Starting phenix.real_space_refine on Thu Aug 6 19:08:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf0_45525/08_2026/9cf0_45525_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf0_45525/08_2026/9cf0_45525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cf0_45525/08_2026/9cf0_45525_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf0_45525/08_2026/9cf0_45525_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cf0_45525/08_2026/9cf0_45525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf0_45525/08_2026/9cf0_45525.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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 79 5.49 5 S 35 5.16 5 C 5386 2.51 5 N 1558 2.21 5 O 1816 1.98 5 H 8166 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17040 Number of models: 1 Model: "" Number of chains: 5 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: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 446 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "W" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1722 Classifications: {'DNA': 13, 'RNA': 41} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 11, 'rna3p': 42} Time building chain proxies: 2.63, per 1000 atoms: 0.15 Number of scatterers: 17040 At special positions: 0 Unit cell: (78.375, 119.625, 120.45, 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 79 15.00 O 1816 8.00 N 1558 7.00 C 5386 6.00 H 8166 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: 1.78 Conformation dependent library (CDL) restraints added in 626.5 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: 39 helices and 8 sheets defined 51.7% alpha, 12.0% beta 22 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 3.15 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 142 Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 119 through 121 No H-bonds generated for 'chain 'P' and resid 119 through 121' Processing helix chain 'P' and resid 122 through 153 removed outlier: 3.549A pdb=" N LEU P 126 " --> pdb=" O TYR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 164 removed outlier: 3.668A pdb=" N ILE P 164 " --> pdb=" O ASN P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.521A pdb=" N PHE P 169 " --> pdb=" O THR P 165 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU P 171 " --> pdb=" O ASP P 167 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU P 176 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 210 removed outlier: 3.869A pdb=" N HIS P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASP P 203 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA P 204 " --> pdb=" O LYS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 254 removed outlier: 4.330A pdb=" N LYS P 229 " --> pdb=" O TYR P 225 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN P 244 " --> pdb=" O ALA P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 270 Processing helix chain 'P' and resid 273 through 285 removed outlier: 3.876A pdb=" N LYS P 283 " --> pdb=" O GLN P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 298 removed outlier: 3.671A pdb=" N LYS P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) 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: 4.579A 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 381 through 388 removed outlier: 3.825A pdb=" N TYR P 386 " --> pdb=" O LYS P 382 " (cutoff:3.500A) 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: 3.750A pdb=" N ARG P 406 " --> pdb=" O ASN P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 416 removed outlier: 3.687A pdb=" N PHE P 415 " --> pdb=" O ARG P 412 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS P 416 " --> pdb=" O LYS P 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 412 through 416' 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 511 through 516 Processing helix chain 'P' and resid 516 through 529 Processing helix chain 'P' and resid 531 through 542 Processing helix chain 'P' and resid 550 through 574 removed outlier: 3.572A pdb=" N VAL P 564 " --> pdb=" O ALA P 560 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASP P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE P 567 " --> pdb=" O SER P 563 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU P 570 " --> pdb=" O ASP P 566 " (cutoff:3.500A) Processing helix chain 'P' and resid 622 through 639 removed outlier: 3.900A pdb=" N LYS P 626 " --> pdb=" O ASP P 622 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 645 Processing helix chain 'P' and resid 648 through 663 removed outlier: 3.823A pdb=" N LEU P 663 " --> pdb=" O ALA P 659 " (cutoff:3.500A) Processing helix chain 'P' and resid 668 through 679 removed outlier: 4.300A pdb=" N LYS P 672 " --> pdb=" O GLU P 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 680 through 684 removed outlier: 3.874A pdb=" N ARG P 683 " --> pdb=" O GLY P 680 " (cutoff:3.500A) Processing helix chain 'P' and resid 686 through 713 removed outlier: 3.855A pdb=" N LYS P 711 " --> pdb=" O LYS P 707 " (cutoff:3.500A) Processing helix chain 'P' and resid 736 through 747 removed outlier: 3.746A pdb=" N LEU P 740 " --> pdb=" O ARG P 736 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG P 742 " --> pdb=" O LYS P 738 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET P 743 " --> pdb=" O GLY P 739 " (cutoff:3.500A) Processing helix chain 'P' and resid 780 through 785 removed outlier: 4.662A pdb=" N GLU P 785 " --> pdb=" O PRO P 781 " (cutoff:3.500A) Processing helix chain 'P' and resid 801 through 806 removed outlier: 3.988A pdb=" N GLU P 805 " --> pdb=" O SER P 802 " (cutoff:3.500A) 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: 3.642A pdb=" N ARG B 53 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 95 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET B 98 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 126 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 19 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA B 10 " --> pdb=" O PRO B 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 2 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 158 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU B 9 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.700A 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: 4.119A pdb=" N LEU P 440 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR P 429 " --> pdb=" O LEU P 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 107 through 113 Processing sheet with id=AA4, first strand: chain 'P' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'P' and resid 507 through 510 removed outlier: 6.432A pdb=" N LEU P 719 " --> pdb=" O TYR P 752 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 592 through 593 removed outlier: 3.801A pdb=" N ALA P 607 " --> pdb=" O LEU P 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 770 through 772 Processing sheet with id=AA8, first strand: chain 'P' and resid 775 through 777 348 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 8149 1.12 - 1.30: 1306 1.30 - 1.47: 3741 1.47 - 1.65: 4146 1.65 - 1.82: 53 Bond restraints: 17395 Sorted by residual: bond pdb=" N SER P 693 " pdb=" H SER P 693 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL P 407 " pdb=" H VAL P 407 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP P 380 " pdb=" H ASP P 380 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH2 ARG P 193 " pdb="HH21 ARG P 193 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" ND2 ASN P 237 " pdb="HD21 ASN P 237 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 17390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 27200 2.72 - 5.43: 3380 5.43 - 8.15: 825 8.15 - 10.87: 25 10.87 - 13.58: 18 Bond angle restraints: 31448 Sorted by residual: angle pdb=" O5' A W 33 " pdb=" C5' A W 33 " pdb=" C4' A W 33 " ideal model delta sigma weight residual 109.40 118.85 -9.45 8.00e-01 1.56e+00 1.39e+02 angle pdb=" O4' A W 33 " pdb=" C1' A W 33 " pdb=" N9 A W 33 " ideal model delta sigma weight residual 108.50 116.53 -8.03 7.00e-01 2.04e+00 1.32e+02 angle pdb=" O4' U W 30 " pdb=" C1' U W 30 " pdb=" N1 U W 30 " ideal model delta sigma weight residual 108.20 116.50 -8.30 8.00e-01 1.56e+00 1.08e+02 angle pdb=" O4' U W 17 " pdb=" C1' U W 17 " pdb=" N1 U W 17 " ideal model delta sigma weight residual 108.20 116.38 -8.18 8.00e-01 1.56e+00 1.05e+02 angle pdb=" O4' U W 40 " pdb=" C1' U W 40 " pdb=" N1 U W 40 " ideal model delta sigma weight residual 108.50 115.45 -6.95 7.00e-01 2.04e+00 9.87e+01 ... (remaining 31443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 7572 35.73 - 71.46: 451 71.46 - 107.19: 27 107.19 - 142.92: 8 142.92 - 178.65: 5 Dihedral angle restraints: 8063 sinusoidal: 4937 harmonic: 3126 Sorted by residual: dihedral pdb=" C5' A W 32 " pdb=" C4' A W 32 " pdb=" C3' A W 32 " pdb=" O3' A W 32 " ideal model delta sinusoidal sigma weight residual 147.00 77.23 69.77 1 8.00e+00 1.56e-02 9.81e+01 dihedral pdb=" O4' A W 32 " pdb=" C4' A W 32 " pdb=" C3' A W 32 " pdb=" C2' A W 32 " ideal model delta sinusoidal sigma weight residual 24.00 -34.44 58.44 1 8.00e+00 1.56e-02 7.15e+01 dihedral pdb=" O4' C W 18 " pdb=" C1' C W 18 " pdb=" N1 C W 18 " pdb=" C2 C W 18 " ideal model delta sinusoidal sigma weight residual 200.00 75.60 124.40 1 1.50e+01 4.44e-03 6.68e+01 ... (remaining 8060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1139 0.117 - 0.234: 249 0.234 - 0.350: 27 0.350 - 0.467: 6 0.467 - 0.584: 1 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA TYR P 613 " pdb=" N TYR P 613 " pdb=" C TYR P 613 " pdb=" CB TYR P 613 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" C3' DT T 0 " pdb=" C4' DT T 0 " pdb=" O3' DT T 0 " pdb=" C2' DT T 0 " both_signs ideal model delta sigma weight residual False -2.73 -2.29 -0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" C1' G W 19 " pdb=" O4' G W 19 " pdb=" C2' G W 19 " pdb=" N9 G W 19 " both_signs ideal model delta sigma weight residual False 2.47 2.04 0.43 2.00e-01 2.50e+01 4.58e+00 ... (remaining 1419 not shown) Planarity restraints: 2258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G W 19 " 0.735 2.00e-02 2.50e+03 2.58e-01 2.34e+03 pdb=" N9 G W 19 " -0.049 2.00e-02 2.50e+03 pdb=" C8 G W 19 " -0.147 2.00e-02 2.50e+03 pdb=" N7 G W 19 " -0.166 2.00e-02 2.50e+03 pdb=" C5 G W 19 " -0.120 2.00e-02 2.50e+03 pdb=" C6 G W 19 " 0.048 2.00e-02 2.50e+03 pdb=" O6 G W 19 " 0.284 2.00e-02 2.50e+03 pdb=" N1 G W 19 " 0.043 2.00e-02 2.50e+03 pdb=" C2 G W 19 " -0.162 2.00e-02 2.50e+03 pdb=" N2 G W 19 " -0.088 2.00e-02 2.50e+03 pdb=" N3 G W 19 " -0.296 2.00e-02 2.50e+03 pdb=" C4 G W 19 " -0.224 2.00e-02 2.50e+03 pdb=" H8 G W 19 " -0.104 2.00e-02 2.50e+03 pdb=" H1 G W 19 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U W 30 " 0.641 2.00e-02 2.50e+03 2.46e-01 1.82e+03 pdb=" N1 U W 30 " -0.042 2.00e-02 2.50e+03 pdb=" C2 U W 30 " -0.192 2.00e-02 2.50e+03 pdb=" O2 U W 30 " -0.304 2.00e-02 2.50e+03 pdb=" N3 U W 30 " -0.043 2.00e-02 2.50e+03 pdb=" C4 U W 30 " 0.092 2.00e-02 2.50e+03 pdb=" O4 U W 30 " 0.322 2.00e-02 2.50e+03 pdb=" C5 U W 30 " -0.077 2.00e-02 2.50e+03 pdb=" C6 U W 30 " -0.148 2.00e-02 2.50e+03 pdb=" H5 U W 30 " -0.075 2.00e-02 2.50e+03 pdb=" H3 U W 30 " 0.020 2.00e-02 2.50e+03 pdb=" H6 U W 30 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U W 17 " 0.416 2.00e-02 2.50e+03 1.74e-01 9.13e+02 pdb=" N1 U W 17 " 0.011 2.00e-02 2.50e+03 pdb=" C2 U W 17 " -0.065 2.00e-02 2.50e+03 pdb=" O2 U W 17 " -0.290 2.00e-02 2.50e+03 pdb=" N3 U W 17 " 0.026 2.00e-02 2.50e+03 pdb=" C4 U W 17 " 0.078 2.00e-02 2.50e+03 pdb=" O4 U W 17 " 0.228 2.00e-02 2.50e+03 pdb=" C5 U W 17 " -0.053 2.00e-02 2.50e+03 pdb=" C6 U W 17 " -0.081 2.00e-02 2.50e+03 pdb=" H5 U W 17 " -0.116 2.00e-02 2.50e+03 pdb=" H3 U W 17 " -0.005 2.00e-02 2.50e+03 pdb=" H6 U W 17 " -0.149 2.00e-02 2.50e+03 ... (remaining 2255 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 830 2.16 - 2.77: 27522 2.77 - 3.38: 46340 3.38 - 3.99: 61268 3.99 - 4.60: 90602 Nonbonded interactions: 226562 Sorted by model distance: nonbonded pdb="HO2' U W 31 " pdb=" OP1 A W 32 " model vdw 1.552 2.450 nonbonded pdb="HO2' U W 17 " pdb=" OP2 C W 18 " model vdw 1.565 2.450 nonbonded pdb="HO2' A W 33 " pdb=" OP1 U W 34 " model vdw 1.584 2.450 nonbonded pdb=" HG1 THR P 499 " pdb=" OE1 GLU P 506 " model vdw 1.586 2.450 nonbonded pdb=" OE2 GLU P 538 " pdb=" HH TYR P 572 " model vdw 1.598 2.450 ... (remaining 226557 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.880 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 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 : 0.013 0.051 9229 Z= 0.970 Angle : 1.845 12.561 12780 Z= 1.608 Chirality : 0.097 0.584 1422 Planarity : 0.022 0.263 1349 Dihedral : 20.150 178.652 3856 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.31 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.20 (0.26), residues: 882 helix: -0.77 (0.23), residues: 375 sheet: 0.01 (0.56), residues: 79 loop : -0.86 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 741 TYR 0.151 0.020 TYR P 146 PHE 0.059 0.011 PHE B 111 TRP 0.077 0.019 TRP P 118 HIS 0.008 0.003 HIS P 628 Details of bonding type rmsd/Z covalent geometry : bond 0.01273 / 0.97 ( 9229) covalent geometry : angle 1.84538 / 1.61 (12780) hydrogen bonds : bond 0.17277 / 11.34 ( 398) hydrogen bonds : angle 7.62491 / 5.39 ( 1102) *********************** 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 166 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 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: 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 539 THR cc_start: 0.8452 (m) cc_final: 0.8128 (p) REVERT: P 745 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8011 (mtpt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3277 time to fit residues: 68.5640 Evaluate side-chains 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 287 GLN P 290 ASN P 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.127096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097745 restraints weight = 57204.112| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.83 r_work: 0.3405 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9229 Z= 0.211 Angle : 0.867 10.200 12780 Z= 0.499 Chirality : 0.054 0.303 1422 Planarity : 0.007 0.083 1349 Dihedral : 23.884 176.419 1998 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.61 % Favored : 97.05 % Rotamer: Outliers : 0.63 % Allowed : 6.69 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.91 (0.26), residues: 882 helix: 0.10 (0.25), residues: 380 sheet: -0.81 (0.49), residues: 90 loop : -1.15 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 814 TYR 0.017 0.002 TYR P 205 PHE 0.029 0.002 PHE B 111 TRP 0.013 0.002 TRP P 724 HIS 0.006 0.002 HIS P 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 ( 9229) covalent geometry : angle 0.86667 / 0.50 (12780) hydrogen bonds : bond 0.07957 / 5.30 ( 398) hydrogen bonds : angle 5.55401 / 3.88 ( 1102) *********************** 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 102 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.485 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: B 9 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7242 (mt-10) REVERT: P 331 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7957 (mm-30) REVERT: P 485 MET cc_start: 0.9284 (mtm) cc_final: 0.9020 (mtp) REVERT: P 689 LYS cc_start: 0.8059 (mttt) cc_final: 0.7138 (mmtt) REVERT: P 745 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8324 (mtpt) REVERT: P 810 GLU cc_start: 0.8067 (tt0) cc_final: 0.7189 (tp30) outliers start: 5 outliers final: 5 residues processed: 99 average time/residue: 0.2171 time to fit residues: 28.5549 Evaluate side-chains 81 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 776 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 628 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.123737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093673 restraints weight = 57822.997| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.77 r_work: 0.3335 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9229 Z= 0.303 Angle : 0.801 10.312 12780 Z= 0.460 Chirality : 0.050 0.267 1422 Planarity : 0.006 0.050 1349 Dihedral : 23.842 179.322 1998 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.56 % Favored : 94.33 % Rotamer: Outliers : 0.88 % Allowed : 8.59 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.17 (0.26), residues: 882 helix: 0.13 (0.24), residues: 376 sheet: -1.35 (0.46), residues: 95 loop : -1.45 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 53 TYR 0.016 0.002 TYR P 335 PHE 0.027 0.002 PHE B 111 TRP 0.009 0.002 TRP P 816 HIS 0.007 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.30 ( 9229) covalent geometry : angle 0.80141 / 0.46 (12780) hydrogen bonds : bond 0.06753 / 4.52 ( 398) hydrogen bonds : angle 5.43972 / 3.83 ( 1102) *********************** 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 83 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.381 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: B 37 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8816 (mm) REVERT: P 298 LYS cc_start: 0.8800 (mttt) cc_final: 0.8497 (pttt) REVERT: P 689 LYS cc_start: 0.8195 (mttt) cc_final: 0.7160 (mmtt) REVERT: P 745 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8211 (mtpt) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.1858 time to fit residues: 20.5831 Evaluate side-chains 78 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 188 LYS Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 507 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.125492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.095539 restraints weight = 56823.323| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.77 r_work: 0.3372 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9229 Z= 0.162 Angle : 0.679 9.247 12780 Z= 0.392 Chirality : 0.046 0.287 1422 Planarity : 0.005 0.040 1349 Dihedral : 23.679 179.819 1998 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 0.88 % Allowed : 8.71 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.76 (0.26), residues: 882 helix: 0.58 (0.25), residues: 376 sheet: -1.14 (0.48), residues: 94 loop : -1.35 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 524 TYR 0.012 0.001 TYR P 205 PHE 0.017 0.001 PHE B 111 TRP 0.008 0.001 TRP P 816 HIS 0.002 0.001 HIS P 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 9229) covalent geometry : angle 0.67929 / 0.39 (12780) hydrogen bonds : bond 0.05681 / 3.86 ( 398) hydrogen bonds : angle 5.03983 / 3.55 ( 1102) *********************** 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 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.299 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 37 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8776 (mm) REVERT: P 485 MET cc_start: 0.9409 (mtm) cc_final: 0.9196 (mtp) REVERT: P 745 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8197 (mtpt) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.2047 time to fit residues: 23.4515 Evaluate side-chains 77 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 546 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.125184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.095325 restraints weight = 56885.328| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.77 r_work: 0.3369 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9229 Z= 0.179 Angle : 0.659 8.844 12780 Z= 0.380 Chirality : 0.045 0.255 1422 Planarity : 0.004 0.038 1349 Dihedral : 23.526 179.952 1998 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.78 % Rotamer: Outliers : 0.88 % Allowed : 8.84 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.54 (0.27), residues: 882 helix: 0.92 (0.26), residues: 374 sheet: -1.23 (0.47), residues: 94 loop : -1.34 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 524 TYR 0.013 0.001 TYR P 572 PHE 0.016 0.001 PHE B 111 TRP 0.006 0.001 TRP B 119 HIS 0.003 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 ( 9229) covalent geometry : angle 0.65931 / 0.38 (12780) hydrogen bonds : bond 0.05324 / 3.62 ( 398) hydrogen bonds : angle 4.94417 / 3.48 ( 1102) *********************** 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 78 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.273 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: B 37 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8761 (mm) REVERT: P 745 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8219 (mtpt) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.1796 time to fit residues: 18.2353 Evaluate side-chains 74 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 188 LYS Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 546 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.125314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095428 restraints weight = 56886.374| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.75 r_work: 0.3373 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9229 Z= 0.175 Angle : 0.642 8.341 12780 Z= 0.369 Chirality : 0.045 0.262 1422 Planarity : 0.004 0.034 1349 Dihedral : 23.455 178.984 1998 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % 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 : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.27), residues: 882 helix: 1.07 (0.26), residues: 374 sheet: -1.16 (0.52), residues: 85 loop : -1.30 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 524 TYR 0.013 0.001 TYR P 572 PHE 0.025 0.002 PHE P 319 TRP 0.007 0.001 TRP B 119 HIS 0.003 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 9229) covalent geometry : angle 0.64223 / 0.37 (12780) hydrogen bonds : bond 0.05097 / 3.48 ( 398) hydrogen bonds : angle 4.87190 / 3.44 ( 1102) *********************** 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 78 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.463 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 745 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8216 (mtpt) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 0.1992 time to fit residues: 20.5103 Evaluate side-chains 68 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 546 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 88 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.0010 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.127240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097352 restraints weight = 57223.846| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.78 r_work: 0.3406 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9229 Z= 0.120 Angle : 0.595 6.823 12780 Z= 0.340 Chirality : 0.043 0.280 1422 Planarity : 0.004 0.032 1349 Dihedral : 23.359 179.092 1998 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 0.88 % Allowed : 9.22 % 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: -0.06 (0.28), residues: 882 helix: 1.38 (0.26), residues: 374 sheet: -1.09 (0.54), residues: 80 loop : -1.13 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 524 TYR 0.013 0.001 TYR P 205 PHE 0.016 0.001 PHE B 111 TRP 0.007 0.001 TRP B 119 HIS 0.005 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 9229) covalent geometry : angle 0.59462 / 0.34 (12780) hydrogen bonds : bond 0.04514 / 3.08 ( 398) hydrogen bonds : angle 4.67417 / 3.30 ( 1102) *********************** 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 78 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 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: symmetry clash outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 0.1743 time to fit residues: 18.6200 Evaluate side-chains 71 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 546 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.126305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.096511 restraints weight = 57071.317| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.75 r_work: 0.3391 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9229 Z= 0.149 Angle : 0.594 6.881 12780 Z= 0.340 Chirality : 0.043 0.268 1422 Planarity : 0.004 0.032 1349 Dihedral : 23.327 178.700 1998 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 1.14 % Allowed : 9.22 % 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: 0.01 (0.28), residues: 882 helix: 1.44 (0.26), residues: 377 sheet: -1.04 (0.52), residues: 85 loop : -1.12 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 524 TYR 0.011 0.001 TYR P 572 PHE 0.048 0.002 PHE P 773 TRP 0.006 0.001 TRP B 119 HIS 0.003 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 9229) covalent geometry : angle 0.59359 / 0.34 (12780) hydrogen bonds : bond 0.04533 / 3.08 ( 398) hydrogen bonds : angle 4.66599 / 3.30 ( 1102) *********************** 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 78 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.425 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: P 254 PHE cc_start: 0.8366 (t80) cc_final: 0.8122 (t80) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.1818 time to fit residues: 19.6775 Evaluate side-chains 71 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 546 THR Chi-restraints excluded: chain P residue 721 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 79 optimal weight: 4.9990 chunk 66 optimal weight: 0.0020 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.127434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.097779 restraints weight = 57066.077| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.77 r_work: 0.3415 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9229 Z= 0.116 Angle : 0.567 5.993 12780 Z= 0.325 Chirality : 0.042 0.292 1422 Planarity : 0.004 0.033 1349 Dihedral : 23.282 178.741 1998 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 1.01 % Allowed : 9.60 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.18 (0.28), residues: 882 helix: 1.68 (0.26), residues: 376 sheet: -1.11 (0.52), residues: 90 loop : -1.08 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 524 TYR 0.012 0.001 TYR P 205 PHE 0.030 0.001 PHE P 773 TRP 0.006 0.001 TRP B 119 HIS 0.005 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 ( 9229) covalent geometry : angle 0.56713 / 0.33 (12780) hydrogen bonds : bond 0.04246 / 2.90 ( 398) hydrogen bonds : angle 4.50074 / 3.18 ( 1102) *********************** 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 79 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.428 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: P 254 PHE cc_start: 0.8367 (t80) cc_final: 0.8109 (t80) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.1730 time to fit residues: 18.4799 Evaluate side-chains 70 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 546 THR Chi-restraints excluded: chain P residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 287 GLN P 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095169 restraints weight = 56889.963| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.72 r_work: 0.3367 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9229 Z= 0.225 Angle : 0.621 6.487 12780 Z= 0.354 Chirality : 0.044 0.278 1422 Planarity : 0.004 0.030 1349 Dihedral : 23.265 178.203 1998 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 0.76 % Allowed : 9.72 % Favored : 89.52 % 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: -0.07 (0.28), residues: 882 helix: 1.48 (0.26), residues: 378 sheet: -0.98 (0.53), residues: 90 loop : -1.30 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 683 TYR 0.014 0.002 TYR P 572 PHE 0.031 0.002 PHE P 773 TRP 0.006 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 ( 9229) covalent geometry : angle 0.62134 / 0.35 (12780) hydrogen bonds : bond 0.04716 / 3.19 ( 398) hydrogen bonds : angle 4.73482 / 3.35 ( 1102) ********************** 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 68 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.436 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: P 254 PHE cc_start: 0.8379 (t80) cc_final: 0.8159 (t80) outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 0.1673 time to fit residues: 15.6736 Evaluate side-chains 65 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 546 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.126126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.096774 restraints weight = 56653.373| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.74 r_work: 0.3396 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9229 Z= 0.126 Angle : 0.570 6.021 12780 Z= 0.327 Chirality : 0.042 0.285 1422 Planarity : 0.004 0.026 1349 Dihedral : 23.273 179.081 1998 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 0.88 % Allowed : 9.72 % Favored : 89.39 % 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: 0.10 (0.28), residues: 882 helix: 1.61 (0.26), residues: 377 sheet: -1.00 (0.53), residues: 85 loop : -1.16 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 524 TYR 0.012 0.001 TYR P 205 PHE 0.031 0.001 PHE P 773 TRP 0.005 0.001 TRP B 119 HIS 0.004 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 9229) covalent geometry : angle 0.57002 / 0.33 (12780) hydrogen bonds : bond 0.04354 / 2.96 ( 398) hydrogen bonds : angle 4.58686 / 3.23 ( 1102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3571.82 seconds wall clock time: 61 minutes 22.74 seconds (3682.74 seconds total)