planarity : 0.004 0.043 1391 Dihedral : 23.175 175.344 2476 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.26 % Allowed : 9.97 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.28), residues: 882 helix: 1.88 (0.25), residues: 380 sheet: 0.21 (0.53), residues: 91 loop : 0.13 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 818 TYR 0.012 0.001 TYR P 600 PHE 0.020 0.002 PHE P 254 TRP 0.007 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00479 (10196) covalent geometry : angle 0.59670 (14269) hydrogen bonds : bond 0.04846 ( 464) hydrogen bonds : angle 4.47766 ( 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 230 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 220 time to evaluate : 0.365 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: B 35 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8284 (ttp80) REVERT: B 46 TYR cc_start: 0.7674 (m-10) cc_final: 0.7266 (m-80) REVERT: P 202 LYS cc_start: 0.8332 (tttt) cc_final: 0.8050 (ttpp) REVERT: P 212 THR cc_start: 0.8227 (m) cc_final: 0.7903 (p) REVERT: P 380 ASP cc_start: 0.6963 (t0) cc_final: 0.6676 (t0) REVERT: P 395 LEU cc_start: 0.8584 (tp) cc_final: 0.8307 (tt) REVERT: P 399 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6968 (mm-30) REVERT: P 422 LYS cc_start: 0.8529 (mttt) cc_final: 0.8284 (mttp) REVERT: P 504 LYS cc_start: 0.8409 (tttt) cc_final: 0.8143 (ttpt) REVERT: P 536 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7555 (mm-30) REVERT: P 565 LYS cc_start: 0.8499 (pttt) cc_final: 0.8228 (pttm) REVERT: P 582 GLU cc_start: 0.7752 (tp30) cc_final: 0.7544 (tm-30) REVERT: P 653 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7433 (mtp180) REVERT: P 660 LYS cc_start: 0.8860 (tttt) cc_final: 0.8657 (tttt) REVERT: P 672 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8448 (mtpt) REVERT: P 695 LYS cc_start: 0.8028 (tppt) cc_final: 0.7451 (tptm) REVERT: P 699 ASP cc_start: 0.7932 (m-30) cc_final: 0.7692 (m-30) REVERT: P 787 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7610 (mm-40) REVERT: P 819 ASP cc_start: 0.7867 (m-30) cc_final: 0.7550 (m-30) REVERT: P 835 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7248 (mt-10) outliers start: 10 outliers final: 8 residues processed: 222 average time/residue: 0.2947 time to fit residues: 81.7819 Evaluate side-chains 217 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 89 HIS 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 643 ILE Chi-restraints excluded: chain P residue 729 THR Chi-restraints excluded: chain P residue 836 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS P 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.147492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122498 restraints weight = 36766.596| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.65 r_work: 0.3452 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10196 Z= 0.245 Angle : 0.603 4.913 14269 Z= 0.348 Chirality : 0.044 0.163 1590 Planarity : 0.004 0.046 1391 Dihedral : 23.254 175.432 2476 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.01 % Allowed : 10.98 % 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 aren not related in a simple way. whole: 1.25 (0.27), residues: 882 helix: 1.88 (0.25), residues: 380 sheet: 0.11 (0.52), residues: 91 loop : 0.08 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 818 TYR 0.015 0.002 TYR P 141 PHE 0.014 0.001 PHE B 110 TRP 0.007 0.001 TRP P 816 HIS 0.007 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00541 (10196) covalent geometry : angle 0.60322 (14269) hydrogen bonds : bond 0.04854 ( 464) hydrogen bonds : angle 4.43459 ( 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 225 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.374 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 46 TYR cc_start: 0.7711 (m-10) cc_final: 0.7313 (m-80) REVERT: P 106 ARG cc_start: 0.6995 (ttt-90) cc_final: 0.6740 (ttt-90) REVERT: P 202 LYS cc_start: 0.8373 (tttt) cc_final: 0.8129 (ttpp) REVERT: P 212 THR cc_start: 0.8282 (m) cc_final: 0.8000 (p) REVERT: P 380 ASP cc_start: 0.6941 (t0) cc_final: 0.6674 (t0) REVERT: P 395 LEU cc_start: 0.8572 (tp) cc_final: 0.8338 (tt) REVERT: P 399 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6958 (mm-30) REVERT: P 422 LYS cc_start: 0.8572 (mttt) cc_final: 0.8330 (mttp) REVERT: P 504 LYS cc_start: 0.8433 (tttt) cc_final: 0.8176 (ttpt) REVERT: P 536 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7574 (mm-30) REVERT: P 565 LYS cc_start: 0.8510 (pttt) cc_final: 0.8258 (pttm) REVERT: P 672 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8461 (mtpt) REVERT: P 695 LYS cc_start: 0.8137 (tppt) cc_final: 0.7565 (tptm) REVERT: P 699 ASP cc_start: 0.7964 (m-30) cc_final: 0.7714 (m-30) REVERT: P 819 ASP cc_start: 0.7943 (m-30) cc_final: 0.7612 (m-30) REVERT: P 835 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7224 (mt-10) outliers start: 8 outliers final: 6 residues processed: 220 average time/residue: 0.2972 time to fit residues: 81.7012 Evaluate side-chains 219 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 701 ASN Chi-restraints excluded: chain P residue 836 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 161 ASN P 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.148632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123780 restraints weight = 36648.901| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.64 r_work: 0.3466 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10196 Z= 0.175 Angle : 0.569 4.646 14269 Z= 0.329 Chirality : 0.041 0.149 1590 Planarity : 0.004 0.037 1391 Dihedral : 23.166 174.515 2476 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.88 % Allowed : 11.36 % Favored : 87.75 % 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 aren not related in a simple way. whole: 1.26 (0.28), residues: 882 helix: 1.92 (0.25), residues: 381 sheet: 0.30 (0.55), residues: 81 loop : 0.00 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.015 0.001 TYR P 571 PHE 0.021 0.001 PHE B 110 TRP 0.008 0.001 TRP P 816 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00380 (10196) covalent geometry : angle 0.56899 (14269) hydrogen bonds : bond 0.04336 ( 464) hydrogen bonds : angle 4.32834 ( 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 222 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.465 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: 0.7617 (t) cc_final: 0.7356 (t) REVERT: B 46 TYR cc_start: 0.7685 (m-10) cc_final: 0.7326 (m-80) REVERT: P 202 LYS cc_start: 0.8341 (tttt) cc_final: 0.8081 (ttpp) REVERT: P 212 THR cc_start: 0.8280 (m) cc_final: 0.8000 (p) REVERT: P 255 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7885 (mmtp) REVERT: P 359 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7678 (mp0) REVERT: P 380 ASP cc_start: 0.6875 (t0) cc_final: 0.6662 (t0) REVERT: P 395 LEU cc_start: 0.8566 (tp) cc_final: 0.8351 (tt) REVERT: P 399 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6910 (mm-30) REVERT: P 422 LYS cc_start: 0.8541 (mttt) cc_final: 0.8317 (mttp) REVERT: P 504 LYS cc_start: 0.8420 (tttt) cc_final: 0.8161 (ttpt) REVERT: P 536 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7544 (mm-30) REVERT: P 565 LYS cc_start: 0.8507 (pttt) cc_final: 0.8266 (pttm) REVERT: P 672 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8468 (mtpt) REVERT: P 695 LYS cc_start: 0.8085 (tppt) cc_final: 0.7547 (tptm) REVERT: P 699 ASP cc_start: 0.7955 (m-30) cc_final: 0.7717 (m-30) REVERT: P 819 ASP cc_start: 0.7851 (m-30) cc_final: 0.7511 (m-30) REVERT: P 835 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7219 (mt-10) outliers start: 7 outliers final: 6 residues processed: 218 average time/residue: 0.3751 time to fit residues: 101.5972 Evaluate side-chains 219 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 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 836 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120418 restraints weight = 36556.839| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.69 r_work: 0.3417 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10196 Z= 0.316 Angle : 0.641 5.005 14269 Z= 0.367 Chirality : 0.048 0.195 1590 Planarity : 0.005 0.052 1391 Dihedral : 23.287 175.831 2476 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.26 % Allowed : 11.36 % Favored : 87.37 % 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 aren not related in a simple way. whole: 0.93 (0.27), residues: 882 helix: 1.63 (0.25), residues: 381 sheet: 0.01 (0.52), residues: 86 loop : -0.14 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 818 TYR 0.018 0.002 TYR P 141 PHE 0.015 0.002 PHE P 235 TRP 0.009 0.002 TRP P 816 HIS 0.006 0.002 HIS P 201 Details of bonding type rmsd covalent geometry : bond 0.00698 (10196) covalent geometry : angle 0.64064 (14269) hydrogen bonds : bond 0.05393 ( 464) hydrogen bonds : angle 4.47938 ( 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 240 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 230 time to evaluate : 0.450 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 27 VAL cc_start: 0.7760 (t) cc_final: 0.7483 (t) REVERT: B 81 PHE cc_start: 0.7773 (p90) cc_final: 0.7472 (p90) REVERT: P 106 ARG cc_start: 0.7097 (ttt-90) cc_final: 0.6860 (ttt-90) REVERT: P 202 LYS cc_start: 0.8402 (tttt) cc_final: 0.8123 (ttpp) REVERT: P 212 THR cc_start: 0.8291 (m) cc_final: 0.8014 (p) REVERT: P 342 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: P 380 ASP cc_start: 0.7041 (t0) cc_final: 0.6755 (t0) REVERT: P 393 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8011 (mttm) REVERT: P 395 LEU cc_start: 0.8626 (tp) cc_final: 0.8404 (tt) REVERT: P 399 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7027 (mm-30) REVERT: P 422 LYS cc_start: 0.8570 (mttt) cc_final: 0.8347 (mttp) REVERT: P 504 LYS cc_start: 0.8453 (tttt) cc_final: 0.8183 (ttmm) REVERT: P 514 ASP cc_start: 0.8292 (t70) cc_final: 0.7976 (t0) REVERT: P 536 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7578 (mm-30) REVERT: P 565 LYS cc_start: 0.8500 (pttt) cc_final: 0.8271 (pttm) REVERT: P 582 GLU cc_start: 0.7745 (tp30) cc_final: 0.7335 (tm-30) REVERT: P 636 ILE cc_start: 0.8672 (mt) cc_final: 0.8464 (tt) REVERT: P 653 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7643 (mtp180) REVERT: P 672 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8477 (mtpt) REVERT: P 695 LYS cc_start: 0.8159 (tppt) cc_final: 0.7622 (tptm) REVERT: P 699 ASP cc_start: 0.7977 (m-30) cc_final: 0.7739 (m-30) REVERT: P 819 ASP cc_start: 0.8023 (m-30) cc_final: 0.7692 (m-30) REVERT: P 835 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7250 (mt-10) outliers start: 10 outliers final: 7 residues processed: 234 average time/residue: 0.3589 time to fit residues: 105.0331 Evaluate side-chains 236 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 296 ILE 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 660 LYS Chi-restraints excluded: chain P residue 836 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124341 restraints weight = 36836.579| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.61 r_work: 0.3455 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10196 Z= 0.177 Angle : 0.574 4.495 14269 Z= 0.332 Chirality : 0.041 0.186 1590 Planarity : 0.004 0.042 1391 Dihedral : 23.162 173.943 2476 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.39 % Allowed : 11.87 % 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 aren not related in a simple way. whole: 1.11 (0.28), residues: 882 helix: 1.89 (0.26), residues: 381 sheet: 0.05 (0.54), residues: 81 loop : -0.15 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 282 TYR 0.017 0.001 TYR P 571 PHE 0.024 0.001 PHE B 110 TRP 0.008 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00387 (10196) covalent geometry : angle 0.57442 (14269) hydrogen bonds : bond 0.04287 ( 464) hydrogen bonds : angle 4.27022 ( 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 237 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 0.476 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: 0.7686 (t) cc_final: 0.7399 (t) REVERT: B 46 TYR cc_start: 0.7702 (m-10) cc_final: 0.7394 (m-80) REVERT: B 109 GLN cc_start: 0.8519 (mt0) cc_final: 0.8295 (mt0) REVERT: P 202 LYS cc_start: 0.8366 (tttt) cc_final: 0.8123 (ttpp) REVERT: P 212 THR cc_start: 0.8286 (m) cc_final: 0.8022 (p) REVERT: P 255 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7903 (mmtp) REVERT: P 359 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7668 (mp0) REVERT: P 380 ASP cc_start: 0.6879 (t0) cc_final: 0.6639 (t0) REVERT: P 393 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8002 (mttm) REVERT: P 395 LEU cc_start: 0.8601 (tp) cc_final: 0.8372 (tt) REVERT: P 399 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6966 (mm-30) REVERT: P 422 LYS cc_start: 0.8548 (mttt) cc_final: 0.8297 (mttm) REVERT: P 504 LYS cc_start: 0.8466 (tttt) cc_final: 0.8201 (ttmm) REVERT: P 536 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7518 (mm-30) REVERT: P 565 LYS cc_start: 0.8499 (pttt) cc_final: 0.8272 (pttm) REVERT: P 582 GLU cc_start: 0.7701 (tp30) cc_final: 0.7347 (tm-30) REVERT: P 653 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7644 (mtp180) REVERT: P 672 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8442 (mtpt) REVERT: P 695 LYS cc_start: 0.8098 (tppt) cc_final: 0.7576 (tptm) REVERT: P 699 ASP cc_start: 0.7947 (m-30) cc_final: 0.7687 (m-30) REVERT: P 819 ASP cc_start: 0.7911 (m-30) cc_final: 0.7572 (m-30) REVERT: P 835 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7229 (mt-10) outliers start: 11 outliers final: 6 residues processed: 230 average time/residue: 0.3725 time to fit residues: 106.7699 Evaluate side-chains 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 315 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 84 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123897 restraints weight = 36675.836| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.61 r_work: 0.3442 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10196 Z= 0.200 Angle : 0.578 4.475 14269 Z= 0.334 Chirality : 0.042 0.170 1590 Planarity : 0.004 0.040 1391 Dihedral : 23.121 174.336 2476 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.88 % Allowed : 12.75 % Favored : 86.36 % 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 aren not related in a simple way. whole: 1.09 (0.28), residues: 882 helix: 1.88 (0.26), residues: 381 sheet: 0.01 (0.54), residues: 81 loop : -0.16 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 282 TYR 0.014 0.001 TYR P 571 PHE 0.016 0.001 PHE B 110 TRP 0.009 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00440 (10196) covalent geometry : angle 0.57815 (14269) hydrogen bonds : bond 0.04422 ( 464) hydrogen bonds : angle 4.26437 ( 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 234 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 0.460 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 27 VAL cc_start: 0.7704 (t) cc_final: 0.7416 (t) REVERT: B 46 TYR cc_start: 0.7715 (m-10) cc_final: 0.7436 (m-80) REVERT: P 202 LYS cc_start: 0.8376 (tttt) cc_final: 0.8133 (ttpp) REVERT: P 212 THR cc_start: 0.8235 (m) cc_final: 0.7982 (p) REVERT: P 255 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7890 (mmtp) REVERT: P 380 ASP cc_start: 0.6900 (t0) cc_final: 0.6660 (t0) REVERT: P 393 LYS cc_start: 0.8441 (ptpp) cc_final: 0.8007 (mttm) REVERT: P 395 LEU cc_start: 0.8605 (tp) cc_final: 0.8385 (tt) REVERT: P 399 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6882 (mm-30) REVERT: P 504 LYS cc_start: 0.8460 (tttt) cc_final: 0.8181 (ttmm) REVERT: P 536 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7515 (mm-30) REVERT: P 565 LYS cc_start: 0.8496 (pttt) cc_final: 0.8267 (pttm) REVERT: P 582 GLU cc_start: 0.7706 (tp30) cc_final: 0.7485 (tm-30) REVERT: P 641 LYS cc_start: 0.8017 (tttt) cc_final: 0.7707 (tttt) REVERT: P 653 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7651 (mtp180) REVERT: P 672 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8485 (mtpt) REVERT: P 695 LYS cc_start: 0.8087 (tppt) cc_final: 0.7527 (tptm) REVERT: P 699 ASP cc_start: 0.7927 (m-30) cc_final: 0.7667 (m-30) REVERT: P 786 LYS cc_start: 0.8574 (mptt) cc_final: 0.8257 (mptt) REVERT: P 819 ASP cc_start: 0.7898 (m-30) cc_final: 0.7551 (m-30) REVERT: P 835 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7260 (mt-10) outliers start: 7 outliers final: 6 residues processed: 230 average time/residue: 0.3657 time to fit residues: 104.6580 Evaluate side-chains 230 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 315 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.149470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125086 restraints weight = 36851.397| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.61 r_work: 0.3471 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10196 Z= 0.155 Angle : 0.556 4.289 14269 Z= 0.322 Chirality : 0.040 0.166 1590 Planarity : 0.004 0.038 1391 Dihedral : 23.053 173.236 2476 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.88 % Allowed : 13.13 % Favored : 85.98 % 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 aren not related in a simple way. whole: 1.21 (0.28), residues: 882 helix: 2.01 (0.26), residues: 381 sheet: 0.04 (0.55), residues: 81 loop : -0.13 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.013 0.001 TYR P 571 PHE 0.025 0.001 PHE B 110 TRP 0.007 0.001 TRP P 816 HIS 0.003 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00338 (10196) covalent geometry : angle 0.55640 (14269) hydrogen bonds : bond 0.04009 ( 464) hydrogen bonds : angle 4.16691 ( 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 236 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 0.441 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: 0.7655 (t) cc_final: 0.7361 (t) REVERT: B 46 TYR cc_start: 0.7705 (m-10) cc_final: 0.7433 (m-80) REVERT: P 202 LYS cc_start: 0.8350 (tttt) cc_final: 0.8115 (ttpp) REVERT: P 212 THR cc_start: 0.8226 (m) cc_final: 0.7976 (p) REVERT: P 255 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7880 (mmtp) REVERT: P 380 ASP cc_start: 0.6813 (t0) cc_final: 0.6608 (t0) REVERT: P 393 LYS cc_start: 0.8418 (ptpp) cc_final: 0.7993 (mttm) REVERT: P 394 VAL cc_start: 0.8854 (t) cc_final: 0.8589 (m) REVERT: P 399 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6846 (mm-30) REVERT: P 504 LYS cc_start: 0.8476 (tttt) cc_final: 0.8196 (ttmm) REVERT: P 536 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7516 (mm-30) REVERT: P 565 LYS cc_start: 0.8486 (pttt) cc_final: 0.8261 (pttm) REVERT: P 582 GLU cc_start: 0.7712 (tp30) cc_final: 0.7499 (tm-30) REVERT: P 641 LYS cc_start: 0.7989 (tttt) cc_final: 0.7685 (tttt) REVERT: P 653 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7637 (mtp180) REVERT: P 672 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8453 (mtpt) REVERT: P 695 LYS cc_start: 0.8074 (tppt) cc_final: 0.7532 (tptm) REVERT: P 699 ASP cc_start: 0.7931 (m-30) cc_final: 0.7656 (m-30) REVERT: P 786 LYS cc_start: 0.8547 (mptt) cc_final: 0.8236 (mptt) REVERT: P 819 ASP cc_start: 0.7816 (m-30) cc_final: 0.7467 (m-30) REVERT: P 835 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7241 (mt-10) outliers start: 7 outliers final: 6 residues processed: 232 average time/residue: 0.3571 time to fit residues: 103.2988 Evaluate side-chains 230 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 315 LEU 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: 3.9990 chunk 3 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 161 ASN P 402 ASN P 427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.147640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123382 restraints weight = 36858.120| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.62 r_work: 0.3439 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10196 Z= 0.253 Angle : 0.602 4.862 14269 Z= 0.346 Chirality : 0.045 0.177 1590 Planarity : 0.004 0.038 1391 Dihedral : 23.099 174.841 2476 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.88 % Allowed : 13.01 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.28), residues: 882 helix: 1.80 (0.26), residues: 381 sheet: 0.05 (0.54), residues: 81 loop : -0.25 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 818 TYR 0.016 0.002 TYR P 141 PHE 0.014 0.002 PHE B 110 TRP 0.009 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00558 (10196) covalent geometry : angle 0.60162 (14269) hydrogen bonds : bond 0.04750 ( 464) hydrogen bonds : angle 4.28832 ( 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 230 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 223 time to evaluate : 0.448 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: B 27 VAL cc_start: 0.7748 (t) cc_final: 0.7460 (t) REVERT: B 46 TYR cc_start: 0.7713 (m-10) cc_final: 0.7449 (m-80) REVERT: B 81 PHE cc_start: 0.7837 (p90) cc_final: 0.7509 (p90) REVERT: P 202 LYS cc_start: 0.8394 (tttt) cc_final: 0.8150 (ttpp) REVERT: P 255 LYS cc_start: 0.8307 (mmmt) cc_final: 0.7921 (mmtp) REVERT: P 380 ASP cc_start: 0.6924 (t0) cc_final: 0.6655 (t0) REVERT: P 393 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8014 (mttm) REVERT: P 394 VAL cc_start: 0.8855 (t) cc_final: 0.8582 (m) REVERT: P 399 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6879 (mm-30) REVERT: P 504 LYS cc_start: 0.8489 (tttt) cc_final: 0.8209 (ttmm) REVERT: P 536 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7534 (mm-30) REVERT: P 565 LYS cc_start: 0.8492 (pttt) cc_final: 0.8269 (pttm) REVERT: P 582 GLU cc_start: 0.7728 (tp30) cc_final: 0.7503 (tm-30) REVERT: P 641 LYS cc_start: 0.8019 (tttt) cc_final: 0.7669 (tttt) REVERT: P 653 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7690 (mtp180) REVERT: P 672 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8472 (mtpt) REVERT: P 695 LYS cc_start: 0.8104 (tppt) cc_final: 0.7548 (tptm) REVERT: P 699 ASP cc_start: 0.7951 (m-30) cc_final: 0.7690 (m-30) REVERT: P 787 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7733 (mm110) REVERT: P 819 ASP cc_start: 0.7954 (m-30) cc_final: 0.7621 (m-30) outliers start: 7 outliers final: 6 residues processed: 226 average time/residue: 0.3375 time to fit residues: 95.5081 Evaluate side-chains 227 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 221 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 315 LEU 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 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.149144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124526 restraints weight = 37260.055| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.68 r_work: 0.3452 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10196 Z= 0.165 Angle : 0.565 4.646 14269 Z= 0.326 Chirality : 0.041 0.162 1590 Planarity : 0.004 0.038 1391 Dihedral : 23.018 173.461 2476 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.76 % Allowed : 13.26 % Favored : 85.98 % 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 aren not related in a simple way. whole: 1.14 (0.28), residues: 882 helix: 1.99 (0.26), residues: 381 sheet: 0.10 (0.54), residues: 81 loop : -0.21 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 282 TYR 0.013 0.001 TYR P 571 PHE 0.013 0.001 PHE B 110 TRP 0.008 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00362 (10196) covalent geometry : angle 0.56458 (14269) hydrogen bonds : bond 0.04114 ( 464) hydrogen bonds : angle 4.17202 ( 1220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5678.10 seconds wall clock time: 97 minutes 0.65 seconds (5820.65 seconds total)