Starting phenix.real_space_refine on Fri Jul 3 23:20:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf0_45525/07_2026/9cf0_45525_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf0_45525/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cf0_45525/07_2026/9cf0_45525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf0_45525/07_2026/9cf0_45525.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf0_45525/07_2026/9cf0_45525_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf0_45525/07_2026/9cf0_45525_neut.cif" } 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-dev-6108/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: 2.81, per 1000 atoms: 0.16 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: 1.55 Conformation dependent library (CDL) restraints added in 441.4 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: 2.63 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: 3.47 Time building geometry restraints manager: 2.15 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: 27219 2.72 - 5.43: 3368 5.43 - 8.15: 819 8.15 - 10.87: 24 10.87 - 13.58: 18 Bond angle restraints: 31448 Sorted by residual: angle pdb=" N6 DA W 55 " pdb=" C6 DA W 55 " pdb=" N1 DA W 55 " ideal model delta sigma weight residual 118.60 112.75 5.85 6.00e-01 2.78e+00 9.51e+01 angle pdb=" N6 A W 41 " pdb=" C6 A W 41 " pdb=" N1 A W 41 " ideal model delta sigma weight residual 118.60 112.80 5.80 6.00e-01 2.78e+00 9.33e+01 angle pdb=" N6 DA W 56 " pdb=" C6 DA W 56 " pdb=" N1 DA W 56 " ideal model delta sigma weight residual 118.60 112.89 5.71 6.00e-01 2.78e+00 9.06e+01 angle pdb=" N6 A W 6 " pdb=" C6 A W 6 " pdb=" N1 A W 6 " ideal model delta sigma weight residual 118.60 112.93 5.67 6.00e-01 2.78e+00 8.94e+01 angle pdb=" N6 DA W 57 " pdb=" C6 DA W 57 " pdb=" N1 DA W 57 " ideal model delta sigma weight residual 118.60 113.01 5.59 6.00e-01 2.78e+00 8.68e+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: 1137 0.117 - 0.234: 253 0.234 - 0.350: 25 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 2.46 2.04 0.41 2.00e-01 2.50e+01 4.29e+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: 2.010 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- 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= 0.939 Angle : 1.833 12.561 12780 Z= 1.557 Chirality : 0.096 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 / 0.94 ( 9229) covalent geometry : angle 1.83291 / 1.56 (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 : 0.460 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: 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: 0.8010 (mtpt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3055 time to fit residues: 63.7621 Evaluate side-chains 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 287 GLN P 290 ASN P 291 GLN P 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.127647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097781 restraints weight = 58621.981| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.95 r_work: 0.3393 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9229 Z= 0.211 Angle : 0.851 8.780 12780 Z= 0.496 Chirality : 0.054 0.321 1422 Planarity : 0.006 0.083 1349 Dihedral : 23.854 171.473 1998 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.83 % Favored : 96.83 % Rotamer: Outliers : 0.63 % Allowed : 6.57 % Favored : 92.80 % 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: -0.92 (0.26), residues: 882 helix: 0.10 (0.25), residues: 380 sheet: -0.84 (0.49), residues: 90 loop : -1.17 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 814 TYR 0.019 0.002 TYR P 205 PHE 0.026 0.002 PHE B 111 TRP 0.014 0.002 TRP P 724 HIS 0.005 0.002 HIS P 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 ( 9229) covalent geometry : angle 0.85057 / 0.50 (12780) hydrogen bonds : bond 0.07862 / 5.23 ( 398) hydrogen bonds : angle 5.51292 / 3.86 ( 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 100 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7277 (mt-10) REVERT: P 485 MET cc_start: 0.9278 (mtm) cc_final: 0.9018 (mtp) REVERT: P 689 LYS cc_start: 0.8087 (mttt) cc_final: 0.7161 (mmtt) REVERT: P 745 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8333 (mtpt) outliers start: 5 outliers final: 5 residues processed: 97 average time/residue: 0.2561 time to fit residues: 32.8975 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 : 0.434 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 52 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.124886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094994 restraints weight = 57640.973| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.80 r_work: 0.3360 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9229 Z= 0.239 Angle : 0.734 8.641 12780 Z= 0.431 Chirality : 0.048 0.281 1422 Planarity : 0.005 0.054 1349 Dihedral : 23.729 179.106 1998 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.90 % Rotamer: Outliers : 0.76 % Allowed : 8.59 % Favored : 90.66 % 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: -0.94 (0.26), residues: 882 helix: 0.29 (0.25), residues: 378 sheet: -1.23 (0.46), residues: 94 loop : -1.29 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 53 TYR 0.014 0.002 TYR P 335 PHE 0.025 0.002 PHE B 111 TRP 0.008 0.002 TRP P 816 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 ( 9229) covalent geometry : angle 0.73435 / 0.43 (12780) hydrogen bonds : bond 0.06300 / 4.23 ( 398) hydrogen bonds : angle 5.25541 / 3.69 ( 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 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.315 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: B 37 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8762 (mm) REVERT: P 689 LYS cc_start: 0.8161 (mttt) cc_final: 0.7145 (mmtt) REVERT: P 745 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8193 (mtpt) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.2051 time to fit residues: 22.3892 Evaluate side-chains 75 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.125379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095525 restraints weight = 56871.728| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.78 r_work: 0.3375 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9229 Z= 0.179 Angle : 0.656 7.536 12780 Z= 0.386 Chirality : 0.045 0.246 1422 Planarity : 0.005 0.038 1349 Dihedral : 23.615 177.648 1998 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 0.76 % Allowed : 8.59 % Favored : 90.66 % 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: -0.62 (0.26), residues: 882 helix: 0.69 (0.25), residues: 377 sheet: -1.20 (0.47), residues: 94 loop : -1.24 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 683 TYR 0.012 0.001 TYR P 572 PHE 0.013 0.001 PHE P 158 TRP 0.008 0.001 TRP P 816 HIS 0.003 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 9229) covalent geometry : angle 0.65603 / 0.39 (12780) hydrogen bonds : bond 0.05561 / 3.78 ( 398) hydrogen bonds : angle 5.01224 / 3.53 ( 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 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.445 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: B 37 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8775 (mm) REVERT: P 485 MET cc_start: 0.9405 (mtm) cc_final: 0.9193 (mtp) REVERT: P 745 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8201 (mtpt) outliers start: 6 outliers final: 3 residues processed: 79 average time/residue: 0.2024 time to fit residues: 22.4761 Evaluate side-chains 76 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 78 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.127191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097387 restraints weight = 56916.185| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.80 r_work: 0.3410 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9229 Z= 0.128 Angle : 0.605 7.065 12780 Z= 0.355 Chirality : 0.043 0.233 1422 Planarity : 0.004 0.033 1349 Dihedral : 23.326 178.031 1998 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 0.63 % Allowed : 9.09 % Favored : 90.28 % 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: -0.24 (0.27), residues: 882 helix: 1.15 (0.26), residues: 373 sheet: -1.11 (0.49), residues: 89 loop : -1.14 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 524 TYR 0.014 0.001 TYR P 601 PHE 0.015 0.001 PHE B 111 TRP 0.007 0.001 TRP B 119 HIS 0.004 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 9229) covalent geometry : angle 0.60466 / 0.36 (12780) hydrogen bonds : bond 0.04783 / 3.26 ( 398) hydrogen bonds : angle 4.74319 / 3.35 ( 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 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.434 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: 0.8905 (OUTLIER) cc_final: 0.8695 (mm) REVERT: P 745 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8194 (mtpt) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.2156 time to fit residues: 24.0464 Evaluate side-chains 74 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 315 LEU 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: 2.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.126731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096844 restraints weight = 56898.781| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.77 r_work: 0.3399 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9229 Z= 0.137 Angle : 0.584 7.286 12780 Z= 0.343 Chirality : 0.042 0.243 1422 Planarity : 0.004 0.034 1349 Dihedral : 23.248 177.955 1998 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 0.63 % Allowed : 9.97 % 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: -0.02 (0.28), residues: 882 helix: 1.37 (0.26), residues: 373 sheet: -1.03 (0.48), residues: 95 loop : -1.06 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 797 TYR 0.011 0.001 TYR P 572 PHE 0.042 0.001 PHE P 773 TRP 0.006 0.001 TRP B 119 HIS 0.004 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 9229) covalent geometry : angle 0.58438 / 0.34 (12780) hydrogen bonds : bond 0.04655 / 3.17 ( 398) hydrogen bonds : angle 4.68290 / 3.31 ( 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 77 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.426 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: P 745 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8186 (mtpt) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.2164 time to fit residues: 22.1428 Evaluate side-chains 73 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 613 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.124897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.095002 restraints weight = 56873.986| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.75 r_work: 0.3366 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4649 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= 0.204 Angle : 0.612 7.223 12780 Z= 0.357 Chirality : 0.043 0.258 1422 Planarity : 0.004 0.031 1349 Dihedral : 23.254 179.043 1998 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % 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 : 0.00 % 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: -0.09 (0.28), residues: 882 helix: 1.34 (0.26), residues: 376 sheet: -1.00 (0.50), residues: 95 loop : -1.16 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 797 TYR 0.015 0.002 TYR P 572 PHE 0.023 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 0.00436 / 0.20 ( 9229) covalent geometry : angle 0.61168 / 0.36 (12780) hydrogen bonds : bond 0.04818 / 3.28 ( 398) hydrogen bonds : angle 4.79644 / 3.40 ( 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 74 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.464 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 outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.1942 time to fit residues: 19.1840 Evaluate side-chains 67 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 613 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.126408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.096605 restraints weight = 56692.881| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.77 r_work: 0.3395 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9229 Z= 0.127 Angle : 0.570 6.527 12780 Z= 0.332 Chirality : 0.042 0.243 1422 Planarity : 0.004 0.032 1349 Dihedral : 23.264 177.660 1998 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 0.88 % Allowed : 10.35 % 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 are not related in a simple way. whole: 0.04 (0.28), residues: 882 helix: 1.54 (0.26), residues: 374 sheet: -1.14 (0.48), residues: 100 loop : -1.11 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 524 TYR 0.011 0.001 TYR P 205 PHE 0.024 0.001 PHE P 773 TRP 0.006 0.001 TRP B 119 HIS 0.004 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 9229) covalent geometry : angle 0.56994 / 0.33 (12780) hydrogen bonds : bond 0.04458 / 3.03 ( 398) hydrogen bonds : angle 4.59334 / 3.27 ( 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 76 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 PHE cc_start: 0.8367 (t80) cc_final: 0.8113 (t80) outliers start: 7 outliers final: 6 residues processed: 71 average time/residue: 0.1714 time to fit residues: 18.3118 Evaluate side-chains 72 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 613 TYR 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: 3.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.125594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095704 restraints weight = 56844.940| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.74 r_work: 0.3381 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9229 Z= 0.164 Angle : 0.572 6.323 12780 Z= 0.334 Chirality : 0.042 0.255 1422 Planarity : 0.004 0.031 1349 Dihedral : 23.250 177.965 1998 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.78 % Rotamer: Outliers : 0.88 % Allowed : 10.61 % Favored : 88.51 % 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: 0.05 (0.28), residues: 882 helix: 1.56 (0.26), residues: 375 sheet: -1.08 (0.49), residues: 100 loop : -1.14 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 524 TYR 0.012 0.001 TYR P 572 PHE 0.027 0.001 PHE P 773 TRP 0.005 0.001 TRP P 816 HIS 0.003 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 9229) covalent geometry : angle 0.57204 / 0.33 (12780) hydrogen bonds : bond 0.04494 / 3.05 ( 398) hydrogen bonds : angle 4.62890 / 3.28 ( 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 73 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.459 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: 0.8384 (t80) cc_final: 0.8111 (t80) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.1724 time to fit residues: 17.6403 Evaluate side-chains 69 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097360 restraints weight = 56393.565| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.75 r_work: 0.3412 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4948 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= 0.114 Angle : 0.551 5.839 12780 Z= 0.322 Chirality : 0.041 0.243 1422 Planarity : 0.004 0.029 1349 Dihedral : 23.189 177.008 1998 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 0.76 % Allowed : 10.48 % 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 are not related in a simple way. whole: 0.27 (0.28), residues: 882 helix: 1.75 (0.26), residues: 374 sheet: -0.94 (0.52), residues: 90 loop : -1.03 (0.30), residues: 418 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 0.028 0.001 PHE P 773 TRP 0.005 0.001 TRP B 119 HIS 0.005 0.001 HIS P 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 9229) covalent geometry : angle 0.55097 / 0.32 (12780) hydrogen bonds : bond 0.04247 / 2.88 ( 398) hydrogen bonds : angle 4.50070 / 3.20 ( 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 74 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 PHE cc_start: 0.8382 (t80) cc_final: 0.8122 (t80) REVERT: P 328 PHE cc_start: 0.7540 (m-80) cc_final: 0.7133 (m-10) outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.1817 time to fit residues: 18.7191 Evaluate side-chains 69 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 139 LYS 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 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.125723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096274 restraints weight = 56687.488| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.72 r_work: 0.3390 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9229 Z= 0.156 Angle : 0.560 5.995 12780 Z= 0.326 Chirality : 0.041 0.253 1422 Planarity : 0.004 0.025 1349 Dihedral : 23.133 177.175 1998 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.78 % Rotamer: Outliers : 0.88 % Allowed : 10.23 % Favored : 88.89 % 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: 0.23 (0.28), residues: 882 helix: 1.70 (0.26), residues: 374 sheet: -0.95 (0.50), residues: 95 loop : -1.04 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 524 TYR 0.012 0.001 TYR P 572 PHE 0.026 0.001 PHE P 773 TRP 0.005 0.001 TRP B 119 HIS 0.003 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 9229) covalent geometry : angle 0.55972 / 0.33 (12780) hydrogen bonds : bond 0.04323 / 2.94 ( 398) hydrogen bonds : angle 4.59842 / 3.26 ( 1102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3802.43 seconds wall clock time: 65 minutes 24.56 seconds (3924.56 seconds total)