Starting phenix.real_space_refine on Wed Feb 12 16:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wxu_32881/02_2025/7wxu_32881_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wxu_32881/02_2025/7wxu_32881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wxu_32881/02_2025/7wxu_32881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wxu_32881/02_2025/7wxu_32881.map" model { file = "/net/cci-nas-00/data/ceres_data/7wxu_32881/02_2025/7wxu_32881_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wxu_32881/02_2025/7wxu_32881_neut.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5175 2.51 5 N 1401 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8116 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1928 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2179 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Time building chain proxies: 4.88, per 1000 atoms: 0.60 Number of scatterers: 8116 At special positions: 0 Unit cell: (80.3, 101.2, 134.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1488 8.00 N 1401 7.00 C 5175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=1.93 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: 2.00 Conformation dependent library (CDL) restraints added in 1.2 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1938 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 40.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 removed outlier: 3.779A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.594A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.853A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.550A pdb=" N LEU A 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.634A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.816A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.615A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.579A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.797A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.061A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.641A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.685A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 568 through 573 removed outlier: 3.728A pdb=" N ILE R 571 " --> pdb=" O SER R 568 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU R 572 " --> pdb=" O PHE R 569 " (cutoff:3.500A) Processing helix chain 'R' and resid 578 through 580 No H-bonds generated for 'chain 'R' and resid 578 through 580' Processing helix chain 'R' and resid 581 through 610 removed outlier: 3.567A pdb=" N VAL R 585 " --> pdb=" O ILE R 581 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS R 586 " --> pdb=" O PHE R 582 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE R 588 " --> pdb=" O VAL R 584 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR R 589 " --> pdb=" O VAL R 585 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY R 594 " --> pdb=" O TYR R 590 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 614 removed outlier: 3.725A pdb=" N ILE R 614 " --> pdb=" O TRP R 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 611 through 614' Processing helix chain 'R' and resid 617 through 646 removed outlier: 3.532A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 685 removed outlier: 3.591A pdb=" N ALA R 659 " --> pdb=" O GLY R 655 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL R 661 " --> pdb=" O CYS R 657 " (cutoff:3.500A) Processing helix chain 'R' and resid 694 through 707 removed outlier: 3.548A pdb=" N MET R 698 " --> pdb=" O ALA R 694 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR R 707 " --> pdb=" O PHE R 703 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 722 Processing helix chain 'R' and resid 723 through 725 No H-bonds generated for 'chain 'R' and resid 723 through 725' Processing helix chain 'R' and resid 744 through 770 Proline residue: R 750 - end of helix removed outlier: 4.534A pdb=" N ILE R 754 " --> pdb=" O PRO R 750 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL R 755 " --> pdb=" O ALA R 751 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL R 757 " --> pdb=" O ALA R 753 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL R 760 " --> pdb=" O ALA R 756 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 801 removed outlier: 3.728A pdb=" N LEU R 796 " --> pdb=" O SER R 792 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR R 797 " --> pdb=" O LEU R 793 " (cutoff:3.500A) Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 811 removed outlier: 3.834A pdb=" N THR R 810 " --> pdb=" O PHE R 806 " (cutoff:3.500A) Processing helix chain 'R' and resid 821 through 829 removed outlier: 3.943A pdb=" N PHE R 829 " --> pdb=" O LEU R 825 " (cutoff:3.500A) Processing helix chain 'R' and resid 829 through 838 Processing helix chain 'R' and resid 843 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.299A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 291 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.058A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.042A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.160A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.960A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.959A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.768A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.252A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2601 1.34 - 1.46: 1772 1.46 - 1.58: 3836 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 8283 Sorted by residual: bond pdb=" N GLN N 39 " pdb=" CA GLN N 39 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.24e-02 6.50e+03 7.98e+00 bond pdb=" N HIS R 820 " pdb=" CA HIS R 820 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.33e-02 5.65e+03 6.12e+00 bond pdb=" N ASN R 816 " pdb=" CA ASN R 816 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.78e+00 bond pdb=" N GLN R 815 " pdb=" CA GLN R 815 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.68e+00 bond pdb=" N LEU R 817 " pdb=" CA LEU R 817 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.51e+00 ... (remaining 8278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 10718 1.76 - 3.51: 419 3.51 - 5.27: 65 5.27 - 7.02: 16 7.02 - 8.78: 8 Bond angle restraints: 11226 Sorted by residual: angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 112.03 119.60 -7.57 1.31e+00 5.83e-01 3.34e+01 angle pdb=" N TYR N 94 " pdb=" CA TYR N 94 " pdb=" C TYR N 94 " ideal model delta sigma weight residual 108.90 115.35 -6.45 1.63e+00 3.76e-01 1.57e+01 angle pdb=" C LYS R 728 " pdb=" CA LYS R 728 " pdb=" CB LYS R 728 " ideal model delta sigma weight residual 109.79 117.66 -7.87 2.05e+00 2.38e-01 1.47e+01 angle pdb=" C LEU B 55 " pdb=" CA LEU B 55 " pdb=" CB LEU B 55 " ideal model delta sigma weight residual 109.55 103.30 6.25 1.68e+00 3.54e-01 1.38e+01 angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 112.96 109.25 3.71 1.00e+00 1.00e+00 1.37e+01 ... (remaining 11221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4489 17.88 - 35.75: 361 35.75 - 53.63: 52 53.63 - 71.51: 9 71.51 - 89.39: 7 Dihedral angle restraints: 4918 sinusoidal: 1924 harmonic: 2994 Sorted by residual: dihedral pdb=" CB CYS R 657 " pdb=" SG CYS R 657 " pdb=" SG CYS R 733 " pdb=" CB CYS R 733 " ideal model delta sinusoidal sigma weight residual -86.00 -126.14 40.14 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASN R 736 " pdb=" C ASN R 736 " pdb=" N TRP R 737 " pdb=" CA TRP R 737 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1074 0.072 - 0.145: 196 0.145 - 0.217: 15 0.217 - 0.289: 0 0.289 - 0.362: 1 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA PHE R 663 " pdb=" N PHE R 663 " pdb=" C PHE R 663 " pdb=" CB PHE R 663 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 1283 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 666 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C PHE R 666 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE R 666 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE R 667 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 664 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C THR R 664 " -0.041 2.00e-02 2.50e+03 pdb=" O THR R 664 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS R 665 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 678 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" C LEU R 678 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU R 678 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY R 679 " 0.013 2.00e-02 2.50e+03 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1133 2.75 - 3.29: 7091 3.29 - 3.82: 11990 3.82 - 4.36: 13614 4.36 - 4.90: 25084 Nonbonded interactions: 58912 Sorted by model distance: nonbonded pdb=" O ALA R 818 " pdb=" CG2 ILE R 822 " model vdw 2.209 3.460 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.246 3.040 nonbonded pdb=" O ASP B 186 " pdb=" O ALA B 203 " model vdw 2.269 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.374 3.040 nonbonded pdb=" NE2 GLN A 59 " pdb=" O SER A 366 " model vdw 2.380 3.120 ... (remaining 58907 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: 1.270 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.009 0.052 8283 Z= 0.576 Angle : 0.838 8.781 11226 Z= 0.483 Chirality : 0.054 0.362 1286 Planarity : 0.006 0.050 1417 Dihedral : 13.411 89.387 2977 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1020 helix: 0.11 (0.27), residues: 367 sheet: 0.57 (0.35), residues: 220 loop : -2.04 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 234 HIS 0.007 0.002 HIS B 62 PHE 0.023 0.003 PHE B 151 TYR 0.025 0.003 TYR N 80 ARG 0.027 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.852 Fit side-chains REVERT: A 221 MET cc_start: 0.8814 (ttp) cc_final: 0.8590 (ttm) REVERT: A 299 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6742 (mm-30) REVERT: G 21 MET cc_start: 0.7060 (ttm) cc_final: 0.6797 (ttm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 1.3045 time to fit residues: 254.9825 Evaluate side-chains 162 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 75 GLN R 815 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111372 restraints weight = 11475.287| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.26 r_work: 0.3319 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8283 Z= 0.240 Angle : 0.588 7.477 11226 Z= 0.320 Chirality : 0.044 0.152 1286 Planarity : 0.004 0.047 1417 Dihedral : 4.816 27.224 1114 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.25 % Allowed : 9.02 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1020 helix: 1.07 (0.27), residues: 375 sheet: 0.63 (0.34), residues: 228 loop : -1.79 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.013 0.002 TYR B 59 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.854 Fit side-chains REVERT: A 221 MET cc_start: 0.8988 (ttp) cc_final: 0.8787 (ttm) REVERT: A 299 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 305 LYS cc_start: 0.8371 (mttt) cc_final: 0.8169 (mttt) REVERT: G 21 MET cc_start: 0.7893 (ttm) cc_final: 0.7570 (ttm) outliers start: 20 outliers final: 9 residues processed: 177 average time/residue: 1.2778 time to fit residues: 239.5243 Evaluate side-chains 169 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 643 VAL Chi-restraints excluded: chain R residue 792 SER Chi-restraints excluded: chain R residue 797 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 392 ASN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110664 restraints weight = 11628.344| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.29 r_work: 0.3320 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8283 Z= 0.253 Angle : 0.573 7.201 11226 Z= 0.310 Chirality : 0.044 0.151 1286 Planarity : 0.004 0.046 1417 Dihedral : 4.688 24.903 1114 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.59 % Allowed : 11.50 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1020 helix: 1.47 (0.27), residues: 371 sheet: 0.64 (0.33), residues: 237 loop : -1.67 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.015 0.002 TYR N 95 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.855 Fit side-chains REVERT: A 299 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 302 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8365 (mt) REVERT: A 305 LYS cc_start: 0.8332 (mttt) cc_final: 0.7798 (mttt) REVERT: A 307 LYS cc_start: 0.8345 (mppt) cc_final: 0.7839 (mppt) REVERT: B 263 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8187 (t) REVERT: R 705 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8184 (tt) outliers start: 23 outliers final: 12 residues processed: 172 average time/residue: 1.4059 time to fit residues: 254.5585 Evaluate side-chains 172 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 643 VAL Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 792 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 155 ASN R 696 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111727 restraints weight = 11517.149| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.25 r_work: 0.3335 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8283 Z= 0.217 Angle : 0.551 7.564 11226 Z= 0.298 Chirality : 0.043 0.147 1286 Planarity : 0.004 0.044 1417 Dihedral : 4.565 25.403 1114 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.71 % Allowed : 12.74 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 1020 helix: 1.70 (0.28), residues: 371 sheet: 0.70 (0.33), residues: 241 loop : -1.59 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.014 0.001 TYR N 95 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.897 Fit side-chains REVERT: A 302 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8345 (mt) REVERT: R 588 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6574 (pt) REVERT: R 705 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8162 (tt) outliers start: 24 outliers final: 12 residues processed: 175 average time/residue: 1.3288 time to fit residues: 245.2285 Evaluate side-chains 174 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 643 VAL Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 792 SER Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.131514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110241 restraints weight = 11365.556| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.24 r_work: 0.3319 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8283 Z= 0.278 Angle : 0.582 8.154 11226 Z= 0.315 Chirality : 0.044 0.142 1286 Planarity : 0.004 0.044 1417 Dihedral : 4.646 25.937 1114 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.04 % Allowed : 14.32 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1020 helix: 1.65 (0.27), residues: 372 sheet: 0.72 (0.33), residues: 235 loop : -1.57 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.016 0.002 TYR N 95 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.845 Fit side-chains REVERT: A 302 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 59 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: R 588 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6578 (pt) REVERT: R 705 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8166 (tt) outliers start: 27 outliers final: 16 residues processed: 173 average time/residue: 1.3544 time to fit residues: 247.1385 Evaluate side-chains 176 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 643 VAL Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 792 SER Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112093 restraints weight = 11573.609| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.25 r_work: 0.3341 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8283 Z= 0.202 Angle : 0.538 7.385 11226 Z= 0.291 Chirality : 0.042 0.142 1286 Planarity : 0.004 0.043 1417 Dihedral : 4.464 25.528 1114 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.82 % Allowed : 14.77 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1020 helix: 1.83 (0.28), residues: 372 sheet: 0.75 (0.33), residues: 239 loop : -1.53 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.001 TYR N 95 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.790 Fit side-chains REVERT: A 272 ASP cc_start: 0.8088 (m-30) cc_final: 0.7861 (m-30) REVERT: A 302 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8345 (mt) REVERT: B 318 LEU cc_start: 0.8614 (tt) cc_final: 0.8191 (tp) REVERT: R 705 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8172 (tt) outliers start: 25 outliers final: 14 residues processed: 172 average time/residue: 1.3131 time to fit residues: 239.6867 Evaluate side-chains 175 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 643 VAL Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 792 SER Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111873 restraints weight = 11549.614| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.24 r_work: 0.3338 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8283 Z= 0.218 Angle : 0.544 6.879 11226 Z= 0.294 Chirality : 0.043 0.148 1286 Planarity : 0.004 0.042 1417 Dihedral : 4.464 25.836 1114 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.82 % Allowed : 15.22 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1020 helix: 1.88 (0.28), residues: 372 sheet: 0.73 (0.33), residues: 240 loop : -1.48 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.001 TYR N 95 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.864 Fit side-chains REVERT: A 272 ASP cc_start: 0.8069 (m-30) cc_final: 0.7859 (m-30) REVERT: R 588 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6634 (pt) REVERT: R 705 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8169 (tt) outliers start: 25 outliers final: 16 residues processed: 170 average time/residue: 1.3972 time to fit residues: 250.3738 Evaluate side-chains 173 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 643 VAL Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 792 SER Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112571 restraints weight = 11691.974| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.27 r_work: 0.3345 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8283 Z= 0.193 Angle : 0.533 6.268 11226 Z= 0.288 Chirality : 0.042 0.150 1286 Planarity : 0.003 0.041 1417 Dihedral : 4.368 25.231 1114 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.59 % Allowed : 16.12 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1020 helix: 1.98 (0.28), residues: 372 sheet: 0.76 (0.33), residues: 241 loop : -1.47 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR N 95 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.770 Fit side-chains REVERT: A 272 ASP cc_start: 0.8089 (m-30) cc_final: 0.7863 (m-30) REVERT: B 75 GLN cc_start: 0.8551 (tp40) cc_final: 0.8202 (tt0) REVERT: R 705 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8093 (tt) outliers start: 23 outliers final: 16 residues processed: 169 average time/residue: 1.4233 time to fit residues: 253.4128 Evaluate side-chains 169 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 643 VAL Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 792 SER Chi-restraints excluded: chain R residue 810 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.4980 chunk 37 optimal weight: 0.0970 chunk 15 optimal weight: 0.0050 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 84 optimal weight: 0.5980 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114605 restraints weight = 11853.299| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.28 r_work: 0.3384 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8283 Z= 0.136 Angle : 0.492 6.644 11226 Z= 0.265 Chirality : 0.041 0.147 1286 Planarity : 0.003 0.041 1417 Dihedral : 4.086 23.860 1114 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.69 % Allowed : 17.81 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1020 helix: 2.19 (0.28), residues: 370 sheet: 0.89 (0.34), residues: 239 loop : -1.41 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.953 Fit side-chains REVERT: A 272 ASP cc_start: 0.8052 (m-30) cc_final: 0.7820 (m-30) REVERT: B 75 GLN cc_start: 0.8478 (tp40) cc_final: 0.8210 (tt0) REVERT: B 318 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8314 (tp) REVERT: N 27 PHE cc_start: 0.8061 (p90) cc_final: 0.7776 (p90) REVERT: R 632 LEU cc_start: 0.8086 (tt) cc_final: 0.7782 (tp) REVERT: R 705 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7946 (tt) outliers start: 15 outliers final: 4 residues processed: 170 average time/residue: 1.3108 time to fit residues: 235.2413 Evaluate side-chains 159 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110923 restraints weight = 11530.408| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.25 r_work: 0.3340 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8283 Z= 0.241 Angle : 0.560 7.965 11226 Z= 0.301 Chirality : 0.043 0.145 1286 Planarity : 0.004 0.041 1417 Dihedral : 4.316 25.553 1114 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.35 % Allowed : 18.71 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1020 helix: 2.05 (0.28), residues: 372 sheet: 0.75 (0.34), residues: 242 loop : -1.31 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.022 0.002 TYR N 80 ARG 0.009 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.893 Fit side-chains REVERT: A 272 ASP cc_start: 0.8053 (m-30) cc_final: 0.7837 (m-30) REVERT: G 21 MET cc_start: 0.7896 (ttm) cc_final: 0.7455 (mtp) REVERT: R 705 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7971 (tt) REVERT: R 724 SER cc_start: 0.8199 (m) cc_final: 0.7930 (t) outliers start: 12 outliers final: 8 residues processed: 156 average time/residue: 1.3667 time to fit residues: 224.9905 Evaluate side-chains 159 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 67 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112673 restraints weight = 11658.922| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.27 r_work: 0.3344 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8283 Z= 0.211 Angle : 0.546 7.671 11226 Z= 0.293 Chirality : 0.043 0.147 1286 Planarity : 0.004 0.042 1417 Dihedral : 4.305 25.222 1114 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.92 % Allowed : 18.49 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1020 helix: 2.06 (0.28), residues: 372 sheet: 0.74 (0.34), residues: 242 loop : -1.30 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.020 0.001 TYR N 80 ARG 0.010 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6681.08 seconds wall clock time: 118 minutes 16.20 seconds (7096.20 seconds total)