Starting phenix.real_space_refine on Wed Sep 17 17:26:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6p_38994/09_2025/8y6p_38994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6p_38994/09_2025/8y6p_38994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y6p_38994/09_2025/8y6p_38994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6p_38994/09_2025/8y6p_38994.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6p_38994/09_2025/8y6p_38994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6p_38994/09_2025/8y6p_38994_neut.cif" } resolution = 3.9 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= 0.000 sd= 0.031 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 50 5.16 5 C 6415 2.51 5 N 1684 2.21 5 O 1828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9977 Number of models: 1 Model: "" Number of chains: 1 Chain: "Q" Number of atoms: 9977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1228, 9977 Classifications: {'peptide': 1228} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1185} Chain breaks: 10 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 2.43, per 1000 atoms: 0.24 Number of scatterers: 9977 At special positions: 0 Unit cell: (101.85, 108.64, 126.1, 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 50 16.00 O 1828 8.00 N 1684 7.00 C 6415 6.00 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: 0.99 Conformation dependent library (CDL) restraints added in 379.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 19 sheets defined 29.8% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'Q' and resid 11 through 17 removed outlier: 3.662A pdb=" N ILE Q 15 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER Q 17 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 27 Processing helix chain 'Q' and resid 41 through 50 Processing helix chain 'Q' and resid 53 through 68 Processing helix chain 'Q' and resid 69 through 79 removed outlier: 4.843A pdb=" N LYS Q 75 " --> pdb=" O GLU Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 85 removed outlier: 4.125A pdb=" N ASN Q 84 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 96 removed outlier: 3.773A pdb=" N SER Q 90 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) Proline residue: Q 91 - end of helix Processing helix chain 'Q' and resid 100 through 117 Processing helix chain 'Q' and resid 117 through 123 removed outlier: 3.794A pdb=" N ALA Q 121 " --> pdb=" O ASN Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 141 Processing helix chain 'Q' and resid 156 through 167 removed outlier: 3.516A pdb=" N SER Q 167 " --> pdb=" O ASP Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 174 Processing helix chain 'Q' and resid 190 through 204 removed outlier: 3.513A pdb=" N GLU Q 194 " --> pdb=" O GLU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 216 through 233 removed outlier: 3.909A pdb=" N ARG Q 220 " --> pdb=" O ASN Q 216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 238 Processing helix chain 'Q' and resid 249 through 257 removed outlier: 3.567A pdb=" N TRP Q 253 " --> pdb=" O ASN Q 249 " (cutoff:3.500A) Processing helix chain 'Q' and resid 268 through 275 removed outlier: 3.708A pdb=" N THR Q 272 " --> pdb=" O PHE Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 303 Processing helix chain 'Q' and resid 322 through 333 removed outlier: 3.522A pdb=" N ILE Q 327 " --> pdb=" O ARG Q 323 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 345 Processing helix chain 'Q' and resid 350 through 355 Processing helix chain 'Q' and resid 364 through 371 Processing helix chain 'Q' and resid 372 through 374 No H-bonds generated for 'chain 'Q' and resid 372 through 374' Processing helix chain 'Q' and resid 383 through 390 removed outlier: 3.585A pdb=" N LEU Q 388 " --> pdb=" O ILE Q 384 " (cutoff:3.500A) Processing helix chain 'Q' and resid 397 through 409 removed outlier: 3.707A pdb=" N SER Q 409 " --> pdb=" O LEU Q 405 " (cutoff:3.500A) Processing helix chain 'Q' and resid 438 through 449 Processing helix chain 'Q' and resid 465 through 470 Processing helix chain 'Q' and resid 470 through 477 removed outlier: 3.842A pdb=" N HIS Q 474 " --> pdb=" O HIS Q 470 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN Q 477 " --> pdb=" O HIS Q 473 " (cutoff:3.500A) Processing helix chain 'Q' and resid 479 through 485 Processing helix chain 'Q' and resid 493 through 502 removed outlier: 3.512A pdb=" N LEU Q 497 " --> pdb=" O ASP Q 493 " (cutoff:3.500A) Processing helix chain 'Q' and resid 517 through 522 Processing helix chain 'Q' and resid 523 through 528 Processing helix chain 'Q' and resid 536 through 553 Proline residue: Q 547 - end of helix Processing helix chain 'Q' and resid 563 through 570 removed outlier: 4.119A pdb=" N MET Q 567 " --> pdb=" O ARG Q 563 " (cutoff:3.500A) Processing helix chain 'Q' and resid 574 through 583 removed outlier: 3.857A pdb=" N HIS Q 578 " --> pdb=" O PHE Q 574 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL Q 581 " --> pdb=" O ALA Q 577 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1011 through 1017 Processing helix chain 'Q' and resid 1130 through 1134 removed outlier: 3.533A pdb=" N PHE Q1134 " --> pdb=" O PRO Q1131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1260 through 1266 removed outlier: 3.560A pdb=" N ASN Q1266 " --> pdb=" O HIS Q1262 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1319 through 1323 Processing sheet with id=AA1, first strand: chain 'Q' and resid 178 through 182 removed outlier: 6.845A pdb=" N PHE Q 179 " --> pdb=" O VAL Q 243 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU Q 245 " --> pdb=" O PHE Q 179 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU Q 181 " --> pdb=" O LEU Q 245 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL Q 247 " --> pdb=" O LEU Q 181 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL Q 147 " --> pdb=" O LEU Q 264 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR Q 266 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE Q 149 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN Q 146 " --> pdb=" O THR Q 281 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE Q 283 " --> pdb=" O ASN Q 146 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU Q 148 " --> pdb=" O ILE Q 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 380 through 382 Processing sheet with id=AA3, first strand: chain 'Q' and resid 590 through 591 Processing sheet with id=AA4, first strand: chain 'Q' and resid 603 through 604 removed outlier: 6.014A pdb=" N VAL Q 928 " --> pdb=" O ALA Q 923 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA Q 923 " --> pdb=" O VAL Q 928 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR Q 917 " --> pdb=" O LEU Q 934 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LYS Q 916 " --> pdb=" O GLU Q 909 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU Q 909 " --> pdb=" O LYS Q 916 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE Q 918 " --> pdb=" O ILE Q 907 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE Q 907 " --> pdb=" O ILE Q 918 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU Q 920 " --> pdb=" O VAL Q 905 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL Q 905 " --> pdb=" O LEU Q 920 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY Q 922 " --> pdb=" O GLU Q 903 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 603 through 604 Processing sheet with id=AA6, first strand: chain 'Q' and resid 610 through 616 removed outlier: 3.624A pdb=" N PHE Q 620 " --> pdb=" O LEU Q 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 654 through 660 Processing sheet with id=AA8, first strand: chain 'Q' and resid 714 through 720 removed outlier: 3.664A pdb=" N ALA Q 716 " --> pdb=" O ALA Q 735 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASP Q 740 " --> pdb=" O PHE Q 736 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 714 through 720 removed outlier: 3.664A pdb=" N ALA Q 716 " --> pdb=" O ALA Q 735 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASP Q 740 " --> pdb=" O PHE Q 736 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU Q 761 " --> pdb=" O VAL Q 741 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 768 through 774 removed outlier: 4.740A pdb=" N LEU Q 788 " --> pdb=" O LEU Q 801 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 815 through 817 removed outlier: 4.240A pdb=" N VAL Q 836 " --> pdb=" O VAL Q 854 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 862 through 867 removed outlier: 3.719A pdb=" N CYS Q 864 " --> pdb=" O GLY Q 877 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP Q 886 " --> pdb=" O PRO Q 892 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 971 through 977 removed outlier: 5.893A pdb=" N LEU Q 974 " --> pdb=" O VAL Q 987 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL Q 987 " --> pdb=" O LEU Q 974 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 1020 through 1025 removed outlier: 3.514A pdb=" N THR Q1047 " --> pdb=" O ASP Q1042 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 1060 through 1062 removed outlier: 3.727A pdb=" N TYR Q1060 " --> pdb=" O SER Q1072 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 1104 through 1110 removed outlier: 6.479A pdb=" N PHE Q1118 " --> pdb=" O LYS Q1105 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA Q1107 " --> pdb=" O ILE Q1116 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE Q1116 " --> pdb=" O ALA Q1107 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU Q1109 " --> pdb=" O TYR Q1114 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR Q1114 " --> pdb=" O LEU Q1109 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 1144 through 1150 removed outlier: 3.519A pdb=" N GLY Q1146 " --> pdb=" O ALA Q1157 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE Q1162 " --> pdb=" O TYR Q1158 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG Q1167 " --> pdb=" O GLN Q1179 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLN Q1179 " --> pdb=" O ARG Q1167 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE Q1169 " --> pdb=" O TYR Q1177 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR Q1177 " --> pdb=" O ILE Q1169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 1191 through 1196 removed outlier: 6.861A pdb=" N GLY Q1206 " --> pdb=" O SER Q1192 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU Q1194 " --> pdb=" O ALA Q1204 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA Q1204 " --> pdb=" O LEU Q1194 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA Q1196 " --> pdb=" O MET Q1202 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET Q1202 " --> pdb=" O ALA Q1196 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA Q1216 " --> pdb=" O LEU Q1224 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU Q1224 " --> pdb=" O ALA Q1216 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N GLU Q1218 " --> pdb=" O VAL Q1222 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL Q1222 " --> pdb=" O GLU Q1218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 1238 through 1241 removed outlier: 3.548A pdb=" N ALA Q1336 " --> pdb=" O PHE Q1257 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN Q1259 " --> pdb=" O LEU Q1334 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU Q1334 " --> pdb=" O ASN Q1259 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1020 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: 2.14 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1978 1.33 - 1.45: 2414 1.45 - 1.57: 5724 1.57 - 1.69: 1 1.69 - 1.82: 74 Bond restraints: 10191 Sorted by residual: bond pdb=" CA PRO Q 321 " pdb=" C PRO Q 321 " ideal model delta sigma weight residual 1.520 1.469 0.051 9.50e-03 1.11e+04 2.88e+01 bond pdb=" N ALA Q 333 " pdb=" CA ALA Q 333 " ideal model delta sigma weight residual 1.457 1.518 -0.061 1.29e-02 6.01e+03 2.23e+01 bond pdb=" CA ASN Q 320 " pdb=" C ASN Q 320 " ideal model delta sigma weight residual 1.527 1.480 0.047 1.02e-02 9.61e+03 2.11e+01 bond pdb=" CA THR Q 337 " pdb=" C THR Q 337 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.30e-02 5.92e+03 1.93e+01 bond pdb=" CA ARG Q 323 " pdb=" C ARG Q 323 " ideal model delta sigma weight residual 1.523 1.474 0.050 1.30e-02 5.92e+03 1.46e+01 ... (remaining 10186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 13597 3.16 - 6.32: 168 6.32 - 9.48: 37 9.48 - 12.64: 6 12.64 - 15.80: 1 Bond angle restraints: 13809 Sorted by residual: angle pdb=" N ARG Q 323 " pdb=" CA ARG Q 323 " pdb=" C ARG Q 323 " ideal model delta sigma weight residual 111.28 95.48 15.80 1.09e+00 8.42e-01 2.10e+02 angle pdb=" N PRO Q 321 " pdb=" CA PRO Q 321 " pdb=" C PRO Q 321 " ideal model delta sigma weight residual 114.68 102.54 12.14 1.04e+00 9.25e-01 1.36e+02 angle pdb=" CA PRO Q 857 " pdb=" N PRO Q 857 " pdb=" CD PRO Q 857 " ideal model delta sigma weight residual 112.00 99.75 12.25 1.40e+00 5.10e-01 7.66e+01 angle pdb=" N ILE Q 514 " pdb=" CA ILE Q 514 " pdb=" C ILE Q 514 " ideal model delta sigma weight residual 113.53 106.30 7.23 9.80e-01 1.04e+00 5.44e+01 angle pdb=" N THR Q 337 " pdb=" CA THR Q 337 " pdb=" C THR Q 337 " ideal model delta sigma weight residual 111.28 103.56 7.72 1.09e+00 8.42e-01 5.02e+01 ... (remaining 13804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5217 17.72 - 35.44: 712 35.44 - 53.16: 171 53.16 - 70.89: 19 70.89 - 88.61: 10 Dihedral angle restraints: 6129 sinusoidal: 2479 harmonic: 3650 Sorted by residual: dihedral pdb=" CA SER Q 409 " pdb=" C SER Q 409 " pdb=" N LEU Q 410 " pdb=" CA LEU Q 410 " ideal model delta harmonic sigma weight residual -180.00 -147.48 -32.52 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA LEU Q 521 " pdb=" C LEU Q 521 " pdb=" N LYS Q 522 " pdb=" CA LYS Q 522 " ideal model delta harmonic sigma weight residual 180.00 151.83 28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA PHE Q 523 " pdb=" C PHE Q 523 " pdb=" N TYR Q 524 " pdb=" CA TYR Q 524 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1426 0.084 - 0.168: 148 0.168 - 0.253: 1 0.253 - 0.337: 2 0.337 - 0.421: 1 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA LEU Q 317 " pdb=" N LEU Q 317 " pdb=" C LEU Q 317 " pdb=" CB LEU Q 317 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE Q 743 " pdb=" CA ILE Q 743 " pdb=" CG1 ILE Q 743 " pdb=" CG2 ILE Q 743 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA PRO Q 857 " pdb=" N PRO Q 857 " pdb=" C PRO Q 857 " pdb=" CB PRO Q 857 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1575 not shown) Planarity restraints: 1739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 333 " 0.023 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ALA Q 333 " -0.077 2.00e-02 2.50e+03 pdb=" O ALA Q 333 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY Q 334 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 856 " -0.070 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO Q 857 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO Q 857 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO Q 857 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 525 " -0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO Q 526 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO Q 526 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 526 " -0.045 5.00e-02 4.00e+02 ... (remaining 1736 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 176 2.63 - 3.20: 9307 3.20 - 3.77: 15320 3.77 - 4.33: 20512 4.33 - 4.90: 32877 Nonbonded interactions: 78192 Sorted by model distance: nonbonded pdb=" OG1 THR Q1079 " pdb=" O VAL Q1102 " model vdw 2.064 3.040 nonbonded pdb=" OG SER Q1024 " pdb=" OE1 GLN Q1063 " model vdw 2.072 3.040 nonbonded pdb=" OG SER Q1171 " pdb=" O GLN Q1174 " model vdw 2.188 3.040 nonbonded pdb=" O PHE Q 590 " pdb=" OG1 THR Q 591 " model vdw 2.189 3.040 nonbonded pdb=" NE2 GLN Q 731 " pdb=" O LEU Q 744 " model vdw 2.213 3.120 ... (remaining 78187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 10191 Z= 0.236 Angle : 0.904 15.801 13809 Z= 0.512 Chirality : 0.049 0.421 1578 Planarity : 0.006 0.098 1739 Dihedral : 16.866 88.607 3743 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 1.08 % Allowed : 7.13 % Favored : 91.79 % Rotamer: Outliers : 1.34 % Allowed : 29.52 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.25), residues: 1206 helix: -0.32 (0.31), residues: 302 sheet: 0.58 (0.29), residues: 329 loop : -1.58 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 595 TYR 0.056 0.002 TYR Q1366 PHE 0.010 0.001 PHE Q1349 TRP 0.045 0.002 TRP Q 341 HIS 0.004 0.001 HIS Q 593 Details of bonding type rmsd covalent geometry : bond 0.00409 (10191) covalent geometry : angle 0.90351 (13809) hydrogen bonds : bond 0.16226 ( 360) hydrogen bonds : angle 6.89999 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 283 ILE cc_start: 0.8925 (mm) cc_final: 0.8624 (mm) REVERT: Q 323 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6748 (tpp80) REVERT: Q 340 ASN cc_start: 0.5851 (OUTLIER) cc_final: 0.5581 (m-40) REVERT: Q 1032 PHE cc_start: 0.8328 (m-80) cc_final: 0.8018 (m-10) outliers start: 15 outliers final: 8 residues processed: 185 average time/residue: 0.1096 time to fit residues: 28.4038 Evaluate side-chains 168 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 331 ILE Chi-restraints excluded: chain Q residue 340 ASN Chi-restraints excluded: chain Q residue 440 HIS Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 933 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 222 HIS ** Q 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS ** Q1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q1368 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.079145 restraints weight = 31369.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081508 restraints weight = 18905.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083113 restraints weight = 13270.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084283 restraints weight = 10293.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085113 restraints weight = 8446.828| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 10191 Z= 0.347 Angle : 0.873 11.790 13809 Z= 0.452 Chirality : 0.051 0.251 1578 Planarity : 0.006 0.093 1739 Dihedral : 7.056 48.907 1339 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.71 % Favored : 90.30 % Rotamer: Outliers : 8.14 % Allowed : 23.17 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.25), residues: 1206 helix: -0.70 (0.29), residues: 317 sheet: 0.35 (0.29), residues: 340 loop : -1.82 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 332 TYR 0.057 0.003 TYR Q 527 PHE 0.020 0.003 PHE Q 494 TRP 0.022 0.002 TRP Q1006 HIS 0.007 0.001 HIS Q 757 Details of bonding type rmsd covalent geometry : bond 0.00773 (10191) covalent geometry : angle 0.87285 (13809) hydrogen bonds : bond 0.04676 ( 360) hydrogen bonds : angle 6.40300 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 160 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 283 ILE cc_start: 0.8865 (mm) cc_final: 0.8627 (mm) REVERT: Q 317 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6468 (mt) REVERT: Q 323 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.6142 (mmt90) REVERT: Q 368 MET cc_start: 0.9269 (mmm) cc_final: 0.8638 (tmm) REVERT: Q 462 TYR cc_start: 0.7032 (t80) cc_final: 0.4693 (t80) REVERT: Q 516 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8692 (t0) REVERT: Q 977 MET cc_start: 0.5929 (ttt) cc_final: 0.5527 (ttp) REVERT: Q 1156 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8253 (tp) REVERT: Q 1182 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: Q 1263 MET cc_start: 0.9031 (mmm) cc_final: 0.8802 (mtt) REVERT: Q 1361 ASP cc_start: 0.8848 (p0) cc_final: 0.8524 (p0) outliers start: 91 outliers final: 48 residues processed: 222 average time/residue: 0.1007 time to fit residues: 31.8267 Evaluate side-chains 194 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 159 TRP Chi-restraints excluded: chain Q residue 164 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 340 ASN Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 425 ILE Chi-restraints excluded: chain Q residue 440 HIS Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 453 PHE Chi-restraints excluded: chain Q residue 475 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 495 ARG Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 501 ILE Chi-restraints excluded: chain Q residue 516 ASN Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 558 TYR Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 642 THR Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 774 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1017 ASN Chi-restraints excluded: chain Q residue 1040 ILE Chi-restraints excluded: chain Q residue 1046 ASP Chi-restraints excluded: chain Q residue 1080 VAL Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1154 LEU Chi-restraints excluded: chain Q residue 1156 LEU Chi-restraints excluded: chain Q residue 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1182 GLU Chi-restraints excluded: chain Q residue 1222 VAL Chi-restraints excluded: chain Q residue 1341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 499 GLN ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 927 GLN Q 952 HIS Q1232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083341 restraints weight = 30839.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085982 restraints weight = 17536.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087788 restraints weight = 11857.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089047 restraints weight = 8911.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089892 restraints weight = 7184.812| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10191 Z= 0.139 Angle : 0.714 7.972 13809 Z= 0.360 Chirality : 0.047 0.201 1578 Planarity : 0.005 0.089 1739 Dihedral : 6.428 50.953 1334 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 1.08 % Allowed : 8.04 % Favored : 90.88 % Rotamer: Outliers : 4.92 % Allowed : 24.60 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.25), residues: 1206 helix: -0.18 (0.31), residues: 310 sheet: 0.57 (0.30), residues: 333 loop : -1.78 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 595 TYR 0.056 0.002 TYR Q 527 PHE 0.011 0.001 PHE Q 494 TRP 0.027 0.002 TRP Q 341 HIS 0.006 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00318 (10191) covalent geometry : angle 0.71351 (13809) hydrogen bonds : bond 0.03814 ( 360) hydrogen bonds : angle 5.87877 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 89 MET cc_start: 0.7006 (mmt) cc_final: 0.6719 (mmt) REVERT: Q 323 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.6268 (mmt90) REVERT: Q 462 TYR cc_start: 0.7023 (t80) cc_final: 0.6550 (t80) REVERT: Q 977 MET cc_start: 0.5707 (ttt) cc_final: 0.5422 (ttp) REVERT: Q 1185 ILE cc_start: 0.8692 (mm) cc_final: 0.8492 (mm) REVERT: Q 1361 ASP cc_start: 0.8752 (p0) cc_final: 0.8453 (p0) outliers start: 55 outliers final: 32 residues processed: 200 average time/residue: 0.1069 time to fit residues: 30.0871 Evaluate side-chains 173 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 260 CYS Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 425 ILE Chi-restraints excluded: chain Q residue 440 HIS Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 453 PHE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 495 ARG Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1040 ILE Chi-restraints excluded: chain Q residue 1054 ILE Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1205 MET Chi-restraints excluded: chain Q residue 1222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 516 ASN ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.100653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084361 restraints weight = 31010.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086852 restraints weight = 18568.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088516 restraints weight = 12884.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089732 restraints weight = 9873.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.090618 restraints weight = 8056.007| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10191 Z= 0.130 Angle : 0.697 15.737 13809 Z= 0.346 Chirality : 0.046 0.210 1578 Planarity : 0.005 0.085 1739 Dihedral : 6.112 55.838 1332 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.21 % Favored : 91.79 % Rotamer: Outliers : 5.37 % Allowed : 24.60 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.25), residues: 1206 helix: -0.05 (0.31), residues: 313 sheet: 0.78 (0.30), residues: 326 loop : -1.77 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 595 TYR 0.051 0.002 TYR Q 527 PHE 0.010 0.001 PHE Q 523 TRP 0.023 0.002 TRP Q 589 HIS 0.005 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00301 (10191) covalent geometry : angle 0.69722 (13809) hydrogen bonds : bond 0.03420 ( 360) hydrogen bonds : angle 5.61926 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 317 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.6029 (mt) REVERT: Q 323 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6335 (mmt90) REVERT: Q 462 TYR cc_start: 0.6962 (t80) cc_final: 0.6504 (t80) REVERT: Q 576 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6227 (tm-30) REVERT: Q 775 LEU cc_start: 0.7923 (tt) cc_final: 0.7690 (tp) REVERT: Q 910 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8182 (tt) REVERT: Q 977 MET cc_start: 0.5661 (ttt) cc_final: 0.5448 (ttp) REVERT: Q 1185 ILE cc_start: 0.8631 (mm) cc_final: 0.8427 (mm) REVERT: Q 1361 ASP cc_start: 0.8754 (p0) cc_final: 0.8521 (p0) outliers start: 60 outliers final: 36 residues processed: 206 average time/residue: 0.1022 time to fit residues: 29.8773 Evaluate side-chains 186 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 114 TYR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 260 CYS Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 440 HIS Chi-restraints excluded: chain Q residue 444 VAL Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 453 PHE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 495 ARG Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 576 GLU Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 669 LEU Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 910 LEU Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1024 SER Chi-restraints excluded: chain Q residue 1040 ILE Chi-restraints excluded: chain Q residue 1046 ASP Chi-restraints excluded: chain Q residue 1054 ILE Chi-restraints excluded: chain Q residue 1103 SER Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.0030 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 0.0010 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 516 ASN ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084891 restraints weight = 30781.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087554 restraints weight = 17430.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089364 restraints weight = 11756.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090692 restraints weight = 8821.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091601 restraints weight = 7077.944| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10191 Z= 0.120 Angle : 0.695 13.026 13809 Z= 0.342 Chirality : 0.045 0.222 1578 Planarity : 0.005 0.087 1739 Dihedral : 6.007 58.472 1332 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.46 % Favored : 91.54 % Rotamer: Outliers : 4.92 % Allowed : 26.65 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.25), residues: 1206 helix: -0.06 (0.31), residues: 314 sheet: 0.80 (0.30), residues: 328 loop : -1.70 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 220 TYR 0.055 0.002 TYR Q 527 PHE 0.014 0.001 PHE Q1215 TRP 0.040 0.002 TRP Q 341 HIS 0.008 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00276 (10191) covalent geometry : angle 0.69519 (13809) hydrogen bonds : bond 0.03242 ( 360) hydrogen bonds : angle 5.51360 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7569 (tm-30) cc_final: 0.6976 (tm-30) REVERT: Q 323 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.6392 (mmt90) REVERT: Q 462 TYR cc_start: 0.6939 (t80) cc_final: 0.6502 (t80) REVERT: Q 545 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7455 (t80) REVERT: Q 576 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6184 (tm-30) REVERT: Q 775 LEU cc_start: 0.8003 (tt) cc_final: 0.7777 (tp) REVERT: Q 910 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8169 (tt) REVERT: Q 977 MET cc_start: 0.5604 (ttt) cc_final: 0.5397 (ttp) REVERT: Q 1185 ILE cc_start: 0.8669 (mm) cc_final: 0.8450 (mm) REVERT: Q 1361 ASP cc_start: 0.8758 (p0) cc_final: 0.8530 (p0) outliers start: 55 outliers final: 35 residues processed: 199 average time/residue: 0.1026 time to fit residues: 29.0688 Evaluate side-chains 190 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 114 TYR Chi-restraints excluded: chain Q residue 148 LEU Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 260 CYS Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 265 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 444 VAL Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 545 PHE Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 576 GLU Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 621 CYS Chi-restraints excluded: chain Q residue 669 LEU Chi-restraints excluded: chain Q residue 737 ILE Chi-restraints excluded: chain Q residue 768 ILE Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 910 LEU Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1013 HIS Chi-restraints excluded: chain Q residue 1046 ASP Chi-restraints excluded: chain Q residue 1103 SER Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.0050 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.101786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085660 restraints weight = 30589.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088135 restraints weight = 18297.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.089822 restraints weight = 12680.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090946 restraints weight = 9694.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.091906 restraints weight = 7910.594| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10191 Z= 0.115 Angle : 0.685 11.159 13809 Z= 0.338 Chirality : 0.045 0.219 1578 Planarity : 0.005 0.091 1739 Dihedral : 5.583 47.719 1327 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.05 % Favored : 92.04 % Rotamer: Outliers : 5.19 % Allowed : 26.03 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.25), residues: 1206 helix: -0.05 (0.31), residues: 314 sheet: 0.81 (0.30), residues: 328 loop : -1.66 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 595 TYR 0.057 0.002 TYR Q 527 PHE 0.014 0.001 PHE Q1215 TRP 0.019 0.001 TRP Q 207 HIS 0.008 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00263 (10191) covalent geometry : angle 0.68499 (13809) hydrogen bonds : bond 0.03125 ( 360) hydrogen bonds : angle 5.44655 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7556 (tm-30) cc_final: 0.6945 (tm-30) REVERT: Q 283 ILE cc_start: 0.8730 (mm) cc_final: 0.8471 (mm) REVERT: Q 323 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6329 (mmt90) REVERT: Q 462 TYR cc_start: 0.6936 (t80) cc_final: 0.6471 (t80) REVERT: Q 576 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6267 (tm-30) REVERT: Q 660 PHE cc_start: 0.7904 (p90) cc_final: 0.7703 (p90) REVERT: Q 775 LEU cc_start: 0.7959 (tt) cc_final: 0.7742 (tp) REVERT: Q 990 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8499 (mtmt) REVERT: Q 1185 ILE cc_start: 0.8593 (mm) cc_final: 0.8388 (mm) REVERT: Q 1361 ASP cc_start: 0.8810 (p0) cc_final: 0.8610 (p0) outliers start: 58 outliers final: 38 residues processed: 205 average time/residue: 0.1039 time to fit residues: 29.9402 Evaluate side-chains 185 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 114 TYR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 260 CYS Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 265 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 444 VAL Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 576 GLU Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 621 CYS Chi-restraints excluded: chain Q residue 669 LEU Chi-restraints excluded: chain Q residue 768 ILE Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 990 LYS Chi-restraints excluded: chain Q residue 1013 HIS Chi-restraints excluded: chain Q residue 1046 ASP Chi-restraints excluded: chain Q residue 1054 ILE Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Chi-restraints excluded: chain Q residue 1366 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.109469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093827 restraints weight = 31606.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096503 restraints weight = 18199.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.098343 restraints weight = 12329.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.099605 restraints weight = 9211.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.100470 restraints weight = 7407.993| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10191 Z= 0.118 Angle : 0.702 9.930 13809 Z= 0.344 Chirality : 0.046 0.213 1578 Planarity : 0.005 0.086 1739 Dihedral : 5.549 47.298 1327 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.21 % Favored : 91.96 % Rotamer: Outliers : 4.83 % Allowed : 26.92 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.25), residues: 1206 helix: -0.06 (0.31), residues: 314 sheet: 0.79 (0.30), residues: 321 loop : -1.60 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 220 TYR 0.058 0.002 TYR Q 527 PHE 0.026 0.001 PHE Q1155 TRP 0.022 0.001 TRP Q 207 HIS 0.008 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00275 (10191) covalent geometry : angle 0.70237 (13809) hydrogen bonds : bond 0.03069 ( 360) hydrogen bonds : angle 5.42267 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6843 (tm-30) REVERT: Q 283 ILE cc_start: 0.8850 (mm) cc_final: 0.8604 (mm) REVERT: Q 323 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6408 (mmt90) REVERT: Q 462 TYR cc_start: 0.6921 (t80) cc_final: 0.6403 (t80) REVERT: Q 515 LEU cc_start: 0.9003 (mt) cc_final: 0.8654 (mt) REVERT: Q 576 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: Q 990 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (mtmt) REVERT: Q 1185 ILE cc_start: 0.8400 (mm) cc_final: 0.8147 (mm) REVERT: Q 1361 ASP cc_start: 0.8821 (p0) cc_final: 0.8599 (p0) outliers start: 54 outliers final: 40 residues processed: 193 average time/residue: 0.1005 time to fit residues: 27.5021 Evaluate side-chains 189 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 29 CYS Chi-restraints excluded: chain Q residue 114 TYR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 260 CYS Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 265 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 437 TYR Chi-restraints excluded: chain Q residue 444 VAL Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 576 GLU Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 669 LEU Chi-restraints excluded: chain Q residue 737 ILE Chi-restraints excluded: chain Q residue 768 ILE Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 990 LYS Chi-restraints excluded: chain Q residue 1013 HIS Chi-restraints excluded: chain Q residue 1046 ASP Chi-restraints excluded: chain Q residue 1054 ILE Chi-restraints excluded: chain Q residue 1103 SER Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 516 ASN ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.110120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.094386 restraints weight = 31934.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.097092 restraints weight = 18373.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.098898 restraints weight = 12445.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.100172 restraints weight = 9368.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100920 restraints weight = 7535.011| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10191 Z= 0.112 Angle : 0.706 15.100 13809 Z= 0.341 Chirality : 0.045 0.217 1578 Planarity : 0.005 0.085 1739 Dihedral : 5.458 46.553 1327 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.97 % Favored : 92.21 % Rotamer: Outliers : 4.11 % Allowed : 27.28 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.25), residues: 1206 helix: -0.06 (0.31), residues: 312 sheet: 0.88 (0.30), residues: 318 loop : -1.62 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 220 TYR 0.057 0.002 TYR Q 527 PHE 0.022 0.001 PHE Q1155 TRP 0.026 0.001 TRP Q 207 HIS 0.007 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00254 (10191) covalent geometry : angle 0.70644 (13809) hydrogen bonds : bond 0.03000 ( 360) hydrogen bonds : angle 5.32591 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6768 (tm-30) REVERT: Q 283 ILE cc_start: 0.8807 (mm) cc_final: 0.8573 (mm) REVERT: Q 323 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.6362 (mmt90) REVERT: Q 462 TYR cc_start: 0.6877 (t80) cc_final: 0.4690 (t80) REVERT: Q 467 PHE cc_start: 0.7150 (m-80) cc_final: 0.6840 (m-80) REVERT: Q 576 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: Q 678 TRP cc_start: 0.8354 (m100) cc_final: 0.7988 (m100) REVERT: Q 775 LEU cc_start: 0.7918 (tp) cc_final: 0.7529 (tp) REVERT: Q 1205 MET cc_start: 0.7938 (mpp) cc_final: 0.7735 (mpp) REVERT: Q 1361 ASP cc_start: 0.8785 (p0) cc_final: 0.8518 (p0) outliers start: 46 outliers final: 37 residues processed: 195 average time/residue: 0.1020 time to fit residues: 28.0659 Evaluate side-chains 186 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 114 TYR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 260 CYS Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 265 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 576 GLU Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 621 CYS Chi-restraints excluded: chain Q residue 669 LEU Chi-restraints excluded: chain Q residue 737 ILE Chi-restraints excluded: chain Q residue 768 ILE Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 905 VAL Chi-restraints excluded: chain Q residue 933 THR Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1013 HIS Chi-restraints excluded: chain Q residue 1054 ILE Chi-restraints excluded: chain Q residue 1103 SER Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.110094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094658 restraints weight = 31690.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097295 restraints weight = 18474.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099055 restraints weight = 12571.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.100317 restraints weight = 9493.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.101143 restraints weight = 7632.996| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10191 Z= 0.120 Angle : 0.710 13.219 13809 Z= 0.346 Chirality : 0.045 0.208 1578 Planarity : 0.005 0.085 1739 Dihedral : 5.385 46.405 1325 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.46 % Favored : 91.79 % Rotamer: Outliers : 4.47 % Allowed : 27.19 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.25), residues: 1206 helix: -0.07 (0.31), residues: 313 sheet: 0.99 (0.30), residues: 310 loop : -1.71 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Q1264 TYR 0.056 0.002 TYR Q 527 PHE 0.021 0.001 PHE Q1155 TRP 0.028 0.001 TRP Q 207 HIS 0.012 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00279 (10191) covalent geometry : angle 0.71050 (13809) hydrogen bonds : bond 0.03142 ( 360) hydrogen bonds : angle 5.44305 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6812 (tm-30) REVERT: Q 283 ILE cc_start: 0.8832 (mm) cc_final: 0.8616 (mm) REVERT: Q 323 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6371 (mmt90) REVERT: Q 462 TYR cc_start: 0.6917 (t80) cc_final: 0.4695 (t80) REVERT: Q 467 PHE cc_start: 0.7160 (m-80) cc_final: 0.6839 (m-80) REVERT: Q 492 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.5243 (pt) REVERT: Q 515 LEU cc_start: 0.8940 (mt) cc_final: 0.8618 (mt) REVERT: Q 678 TRP cc_start: 0.8383 (m100) cc_final: 0.8032 (m100) REVERT: Q 1205 MET cc_start: 0.7991 (mpp) cc_final: 0.7758 (mpp) REVERT: Q 1361 ASP cc_start: 0.8819 (p0) cc_final: 0.8541 (p0) outliers start: 50 outliers final: 40 residues processed: 186 average time/residue: 0.0959 time to fit residues: 25.7011 Evaluate side-chains 185 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 29 CYS Chi-restraints excluded: chain Q residue 114 TYR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 260 CYS Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 265 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 444 VAL Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 492 LEU Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 621 CYS Chi-restraints excluded: chain Q residue 669 LEU Chi-restraints excluded: chain Q residue 768 ILE Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 905 VAL Chi-restraints excluded: chain Q residue 933 THR Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1013 HIS Chi-restraints excluded: chain Q residue 1046 ASP Chi-restraints excluded: chain Q residue 1054 ILE Chi-restraints excluded: chain Q residue 1103 SER Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 72 optimal weight: 0.0670 chunk 33 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.110171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094745 restraints weight = 31541.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.097370 restraints weight = 18562.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.099124 restraints weight = 12673.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.100384 restraints weight = 9571.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.101246 restraints weight = 7711.873| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10191 Z= 0.122 Angle : 0.739 18.431 13809 Z= 0.355 Chirality : 0.046 0.213 1578 Planarity : 0.005 0.085 1739 Dihedral : 5.372 46.525 1325 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.88 % Favored : 92.37 % Rotamer: Outliers : 4.03 % Allowed : 27.46 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.25), residues: 1206 helix: -0.08 (0.31), residues: 314 sheet: 0.98 (0.30), residues: 310 loop : -1.69 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q1264 TYR 0.061 0.002 TYR Q 527 PHE 0.020 0.001 PHE Q1155 TRP 0.029 0.001 TRP Q 207 HIS 0.012 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00282 (10191) covalent geometry : angle 0.73891 (13809) hydrogen bonds : bond 0.03110 ( 360) hydrogen bonds : angle 5.42164 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 20 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6814 (tm-30) REVERT: Q 283 ILE cc_start: 0.8862 (mm) cc_final: 0.8658 (mm) REVERT: Q 323 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.6403 (mmt90) REVERT: Q 329 GLU cc_start: 0.7599 (tt0) cc_final: 0.7046 (tt0) REVERT: Q 368 MET cc_start: 0.8306 (tpp) cc_final: 0.8102 (tpp) REVERT: Q 462 TYR cc_start: 0.6917 (t80) cc_final: 0.4682 (t80) REVERT: Q 467 PHE cc_start: 0.7135 (m-80) cc_final: 0.6825 (m-80) REVERT: Q 492 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.5235 (pt) REVERT: Q 595 ARG cc_start: 0.6106 (tmm160) cc_final: 0.4925 (mmt-90) REVERT: Q 1202 MET cc_start: 0.7382 (mtt) cc_final: 0.7043 (mtm) REVERT: Q 1361 ASP cc_start: 0.8801 (p0) cc_final: 0.8555 (p0) outliers start: 45 outliers final: 38 residues processed: 181 average time/residue: 0.0982 time to fit residues: 25.7828 Evaluate side-chains 188 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 ILE Chi-restraints excluded: chain Q residue 29 CYS Chi-restraints excluded: chain Q residue 114 TYR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 260 CYS Chi-restraints excluded: chain Q residue 262 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 265 THR Chi-restraints excluded: chain Q residue 322 ARG Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 447 TYR Chi-restraints excluded: chain Q residue 449 ILE Chi-restraints excluded: chain Q residue 458 LEU Chi-restraints excluded: chain Q residue 478 ILE Chi-restraints excluded: chain Q residue 492 LEU Chi-restraints excluded: chain Q residue 497 LEU Chi-restraints excluded: chain Q residue 560 ASP Chi-restraints excluded: chain Q residue 573 ILE Chi-restraints excluded: chain Q residue 599 HIS Chi-restraints excluded: chain Q residue 605 LEU Chi-restraints excluded: chain Q residue 621 CYS Chi-restraints excluded: chain Q residue 669 LEU Chi-restraints excluded: chain Q residue 768 ILE Chi-restraints excluded: chain Q residue 770 CYS Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain Q residue 905 VAL Chi-restraints excluded: chain Q residue 933 THR Chi-restraints excluded: chain Q residue 951 VAL Chi-restraints excluded: chain Q residue 1013 HIS Chi-restraints excluded: chain Q residue 1054 ILE Chi-restraints excluded: chain Q residue 1123 VAL Chi-restraints excluded: chain Q residue 1169 ILE Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 0.0670 chunk 89 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 75 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 952 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.111169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095628 restraints weight = 31886.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.098352 restraints weight = 18248.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.100186 restraints weight = 12291.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.101450 restraints weight = 9184.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.102389 restraints weight = 7366.760| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10191 Z= 0.115 Angle : 0.716 10.431 13809 Z= 0.351 Chirality : 0.046 0.211 1578 Planarity : 0.005 0.086 1739 Dihedral : 5.362 46.053 1325 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.97 % Favored : 92.29 % Rotamer: Outliers : 3.94 % Allowed : 27.64 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.25), residues: 1206 helix: 0.05 (0.32), residues: 306 sheet: 1.01 (0.31), residues: 309 loop : -1.65 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q1264 TYR 0.060 0.001 TYR Q 527 PHE 0.018 0.001 PHE Q1155 TRP 0.029 0.001 TRP Q 207 HIS 0.014 0.001 HIS Q 480 Details of bonding type rmsd covalent geometry : bond 0.00261 (10191) covalent geometry : angle 0.71634 (13809) hydrogen bonds : bond 0.03025 ( 360) hydrogen bonds : angle 5.38982 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.23 seconds wall clock time: 30 minutes 48.06 seconds (1848.06 seconds total)